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Methods using environmental DNA to explore and analyze biodiversity from previously unexplored habitats and ecosystems have become increasingly popular in recent years. This is particularly due to the potential reduction in necessary taxonomic expertise, the opportunity to assess microorganismal communities, and decreased time investments required to cover large spatial extents. In forests, the surface of tree bark is an important habitat for epiphytic diversity. Because of the large surface area rich in micro-niches, the seasonal stability of the substrate, and the longevity of trees, tree bark surfaces provide an ideal habitat for many species. Yet, we lack a comprehensive understanding of their communities and the environmental drivers behind the community assembly. These missing links hinder the exploration of the forest microbiome as a whole and limits our understanding of functions of a large forest habitat and its connections to other forest microbiomes. With a holistic eDNA metabarcoding approach, encompassing samples of three major taxonomic groups (e.g. bacteria, fungi, and green algae), as well as simultaneous collections from multiple forest habitats we can contribute to closing these gaps and increase our knowledge of the forest microbiome.
My dissertation is set within the framework of the Biodiversity Exploratories and was conducted in four parts: I. the establishment of an eDNA metabarcoding workflow to reveal the local diversity of the bark surface microbiome; II. the upscaling of the method to large geographic and environmental gradients to uncover the drivers of the microbiome; III. the integration of soil and bark samples to investigate compositional differences in two important forest habitats; IV. the evaluation of eDNA metabarcoding as a tool for biodiversity assessments of lichen diversity in forests.
In the first part, I developed a simple, cost-effective and fast sampling strategy to acquire eDNA samples from the bark of trees in forest ecosystems. Using readily available medical-specimen-collection swabs I sampled bark surfaces of individual trees in Central German forests and used metabarcoding to amplify marker genes of green algae, fungi and bacteria. From the sequencing reads I calculated the first diversity estimates of the major organismal groups of bark surface microbiomes from Central European forests. Overall the methodology produced reliable results, allowing for an expanded sampling in the second part.
In the second part of the dissertation, I expanded the sampling based on the results of part one. I collected bark surface samples from the three regions of the Biodiversity Exploratories covering large spatial and environmental gradients representative for Central European forests. The collection included composite samples from 150 plots and over 750 trees. Utilizing measurements of climatic and forest structure variables provided by the Biodiversity Exploratories, as well as my own community data, I identified the biotic and abiotic drivers behind alpha and beta diversity of the bark surface microbiome.
In the third part, I studied the differences between the bark surface as an unexplored and the soil as an example of a well characterized forest microbiome. Using only the fungal part of the large sampling campaign and soil samples obtained from the same plots at the same time, I assessed the commonalities and differences of the micro-communities of these distinct forest niches. Furthermore, I included two coniferous and one deciduous tree species to examine, if the effect of tree species, previously shown for soil microbiomes, also holds true for the bark surface.
In the last part of my dissertation, I used eDNA in a more applied way as a tool in biodiversity assessments of lichenized fungi. I compared the results from eDNA metabarcoding to an expert floristic mapping conducted in the same plots in 2007/2008. I assigned functional guilds to the fungal taxa obtained in the large sampling campaign and used a subset that was assigned as lichenized fungi.
In conclusion, I showed that eDNA metabarcoding is a valuable tool to reveal the unknown diversity of microorganisms in forest ecosystems. In particular, my results advance our understanding of the bark surface microbiome, an underexplored habitat within forests. The tightly linked interactions of the three major microbial groups underline that studies need to take holistic approaches across multiple taxonomic groups to deepen our understanding of processes governing the assembly of microbiomes. Results from my dissertation may serve as a foundation to inform hypotheses addressing the functions of forest microbiomes. The massive diversity data collected may also contribute to closing the gap in our understanding of macro-organisms and micro-organisms with respect to diversity distributions and patterns of richness, and serve as a baseline for predictions of biodiversity responses under future anthropogenic change.
From hunting and foraging to clearing land for agriculture, humans modify forest biodiversity, landscapes, and climate. Forests constantly undergo disturbance–recovery dynamics and understanding them is a major objective of ecologists and conservationists. Chronosequences are a useful tool for understanding global restoration efforts. They represent a space-for-time substitution approach suited for the quantification of the resistance of ecosystem properties to withstand disturbance and the resilience of these properties until reaching pre-disturbance levels. Here we introduce a newly established chronosequence with 62 plots (50 ⍰ 50 m) in active cacao plantations and pastures, early and late regeneration, and mature old-growth forests, across a 200 km2 area in the extremely wet Chocó rainforest. Our chronosequence covers by far the largest total area of plots compared to others in the Neotropics. Plots ranged from 159–615 masl in a forested landscape with 74 ± 2.8 % forest cover within a 1-km radius including substantial old-growth forest cover. Land-use legacy and regeneration time were not confounded by elevation. We tested how six forest structure variables (maximum tree height and DBH, basal area, number of stems, vertical vegetation heterogeneity, and light availability), aboveground biomass (AGB), and rarefied tree species richness change along our chronosequence. Forest structure variables, AGB, and tree species richness increased with regeneration time and are predicted to reach similar levels to those in old-growth forests after ca. 30–116, 202, and 108 yrs, respectively. Compared to previous work in the Neotropics, old-growth forests in Canandé accumulate high AGB that takes one of the largest time spans reported until total recovery. Our chronosequence comprises one of the largest tree species pools, covers the largest total area of regenerating and old-growth forests, and has higher forest cover than other Neotropical chronosequences. Hence, our chronosequence can be used to determine the time for recovery and stability (resistance and resilience) of different taxa and ecosystem functions, including species interaction networks. This integrative effort will ultimately help to understand how one of the most diverse forests on the planet recovers from large-scale disturbances.
The snake pipefish, Entelurus aequoreus (Linnaeus, 1758), is a slender, up to 60 cm long, northern Atlantic fish that dwells in open seagrass habitats and has recently expanded its distribution range. The snake pipefish is part of the family Syngnathidae (seahorses and pipefish) that has undergone several characteristic morphological changes, such as loss of pelvic fins and elongated snout. Here, we present a highly contiguous, near chromosome-scale genome of the snake pipefish assembled as part of a university master’s course. The final assembly has a length of 1.6 Gbp in 7,391 scaffolds, a scaffold and contig N50 of 62.3 Mbp and 45.0 Mbp and L50 of 12 and 14, respectively. The largest 28 scaffolds (>21 Mbp) span 89.7% of the assembly length. A BUSCO completeness score of 94.1% and a mapping rate above 98% suggest a high assembly completeness. Repetitive elements cover 74.93% of the genome, one of the highest proportions so far identified in vertebrate genomes. Demographic modeling using the PSMC framework indicates a peak in effective population size (50 – 100 kya) during the last interglacial period and suggests that the species might largely benefit from warmer water conditions, as seen today. Our updated snake pipefish assembly forms an important foundation for further analysis of the morphological and molecular changes unique to the family Syngnathidae.
Highlights
• Genomes for all five Natrix species, two represented by two distinct subspecies each, were sequenced.
• Two genomes were de-novo assembled to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp.
• Evidence for interspecific hybridization, both between allopatric and widely sympatric species.
• Fossil-calibrated molecular clock using genomes indicates that species are ancient several million-year-old lineages.
• Our findings imply that speciation took place despite continued gene flow.
Abstract
Understanding speciation is one of the cornerstones of biological diversity research. Currently, speciation is often understood as a continuous process of divergence that continues until genetic or other incompatibilities minimize or prevent interbreeding. The Palearctic snake genus Natrix is an ideal group to study speciation, as it comprises taxa representing distinct stages of the speciation process, ranging from widely interbreeding parapatric taxa through parapatric species with very limited gene flow in narrow hybrid zones to widely sympatric species. To understand the evolution of reproductive isolation through time, we have sequenced the genomes of all five species within this genus and two additional subspecies. We used both long-read and short-read methods to sequence and de-novo-assemble two high-quality genomes (Natrix h. helvetica, Natrix n. natrix) to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp, respectively, and used these as references to assemble the remaining short-read-based genomes. Our phylogenomic analyses yielded a well-supported dated phylogeny and evidence for a surprisingly complex history of interspecific gene flow, including between widely sympatric species. Furthermore, evidence for gene flow was also found for currently allopatric species pairs. Genetic exchange among these well-defined, distinct, and several million-year-old reptile species emphasizes that speciation and maintenance of species distinctness can occur despite continued genetic exchange.
The tremendous diversity of life in the ocean has proven to be a rich source of inspiration for drug discovery, with success rates for marine natural products up to 4 times higher than other naturally derived compounds. Yet the marine biodiscovery pipeline is characterized by chronic underfunding, bottlenecks and, ultimately, untapped potential. For instance, a lack of taxonomic capacity means that, on average, 20 years pass between the discovery of new organisms and the formal publication of scientific names, a prerequisite to proceed with detecting and isolating promising bioactive metabolites. The need for “edge” research that can spur novel lines of discovery and lengthy high-risk drug discovery processes, are poorly matched with research grant cycles. Here we propose five concrete pathways to broaden the biodiscovery pipeline and open the social and economic potential of the ocean genome for global benefit: (1) investing in fundamental research, even when the links to industry are not immediately apparent; (2) cultivating equitable collaborations between academia and industry that share both risks and benefits for these foundational research stages; (3) providing new opportunities for early-career researchers and under-represented groups to engage in high-risk research without risking their careers; (4) sharing data with global networks; and (5) protecting genetic diversity at its source through strong conservation efforts. The treasures of the ocean have provided fundamental breakthroughs in human health and still remain under-utilised for human benefit, yet that potential may be lost if we allow the biodiscovery pipeline to become blocked in a search for quick-fix solutions.
Mollusca is the second-largest animal phylum with over 100,000 species among eight distinct taxonomic classes. Across 1000 living species in the class Polyplacophora, chitons have a relatively constrained morphology but with some notable deviations. Several genera possess “shell eyes”, true eyes with a lens and retina that are embedded within the dorsal shells, which represent the most recent evolution of animal eyes. The phylogeny of major chiton clades is mostly well established, in a set of superfamily and higher-level taxa supported by various approaches including multiple gene markers, mitogenome-phylogeny and phylotranscritomic approaches as well as morphological studies. However, one critical lineage has remained unclear: Schizochiton was controversially suggested as a potential independent origin of chiton shell eyes. Here, with the draft genome sequencing of Schizochiton incisus (superfamily Schizochitonoidea) plus assembly of transcriptome data from other polyplacophorans, we present phylogenetic reconstructions using both mitochondrial genomes and phylogenomic approaches with multiple methods. Phylogenetic trees from mitogenomic data are inconsistent, reflecting larger scale confounding factors in molluscan mitogenomes. A consistent robust topology was generated with protein coding genes using different models and methods. Our results support Schizochitonoidea is a sister group to other Chitonoidea in Chitonina, in agreement with established classification. This suggests that the earliest origin of shell eyes is in Schizochitonoidea, which were also gained secondarily in other genera in Chitonoidea. Our results have generated a holistic review of the internal relationship within Polyplacophora, and a better understanding on the evolution of Polyplacophora.
Fossil dental remains are an archive of unique information for paleobiological studies. Computed microtomography based on X-ray microfocus sources (X-μCT) and Synchrotron Radiation (SR-μCT) allow subtle quantification at the micron and sub-micron scale of the meso- and microstructural signature imprinted in the mineralized tissues, such as enamel and dentine, through high-resolution “virtual histology”. Nonetheless, depending on the degree of alterations undergone during fossilization, X-ray analyses of tooth tissues do not always provide distinct imaging contrasts, thus preventing the extraction of essential morphological and anatomical details. We illustrate here by three examples the successful application of neutron microtomography (n-μCT) in cases where X-rays have previously failed to deliver contrasts between dental tissues of fossilized specimen.
Significance
Identifying the earliest members of the genus Homo is crucial for understanding when and where selective pressures resulted in its emergence from a Plio-Pleistocene hominin taxon. Our revision of a large part of the dental fossil record from southern Africa provides evidence suggesting a paucity of Homo remains and indicates increased levels of dental variation in australopith taxa. Results of the Ba/Ca, Sr/Ca, and elemental mapping of enamel and dentine also indicate that some of the purported Homo specimens show a paleoecological signal similar to that of the australopiths.
Abstract
The origins of Homo, as well as the diversity and biogeographic distribution of early Homo species, remain critical outstanding issues in paleoanthropology. Debates about the recognition of early Homo, first appearance dates, and taxonomic diversity within Homo are particularly important for determining the role that southern African taxa may have played in the origins of the genus. The correct identification of Homo remains also has implications for reconstructing phylogenetic relationships between species of Australopithecus and Paranthropus, and the links between early Homo species and Homo erectus. We use microcomputed tomography and landmark-free deformation-based three-dimensional geometric morphometrics to extract taxonomically informative data from the internal structure of postcanine teeth attributed to Early Pleistocene Homo in the southern African hominin-bearing sites of Sterkfontein, Swartkrans, Drimolen, and Kromdraai B. Our results indicate that, from our sample of 23 specimens, only 4 are unambiguously attributed to Homo, 3 of them coming from Swartkrans member 1 (SK 27, SK 847, and SKX 21204) and 1 from Sterkfontein (Sts 9). Three other specimens from Sterkfontein (StW 80 and 81, SE 1508, and StW 669) approximate the Homo condition in terms of overall enamel–dentine junction shape, but retain Australopithecus-like dental traits, and their generic status remains unclear. The other specimens, including SK 15, present a dominant australopith dental signature. In light of these results, previous dietary and ecological interpretations can be reevaluated, showing that the geochemical signal of one tooth from Kromdraai (KB 5223) and two from Swartkrans (SK 96 and SKX 268) is consistent with that of australopiths.
Chemical pollution caused by synthetic organic chemicals at low concentrations in the environment poses a growing threat to the ecological status of aquatic ecosystems. These chemicals are regularly released into surface waters through both treated and untreated effluents from wastewater treatment plants (WWTPs), agricultural runoff, and industrial discharges. Consequently, they accumulate in surface waters, distribute amongst environmental compartments according to their physicochemical properties, and cause adverse effects on aquatic organisms. Unfortunately, there is a lack of data regarding the occurrence of synthetic organic chemicals, henceforth micropollutants, in South American freshwater ecosystems, especially in Chile.
To address this research gap, we present a comprehensive dataset comprising concentrations of 153 emerging chemicals, including pesticides, pharmaceutical and personal care products (PPCPs), surfactants, and industrial chemicals. These chemicals were found to co-occur in surface waters within Central Chile, specifically in the River Aconcagua Basin. Our sampling strategy involved collecting surface water samples from streams and rivers with diverse land uses, such as agriculture, urban areas, and natural reserves. For sample extraction, we employed an on-site large-volume solid phase extraction (LVSPE) device. The resulting environmental extracts were then subjected to wide-scope chemical target screening using gas chromatography and liquid chromatography high-resolution mass spectrometry (GC- and LCsingle bondHRMS).
The dataset we present holds significant value in assessing the chemical status of water bodies. It enables comparative analysis of pollution fingerprints associated with emerging chemicals across different freshwater systems. Moreover, the data can be reused for environmental risk assessment studies. Its utilisation will contribute to a better understanding of the impact and extent of chemical pollution in aquatic ecosystems, facilitating the development of effective mitigation strategies.
Highlights
• 153 chemicals of emerging concern detected in complex multi-component mixtures.
• 108 possible mixture risk assessment scenarios were investigated.
• Non-detects, QSARs, and experimental ecotoxicological data were integrated for risk assessment.
• 8 chemicals were the main risk drivers in at least one site across the River Aconcagua basin.
Abstract
Environmental risk assessments strategies that account for the complexity of exposures are needed in order to evaluate the toxic pressure of emerging chemicals, which also provide suggestions for risk mitigation and management, if necessary. Currently, most studies on the co-occurrence and environmental impacts of chemicals of emerging concern (CECs) are conducted in countries of the Global North, leaving massive knowledge gaps in countries of the Global South.
In this study, we implement a multi-scenario risk assessment strategy to improve the assessment of both the exposure and hazard components in the chemical risk assessment process. Our strategy incorporates a systematic consideration and weighting of CECs that were not detected, as well as an evaluation of the uncertainties associated with Quantitative Structure-Activity Relationships (QSARs) predictions for chronic ecotoxicity. Furthermore, we present a novel approach to identifying mixture risk drivers. To expand our knowledge beyond well-studied aquatic ecosystems, we applied this multi-scenario strategy to the River Aconcagua basin of Central Chile. The analysis revealed that the concentrations of CECs exceeded acceptable risk thresholds for selected organism groups and the most vulnerable taxonomic groups. Streams flowing through agricultural areas and sites near the river mouth exhibited the highest risks. Notably, the eight risk drivers among the 153 co-occurring chemicals accounted for 66–92 % of the observed risks in the river basin. Six of them are pesticides and pharmaceuticals, chemical classes known for their high biological activity in specific target organisms.
Neanderthal diet has been on the spotlight of paleoanthropological research for many years. The majority of studies that tried to reconstruct the diet of Neanderthals were based on the analysis of zooarchaeological remains, stable isotopes, dental calculus and dental microwear patterns. In the past few years, there have been a few studies that linked dental macrowear patterns of Neanderthals and modern humans to diet and cultural habits. However, they mostly focused on maxillary molars. Although mandibular molars have been widely used in microwear dietary research, little is known about their usage at the macroscopic scale to detect information about human subsistence strategies. In this study, we compare the macrowear patterns of Neanderthal (NEA), fossil Homo sapiens (FHS), modern hunter-gatherers (MHG), pastoralists, early farmers and Australian Aborigines from Yuendumu mandibular molars in order to assess their utility in collecting any possible information about dietary and cultural habits among diverse human groups. We use the occlusal fingerprint analysis method, a quantitative digital approach that has been successfully employed to reconstruct the diet of living non-human primates and past human populations. Our results show macrowear pattern differences between meat-eater MHG and EF groups. Moreover, while we did not find eco-geographical differences in the macrowear patterns of the fossil sample, we found statistically significant differences between NEA and FHS inhabiting steppe/coniferous forest. This latter result could be associated with the use of distinct technological complexes in these two species, which ultimately could have allowed modern humans to exploit natural resources in a different way compared to NEA.
Climate change affects ecosystems worldwide and is threatening biodiversity. Insects, as ectotherm organisms, are strongly dependent on the thermal environment. Yet, little is known about the effects of summer heat and drought on insect diversity. In the Mediterranean climate zone, a region strongly affected by climate change, hot summers might have severe effects on insect communities. Especially the larval stage might be sensitive to thermal variation, as larvae—compared to other life stages—cannot avoid hot temperatures and drought by dormancy. Here we ask, whether inter-annual fluctuations in Mediterranean moth diversity can be explained by temperature (TLarv) and precipitation during larval development (HLarv). To address our question, we analyzed moth communities of a Mediterranean coastal forest during the last 20 years. For species with summer-developing larvae, species richness was significantly negatively correlated with TLarv, while the community composition was affected by both, TLarv and HLarv. Therefore, summer-developing larvae seem particularly sensitive to climate change, as hot summers might exceed the larval temperature optima and drought reduces food plant quality. Increasing frequency and severity of temperature and drought extremes due to climate change, therefore, might amplify insect decline in the future.
Background: In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa.
Results: We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe.
Conclusions: Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
Background: In the speciation continuum the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa.
Results: We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe.
Conclusions: Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
Nitrogen pollution is a major constituent of global change, threatening local biodiversity, ecosystem services, and causing serious environmental damage. Specifically, in areas with heavy agricultural soil-use, excessive use of nitrogen fertilizer pollutes the groundwaters with nitrates, but also with ammonia and nitrites. Freshwater fish and other aquatic fauna are especially vulnerable to nitrites, which can cause massive mortalities at even low concentrations < 0.1 mg/l NO2- - N. Adaptation of fish to environments with relatively high concentrations of chemicals has occurred throughout the history of life, although contemporary evolution acts at a much more rapid pace. The growing use of land for mass agriculture and livestock industries in the last 50 years in the US has dramatically increased the nutrient loading into the surface and groundwaters. Nitrite poses a serious threat for freshwater fauna as it is rapidly up taken and disturbs ion homeostasis and blood gas transport in fish. In this study, we evaluated, by means of a laboratory experiment, the tolerance of fish to nitrite using six different populations of wild eastern mosquitofish (Gambusia holbrooki) from two regions, North FL and NC, and with different background nitrogen pollution histories. Mosquitofish females were exposed to nitrite in the lab, to either < 0.005 mg/l NO2- (control) or 0.3 mg/l NO2- for ten days and we assessed at the end of the exposure period their blood O2 transport capacity by measuring the concentration of four different types of hemoglobin, their total hematocrit, and their respiratory rates. Preliminary results show significant varying patterns in the response of the exposed fish, depending on the population source, as evidenced by their respiratory rates and the blood erythrocyte counts. Mortality was very low, and hemoglobin profiles indicate high tolerance of G. holbrooki to nitrite contamination – a factor supporting their invasion success in agriculturally dominated regions around the world
Nitrogen pollution is a major constituent of global change, threatening local biodiversity, ecosystem services, and causing serious environmental damage. Specifically, in areas with heavy agricultural soil-use, excessive use of nitrogen fertilizer pollutes the groundwaters with nitrates, but also with ammonia and nitrites. Freshwater fish and other aquatic fauna are especially vulnerable to nitrites, which can cause massive mortalities at even low concentrations < 0.1 mg/l NO2- - N. Adaptation of fish to environments with relatively high concentrations of chemicals has occurred throughout the history of life, although contemporary evolution acts at a much more rapid pace. The growing use of land for mass agriculture and livestock industries in the last 50 years in Florida has dramatically increased the nutrient loading into the groundwaters that feed the springs. Nitrite poses a serious threat for freshwater fauna as it is rapidly up taken and disturbs ion homeostasis and blood gas transport in fish. In this study, we evaluated, by means of a common-garden experiment, the tolerance of fish to nitrite using three different populations of eastern mosquitofish (Gambusia holbrooki) with different background nitrogen pollution histories. Mosquitofish females were exposed to nitrite in the lab, to either < 0.005 mg/l NO2- (control) or 0.3 mg/l NO2- for ten days and we assessed at the end of the exposure period their blood O2 transport capacity by measuring the concentration of four different types of hemoglobin, their total hematocrit, and their respiratory rates. Preliminary results show slight but significant varying patterns in the response of the exposed fish, depending on the population source, as evidenced by their respiratory rates and the blood erythrocyte counts. Mortality was very low, and hemoglobin profiles indicate high tolerance of G. holbrooki to nitrite contamination – a factor supporting their invasion success in agriculturally dominated regions around the world.
Ongoing climate change is a major threat to biodiversity and impacts on species distributions and abundances are already evident. Heterogenous responses of species due to varying abiotic tolerances and dispersal abilities have the potential to further amplify or ameliorate these impacts through changes in species assemblages. Here we investigate the impacts of climate change on terrestrial bird distributions and, subsequently, on species richness as well as on different aspects of phylogenetic diversity of species assemblages across the globe. We go beyond previous work by disentangling the potential impacts on assemblage phylogenetic diversity of species gains vs. losses under climate change and compare the projected impacts to randomized assemblage changes.
We show that climate change might not only affect species numbers and composition of global species assemblages but could also have profound impacts on assemblage phylogenetic diversity, which, across extensive areas, differ significantly from random changes. Both the projected impacts on phylogenetic diversity and on phylogenetic structure vary greatly across the globe. Projected increases in the evolutionary history contained within species assemblages, associated with either increasing phylogenetic diversification or clustering, are most frequent at high northern latitudes. By contrast, projected declines in evolutionary history, associated with increasing phylogenetic over-dispersion or homogenisation, are projected across all continents.
The projected widespread changes in the phylogenetic structure of species assemblages show that changes in species richness do not fully reflect the potential threat from climate change to ecosystems. Our results indicate that the most severe changes to the phylogenetic diversity and structure of species assemblages are likely to be caused by species range shifts rather than range reductions and extinctions. Our findings highlight the importance of considering diverse measures in climate impact assessments and the value of integrating species-specific responses into assessments of entire community changes.
Biodiversity is a cornerstone of human health and well-being. However, while evidence of the contributions of nature to human health is rapidly building, research into how biodiversity relates to human health remains limited in important respects. In particular, a better mechanistic understanding of the range of pathways through which biodiversity can influence human health is needed. These pathways relate to both psychological and social processes as well as biophysical processes. Building on evidence from across the natural, social and health sciences, we present a conceptual framework organizing the pathways linking biodiversity to human health. Four domains of pathways—both beneficial as well as harmful—link biodiversity with human health: (i) reducing harm (e.g. provision of medicines, decreasing exposure to air and noise pollution); (ii) restoring capacities (e.g. attention restoration, stress reduction); (iii) building capacities (e.g. promoting physical activity, transcendent experiences); and (iv) causing harm (e.g. dangerous wildlife, zoonotic diseases, allergens). We discuss how to test components of the biodiversity-health framework with available analytical approaches and existing datasets. In a world with accelerating declines in biodiversity, profound land-use change, and an increase in non-communicable and zoonotic diseases globally, greater understanding of these pathways can reinforce biodiversity conservation as a strategy for the promotion of health for both people and nature. We conclude by identifying research avenues and recommendations for policy and practice to foster biodiversity-focused public health actions.
Aim: Formerly introduced for their presumed value in controlling mosquito-borne diseases, the two mosquitofish Gambusia affinis and G. holbrooki (Poeciliidae) are now among the world's most widespread invasive alien species, negatively impacting aquatic ecosystems around the world. These inconspicuous freshwater fish are, once their presence is noticed, difficult to eradicate. It is, therefore, of utmost importance to assess their geographic potential and to identify their likely ability to persist under novel climatic conditions.
Location Global.
Methods We build species distribution models using occurrence data from the native and introduced distribution ranges to identify putative niche shifts and further ascertain the areas climatically suitable for the establishment and possible spread of mosquitofish.
Results We found significant niche expansions into climatic regions outside their natural climatic conditions, emphasizing the importance of integrating climatic niches of both native and invasive ranges into projections. In particular, there was a marked shift toward tropical regions in Asia and a clear niche shift of European G. holbrooki. This ecological flexibility partly explains the massive success of the two species, and substantially increases the risk for further range expansion. We also showed that the potential for additional expansion resulting from climate change is enormous—especially in Europe.
Main conclusions Despite the successful invasion history and ongoing range expansions, many countries still lack proper preventive measures. Thus, we urge policy makers to carefully evaluate the risk both mosquitofish pose to a particular area and to initiate appropriate management strategies.
Human exposure to endocrine disruptors is well documented by biomonitoring data. However, this information is limited to few chemicals like bisphenol A or phthalate plasticizers. To account for so-far unidentified endocrine disruptors and potential mixture effects we employ bioassays to detect endocrine activity in foodstuff and consequently characterize the integrated exposure to endocrine active compounds. Recently, we reported a broad contamination of commercially available bottled water with estrogenic activity and presented evidence for the plastic packaging being a source of this contamination. In continuation of that work, we here compare different sample preparation methods to extract estrogen-like compounds from bottled water. These data demonstrate that inappropriate extraction methods and sample treatment may lead to false-negative results when testing water extracts in bioassays. Using an optimized sample preparation strategy, we furthermore present data on the estrogenic activity of bottled water from France, Germany, and Italy: eleven of the 18 analyzed water samples (61.1%) induced a significant estrogenic response in a bioassay employing a human carcinoma cell line (MCF7, E-Screen). The relative proliferative effects ranged from 19.8 to 50.2% corresponding to an estrogenic activity of 1.9-12.2 pg estradiol equivalents per liter bottled water. When comparing water of the same spring that is packed in glass or plastic bottles made of polyethylene terephthalate (PET), estrogenic activity is three times higher in water from plastic bottles. These data support the hypothesis that PET packaging materials are a source of estrogen-like compounds. Furthermore, the findings presented here conform to previous studies and indicate that the contamination of bottled water with endocrine disruptors is a transnational phenomenon.
The recent advances in molecular methods and data processing have facilitated research on anisakid nematodes. While most research efforts were made regarding the genus Anisakis, since this genus is held responsible for the majority of reported clinical signs, there is still a demand for data on the genus Pseudoterranova. Several case studies of severe invasive anisakidosis affecting various organs caused by species of the P. decipiens complex have been described. To better understand the way these parasites might infest their fish host, we examined whether parasite location within the fish host affects gene expression. A de novo assembly of the transcriptome of Pseudoterranova bulbosa, isolated from North Atlantic cod, was analysed for patterns of differential gene expression between samples taken from liver and viscera. We additionally searched for homologs to known nematode allergens, to give a first estimate of the potential allergenicity of P. bulbosa. There was a subtle difference in the gene expression of samples taken from liver and viscera. Seventy genes were differentially expressed, 32 genes were upregulated in parasites isolated from liver and 38 genes were upregulated in parasites from viscera. Homologs of five nematode allergens were identified among the genes expressed by P. bulbosa. Our transcriptome of P. bulbosa will be a valuable resource for further meta-analyses and resequencing projects.
The extent of male mate choosiness is driven by a trade-off between various environmental factors associated with the costs of mate acquisition, quality assessment and opportunity costs. Our knowledge about natural variation in male mate choosiness across different populations of the same species, however, remains limited. In this study, we compared male mate choosiness across 10 natural populations of the freshwater amphipod Gammarus roeselii (Gervais 1835), a species with overall high male mating investments, and evaluated the relative influence of population density and sex ratio (both affecting mate availability) on male mate choosiness. We investigated amplexus establishment after separating mating pairs and presenting focal males with a novel, size-matched female from the same population. Our analysis revealed considerable effects of sex ratio and (to a lesser extent) population density on time until amplexus establishment (choosiness). Male amphipods are able to perceive variable social conditions (e.g., sex ratio) and modify their mating strategy accordingly: We found choosiness to be reduced in increasingly male-biased populations, whereas selectivity increases when sex ratio becomes female biased. With this, our study expands our limited knowledge on natural variations in male mate choosiness and illustrates the importance of sex ratio (i.e., level of competition) for male mating decisions in natural environments. Accounting for variation in sex ratios, therefore, allows envisioning a distinctive variation of choosiness in natural populations and highlights the importance of considering social background information in future behavioral studies.
This study describes the chemical composition and in vitro toxicity of the organic fraction of fine particulate matter (PM2.5) at an urban background site, which receives emissions either from Frankfurt international airport or the city centre, respectively. We analysed the chemical composition of filter extracts (PM2.5) using ultrahigh-performance liquid chromatography coupled to a high-resolution mass spectrometer, followed by a non-target analysis. In parallel, we applied the bulk of the filter extracts to a Microtox and acetylcholinesterase-inhibition assay for in vitro toxicity testing. We find that both the chemical composition and toxicity depend on the prevailing wind directions, and the airport operating condition, respectively. The occurrence of the airport marker compounds tricresyl phosphate and pentaerythritol esters depends on the time of the day, reflecting the night flight ban as well as an airport strike event during November 2019. We compared the organic aerosol composition and toxicity from the airport wind-sector against the city centre wind-sector. We find that urban background aerosol shows a higher baseline toxicity and acetylcholinesterase inhibition compared to rural PM2.5 that is advected over the airport. Our results indicate that the concentration and individual composition of PM2.5 influence the toxicity. Suspected drivers of the acetylcholinesterase inhibition are i.e. organophosphorus esters like triphenyl phosphate and cresyldiphenyl phosphate, and the non-ionic surfactant 4-tert-octylphenol ethoxylate. However, further research is necessary to unambiguously identify harmful organic air pollutants and their sources and quantify concentration levels at which adverse effects in humans and the environment can occur.
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 Mb and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb of the genome in which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome- wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
Tree water relations of mature oaks in southwest Germany under extreme drought stress in summer 2018
(2021)
Mature oak stands of different tree height at four sandy valley river sites (Quercus robur) and one south-exposed schist slope (Qu. petraea) in the middle Rhine and lower Main valley were studied from early summer 2017 (normal wet year) until the end of 2018 (extremely hot and dry year). Tree water relations (ΨPD, RWC, sap flow rates) were monitored together with soil water relations, LAI and leaf chl content. In two sandy sites with presumed continuous capillary water access from the groundwater aquifer, sap flow rates of the large trees (30 m) and estimated canopy conductance decreased to about 50% of the maximum value in the course of summer 2018, but recovered in autumn. At two other sites, with smaller trees (14–24 m) and presumed interrupted capillary water access during mid-summer 2018, sap flow rates and canopy conductance broke down completely and trees shed a large proportion of leaves in summer. In one of these sites, ΨPD decreased (reversibly) to -4 MPa, one of the lowest values reported in the literature for central Europe, and tree damage resulted not only in extreme leaf shedding, but also in susceptibility to uprooting (in 2 out of 5 measured trees) by thunderstorm gusts in autumn 2018. At the schist slope site, where oaks reached the lowest height and stand density of all sites, sap flow rates remained similar to the values found at the presumed capillary-water supplied sandy sites, indicating access to rock fissure water even at the peak of the drought period. Our findings corroborate the prediction from vegetation modelling that several Qu. robur stands in the Rhine-Main valleys will be prone to severe forest dieback in the forthcoming decades.
In search for practical silvicultural management tools to identify alternative tree species for predicted Central European climate conditions, a cross-species survey with five evergreen, semi-evergreen, and deciduous Quercus taxa with contrasting morphological leaf traits was performed. Fast chlorophyll fluorescence induction of PSII and relative leaf chlorophyll contents were performed to assess the overall plant vitality at any point in time during two complete vegetation periods in consecutive years (2012 and 2013). Maximum photochemical efficiency of PSII and the performance index on absorption base showed a very conservative relationship to each other and a similar intra-annual progress in all deciduous species, but with a different speed of increase and decrease during leaf development and senescence and thus a different length of vegetation period. The intra-annual variability of OJIP and chlorophyll content parameters is considered with respect to the practicability of measurements in the field for management purposes.
Vampire bats are the only mammals that feed exclusively on blood. To uncover genomic changes associated with this dietary adaptation, we generated a haplotype-resolved genome of the common vampire bat and screened 27 bat species for genes that were specifically lost in the vampire bat lineage. We found previously unknown gene losses that relate to reduced insulin secretion (FFAR1 and SLC30A8), limited glycogen stores (PPP1R3E), and a unique gastric physiology (CTSE). Other gene losses likely reflect the biased nutrient composition (ERN2 and CTRL) and distinct pathogen diversity of blood (RNASE7) and predict the complete lack of cone-based vision in these strictly nocturnal bats (PDE6H and PDE6C). Notably, REP15 loss likely helped vampire bats adapt to high dietary iron levels by enhancing iron excretion, and the loss of CYP39A1 could have contributed to their exceptional cognitive abilities. These findings enhance our understanding of vampire bat biology and the genomic underpinnings of adaptations to blood feeding.
Feeding exclusively on blood, vampire bats represent the only obligate sanguivorous lineage among mammals. To uncover genomic changes associated with adaptations to this unique dietary specialization, we generated a new haplotype-resolved reference-quality genome of the common vampire bat (Desmodus rotundus) and screened 26 bat species for genes that were specifically lost in the vampire bat lineage. We discovered previously-unknown gene losses that relate to metabolic and physiological changes, such as reduced insulin secretion (FFAR1, SLC30A8), limited glycogen stores (PPP1R3E), and a distinct gastric physiology (CTSE). Other gene losses likely reflect the biased nutrient composition (ERN2, CTRL) and distinct pathogen diversity of blood (RNASE7). Interestingly, the loss of REP15 likely helped vampire bats to adapt to high dietary iron levels by enhancing iron excretion and the loss of the 24S-hydroxycholesterol metabolizing enzyme CYP39A1 could contribute to their exceptional cognitive abilities. Finally, losses of key cone phototransduction genes (PDE6H, PDE6C) suggest that these strictly-nocturnal bats completely lack cone-based vision. These findings enhance our understanding of vampire bat biology and the genomic underpinnings of adaptations to sanguivory.
Phylogenetic analyses of nuclear and mitochondrial genomes indicate that polar bears captured the brown bear mitochondrial genome 160,000 years ago, leading to an extinction of the original polar bear mitochondrial genome. However, mitochondrial DNA occasionally integrates into the nuclear genome, forming pseudogenes called numts (nuclear mitochondrial integrations). Screening the polar bear genome identified only 13 numts. Genomic analyses of two additional ursine bears and giant panda indicate that all except one of the discovered numts entered the bear lineage at least 14 million years ago. However, short read genome assemblies might lead to an under-representation of numts or other repetitive sequences. Our findings suggest low integration rates of numts in bears and a loss of the original polar bear mitochondrial genome.
Ochnaceae is a pantropical family with multiple transoceanic disjunctions at deep and shallow levels. Earlier attempts to unravel the processes that led to such biogeographic patterns suffered from insufficient phylogenetic resolution and unclear delimitation of some of the genera. In the present study, we estimated divergence time and ancestral ranges based on a phylogenomic framework with a well-resolved phylogenetic backbone to tackle issues of the timing and direction of dispersal that may explain the modern global distribution of Ochnaceae. The nuclear data provided the more robust framework for divergence time estimation compared to the plastome-scale data, although differences in the inferred clade ages were mostly small. While Ochnaceae most likely originated in West Gondwana during the Late Cretaceous, all crown-group disjunctions are inferred as dispersal-based, most of them as transoceanic long-distance dispersal (LDD) during the Cenozoic. All LDDs occurred in an eastward direction except for the SE Asian clade of Sauvagesieae, which was founded by trans-Pacific dispersal from South America. The most species-rich clade by far, Ochninae, originated from either a widespread neotropical-African ancestor or a solely neotropical ancestor which then dispersed to Africa. The ancestors of this clade then diversified in Africa, followed by subsequent dispersal to the Malagasy region and tropical Asia on multiple instances in three genera during the Miocene-Pliocene. In particular, Ochna might have used the South Arabian land corridor to reach South Asia. Thus, the pantropical distribution of Ochnaceae is the result of LDD either transoceanic or via land bridges/corridors, whereas vicariance might have played a role only along the stem of the family.
Primary biosynthetic enzymes involved in the synthesis of lichen polyphenolic compounds depsides and depsidones are non-reducing polyketide synthases (NR-PKSs), and cytochrome P450s. However, for most depsides and depsidones the corresponding PKSs are unknown. Additionally, in non-lichenized fungi specific fatty acid synthases (FASs) provide starters to the PKSs. Yet, the presence of such FASs in lichenized fungi remains to be investigated. Here we implement comparative genomics and metatranscriptomics to identify the most likely PKS and FASs for olivetoric acid and physodic acid biosynthesis, the primary depside and depsidone defining the two chemotypes of the lichen Pseudevernia furfuracea. We propose that the gene cluster PF33-1_006185, found in both chemotypes, is the most likely candidate for the olivetoric acid and physodic acid biosynthesis. This is the first study to identify the gene cluster and the FAS likely responsible for olivetoric acid and physodic acid biosynthesis in a lichenized fungus. Our findings suggest that gene regulation and other epigenetic factors determine whether the mycobiont produces the depside or the depsidone, providing the first direct indication that chemotype diversity in lichens can arise through regulatory and not only through genetic diversity. Combining these results and existing literature, we propose a detailed scheme for depside/depsidone synthesis.
The European bison was saved from the brink of extinction due to considerable conservation efforts since the early 20th century. The current global population of > 9,500 individuals is the result of successful ex situ breeding based on a stock of only 12 founders, resulting in an extremely low level of genetic variability. Due to the low allelic diversity, traditional molecular tools, such as microsatellites, fail to provide sufficient resolution for accurate genetic assessments in European bison, let alone from non-invasive samples. Here, we present a SNP panel for accurate high-resolution genotyping of European bison, which is suitable for a wide variety of sample types. The panel accommodates 96 markers allowing for individual and parental assignment, sex determination, breeding line discrimination, and cross-species detection. Two applications were shown to be utilisable in further Bos species with potential conservation significance. The new SNP panel will allow to tackle crucial tasks in European bison conservation, including the genetic monitoring of reintroduced populations, and a molecular assessment of pedigree data documented in the world’s first studbook of a threatened species.
The basidiomycete smut fungi are predominantly plant parasitic, causing severe losses in some crops. Most species feature a saprotrophic haploid yeast stage, and several smut fungi are only known from this stage, with some isolated from habitats without suitable hosts, e.g. from Antarctica. Thus, these species are generally believed to be apathogenic, but recent findings that some of these might have a plant pathogenic sexual counterpart, casts doubts on the validity of this hypothesis. Here, four Pseudozyma genomes were re-annotated and compared to published smut pathogens and the well-characterised effector gene Pep1 from these species was checked for its ability to complement a Pep1 deletion strain of Ustilago maydis. It was found that 113 high-confidence putative effector proteins were conserved among smut and Pseudozyma genomes. Among these were several validated effector proteins, including Pep1. By genetic complementation we show that Pep1 homologs from the supposedly apathogenic yeasts restore virulence in Pep1-deficient mutants Ustilago maydis. Thus, it is concluded that Pseudozyma species have retained a suite of effectors. This hints at the possibility that Pseudozyma species have kept an unknown plant pathogenic stage for sexual recombination or that these effectors have positive effects when colonising plant surfaces.
Molluscs are the second most species-rich phylum in the animal kingdom, yet only eleven genomes of this group have been published so far. Here, we present the draft genome sequence of the pulmonate freshwater snail Radix auricularia. Six whole genome shotgun libraries with different layouts were sequenced. The resulting assembly comprises 4,823 scaffolds with a cumulative length of 910 Mb and an overall read coverage of 72x. The assembly contains 94.6 % of a metazoan core gene collection, indicating an almost complete coverage of the coding fraction. The discrepancy of ~690 Mb compared to the estimated genome size of R. auricularia (1.6 Gb) results from a high repeat content of 70 % mainly comprising DNA transposons. The annotation of 17,338 protein coding genes was supported by the use of publicly-available transcriptome data. This draft will serve as starting point for further genomic and population genetic research in this scientifically important phylum.
Molluscs are the second most species-rich phylum in the animal kingdom, yet only 11 genomes of this group have been published so far. Here, we present the draft genome sequence of the pulmonate freshwater snail Radix auricularia. Six whole genome shotgun libraries with different layouts were sequenced. The resulting assembly comprises 4,823 scaffolds with a cumulative length of 910 Mb and an overall read coverage of 72×. The assembly contains 94.6% of a metazoan core gene collection, indicating an almost complete coverage of the coding fraction. The discrepancy of ∼690 Mb compared with the estimated genome size of R. auricularia (1.6 Gb) results from a high repeat content of 70% mainly comprising DNA transposons. The annotation of 17,338 protein coding genes was supported by the use of publicly available transcriptome data. This draft will serve as starting point for further genomic and population genetic research in this scientifically important phylum.
In the course of global climate change, central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) differently: even in the same stand, drought damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance with Pool-GWAS. Contrasting the extreme phenotypes identified 106 significantly associated SNPs throughout the genome. Most annotated genes with associated SNPs (>70%) were previously implicated in the drought reaction of plants. Non-synonymous substitutions led either to a functional amino acid exchange or premature termination. A SNP-assay with 70 loci allowed predicting drought phenotype in 98.6% of a validation sample of 92 trees. Drought resistance in European beech is a moderately polygenic trait that should respond well to natural selection, selective management, and breeding.
The gradual heterogeneity of climatic factors pose varying selection pressures across geographic distances that leave signatures of clinal variation in the genome. Separating signatures of clinal adaptation from signatures of other evolutionary forces, such as demographic processes, genetic drift, and adaptation to non-clinal conditions of the immediate local environment is a major challenge. Here, we examine climate adaptation in five natural populations of the harlequin fly Chironomus riparius sampled along a climatic gradient across Europe. Our study integrates experimental data, individual genome resequencing, Pool-Seq data, and population genetic modelling. Common-garden experiments revealed a positive correlation of population growth rates corresponding to the population origin along the climate gradient, suggesting thermal adaptation on the phenotypic level. Based on a population genomic analysis, we derived empirical estimates of historical demography and migration. We used an FST outlier approach to infer positive selection across the climate gradient, in combination with an environmental association analysis. In total we identified 162 candidate genes as genomic basis of climate adaptation. Enriched functions among these candidate genes involved the apoptotic process and molecular response to heat, as well as functions identified in other studies of climate adaptation in other insects. Our results show that local climate conditions impose strong selection pressures and lead to genomic adaptation despite strong gene flow. Moreover, these results imply that selection to different climatic conditions seems to converge on a functional level, at least between different insect species.
Active transposable elements (TEs) may result in divergent genomic insertion and abundance patterns among conspecific populations. Upon secondary contact, such divergent genetic backgrounds can theoretically give rise to classical Dobzhansky-Muller incompatibilities (DMI), a way how TEs can contribute to the evolution of endogenous genetic barriers and eventually population divergence. We investigated whether differential TE activity created endogenous selection pressures among conspecific populations of the non-biting midge Chironomus riparius, focussing on a Chironomus-specific TE, the minisatellite-like Cla-element, whose activity is associated with speciation in the genus. Using an improved and annotated draft genome for a genomic study with five natural C. riparius populations, we found highly population-specific TE insertion patterns with many private insertions. A highly significant correlation of pairwise population FST from genome-wide SNPs with the FST estimated from TEs suggests drift as the major force driving TE population differentiation. However, the significantly higher Cla-element FST level due to a high proportion of differentially fixed Cla-element insertions indicates that segregating, i.e. heterozygous insertions are selected against. With reciprocal crossing experiments and fluorescent in-situ hybridisation of Cla-elements to polytene chromosomes, we documented phenotypic effects on female fertility and chromosomal mispairings that might be linked to DMI in hybrids. We propose that the inferred negative selection on heterozygous Cla-element insertions causes endogenous genetic barriers and therefore acts as DMI among C. riparius populations. The intrinsic genomic turnover exerted by TEs, thus, may have a direct impact on population divergence that is operationally different from drift and local adaptation.
Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to the closely related polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using three different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains numerous uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to massive amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. The increasing evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.
All giraffe (Giraffa) were previously assigned to a single species (G. Camelopardalis) and nine subspecies. However, multi-locus analyses of all subspecies have shown that there are four genetically distinct clades and suggest four giraffe species. This conclusion might not be fully accepted due to limited data and lack of explicit gene flow analyses. Here we present an extended study based on 21 independent nuclear loci from 137 individuals. Explicit gene flow analyses identify less than one migrant per generation, including between the closely related northern and reticulated giraffe. Thus, gene flow analyses and population genetics of the extended dataset confirm four genetically distinct giraffe clades and support four independent giraffe species. The new findings call for a revision of the IUCN classification of giraffe taxonomy. Three of the four species are threatened with extinction, mostly occurring in politically unstable regions, and as such, require the highest conservation support possible.
Phylogenetic analyses of nuclear and mitochondrial genomes have shown that polar bears captured the mitochondrial genome of brown bears some 160,00 years ago. This hybridization event likely led to an extinction of the original polar bear mitochondrial genome. However, parts of the mitochondrial DNA occasionally integrates into the nuclear genome, forming pseudogenes called numts (nuclear mitochondrial integrations). Screening the polar bear genome for numts, we identified only 13 such integrations. Analyses of whole-genome sequences from additional polar bears, brown and American black bears as well as the giant panda indicates that the discovered numts entered the bear lineage before the initial ursid radiation some 14 million years ago. Our findings suggests a low integration rate of numts in the bear lineage and a complete loss of the original polar bear mitochondrial genome.
Species is the fundamental taxonomic unit in biology and its delimitation has implications for conservation. In giraffe (Giraffa spp.), multiple taxonomic classifications have been proposed since the early 1900s.1 However, one species with nine subspecies has been generally accepted,2 likely due to limited in-depth assessments, subspecies hybridizing in captivity,3,4 and anecdotal reports of hybrids in the wild.5 Giraffe taxonomy received new attention after population genetic studies using traditional genetic markers suggested at least four species.6,7 This view has been met with controversy,8 setting the stage for debate.9,10 Genomics is significantly enhancing our understanding of biodiversity and speciation relative to traditional genetic approaches and thus has important implications for species delineation and conservation.11 We present a high-quality de novo genome assembly of the critically endangered Kordofan giraffe (G. camelopardalis antiquorum)12 and a comprehensive whole-genome analysis of 50 giraffe representing all traditionally recognized subspecies. Population structure and phylogenomic analyses support four separately evolving giraffe lineages, which diverged 230–370 ka ago. These lineages underwent distinct demographic histories and show different levels of heterozygosity and inbreeding. Our results strengthen previous findings of limited gene flow and admixture among putative giraffe species6,7,9 and establish a genomic foundation for recognizing four species and seven subspecies, the latter of which should be considered as evolutionary significant units. Achieving a consensus over the number of species and subspecies in giraffe is essential for adequately assessing their threat level and will improve conservation efforts for these iconic taxa.
Background: Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples.
Results: Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations.
Conclusions: We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales.
Consistent individual differences in behaviour (animal personality) are widespread throughout the Animal Kingdom. This includes variation in risk-taking versus risk-averse behavioural tendencies. Variation in several personality dimensions is associated with distinct fitness consequences and thus, may become a target of natural and/or sexual selection. However, the link between animal personality and mate choice—as a major component of sexual selection—remains understudied. We asked (1) whether females and males of the livebearing fish Poecilia mexicana prefer risk-taking mating partners (directional mating preference), (2) or if their preferences are dependent on the choosing individual’s own personality type (assortative mating). We characterized each test subject for its risk-taking behaviour, assessed as the time to emerge from shelter and enter an unknown area. In dichotomous association preference tests, we offered two potential mating partners that differed in risk-taking behaviour but were matched for other phenotypic traits (body size, shape, and colouration). Females, but not males, exhibited a strong directional preference for risk-taking over risk-averse mating partners. At the same time, the strength of females’ preferences correlated positively with their own risk-taking scores. Our study is the first to demonstrate that a strong overall preference for risk-taking mating partners does not preclude effects of choosing individuals’ own personality type on (subtle) individual variation in mating preferences. More generally, two different preferences functions appear to interact to determine the outcome of individual mate choice decisions.
The plant family Brassicaceae includes some of the most studied hosts of plant microbiomes, targeting microbial diversity, community assembly rules, and effects on host performance. Compared to bacteria, eukaryotes in the brassicaceous microbiome remain understudied, especially under natural settings. Here, we assessed the impact of host identity and age on the assembly of fungal and oomycete root communities, using DNA metabarcoding of roots and associated soil of three annual co-habiting Brassicaceae collected at two time points. Our results showed that fungal communities are more diverse and structured than those of oomycetes. In both cases, plant identity and sampling time had little influence on community variation, whereas root/soil compartment had a strong effect by exerting control on the entry of soil microorganisms into the roots. The enrichment in roots of specific fungi suggests a specialization towards the asymptomatic colonization of plant tissues, which could be relevant to host’s fitness and health.
Wildfires are relatively rare in subarctic tundra ecosystems, but they can strongly change ecosystem properties. Short-term fire effects on subarctic tundra vegetation are well documented, but long-term vegetation recovery has been studied less. The frequency of tundra fires will increase with climate warming. Understanding the long-term effects of fire is necessary to predict future ecosystem changes.
We used a space-for-time approach to assess vegetation recovery after fire over more than four decades. We studied soil and vegetation patterns on three large fire scars (>44, 28 and 12 years old) in dry, lichen-dominated forest tundra in Western Siberia. On 60 plots, we determined soil temperature and permafrost thaw depth, sampled vegetation and measured plant functional traits. We assessed trends in NDVI to support the field-based results on vegetation recovery.
Soil temperature, permafrost thaw depth and total vegetation cover had recovered to pre-fire levels after >44 years, as well as total vegetation cover. In contrast, after >44 years, functional groups had not recovered to the pre-fire state. Burnt areas had lower lichen and higher bryophyte and shrub cover. The dominating shrub species, Betula nana, exhibited a higher vitality (higher specific leaf area and plant height) on burnt compared with control plots, suggesting a fire legacy effect in shrub growth. Our results confirm patterns of shrub encroachment after fire that were detected before in other parts of the Arctic and Subarctic. In the so far poorly studied Western Siberian forest tundra we demonstrate for the first time, long-term fire-legacies on the functional composition of relatively dry shrub- and lichen-dominated vegetation.
Seed harvesting from wild plant populations is key for ecological restoration, but may threaten the persistence of source populations. Consequently, several countries have set guidelines limiting the proportions of harvestable seeds. Here, we use high-resolution data from 298 plant species to model the demographic consequences of seed harvesting. We find that the current guidelines only protect some species, but are insufficient or overly restrictive for others. We show that the maximum possible fraction of seed harvesting is strongly associated with harvesting frequency and generation time of the target species, ranging from 100% in long-lived species to <1% in the most annuals. Our results provide quantitative basis to guide seed harvesting legislation based on species’ generation time and harvesting regime.
Background Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Accumulating evidence suggests that TEs may not be randomly distributed in the genome. Drift and natural selection are important forces shaping TE distribution and accumulation, acting directly on the TE element or indirectly on the host species. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host’s ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold-temperate. We trace the occurrence of the newly identified TEs in populations along three replicated elevation gradients using a Pool-Seq approach, to identify TE insertions of potential adaptive significance.
Results We found that TEs cover 21.26 % of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. Out of a total of 182 TE copies we identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function.
Conclusions This pioneering study into the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution. Particularly, it may serve as a foundation for assessing the impact of TE dynamics on fungal adaptation to the abiotic environment, and the impact of TE activity on the evolution and maintenance of a symbiotic lifestyle.
A candidate gene cluster for the bioactive natural product gyrophoric acid in lichen-forming fungi
(2022)
Natural products of lichen-forming fungi are structurally diverse and have a variety of medicinal properties. Despite this, they a have limited implementation in industry, because the corresponding genes remain unknown for most of the natural products. Here we implement a long-read sequencing and bioinformatic approach to identify the biosynthetic gene cluster of the bioactive natural product gyrophoric acid (GA). Using 15 high-quality genomes representing nine GA-producing species of the lichen-forming fungal genus Umbilicaria, we identify the most likely GA cluster and investigate cluster gene organization and composition across the nine species. Our results show that GA clusters are promiscuous within Umbilicaria, with only three genes that are conserved across species, including the PKS gene. In addition, our results suggest that the same cluster codes for different but structurally similar NPs, i.e., GA, umbilicaric acid and hiascic acid, bringing new evidence that lichen metabolite diversity is also generated through regulatory mechanisms at the molecular level. Ours is the first study to identify the most likely GA cluster, and thus provides essential information to open new avenues for biotechnological approaches to producing and modifying GA and similar lichen-derived compounds. We show that bioinformatics approaches are useful in linking genes and potentially associated natural products. Genome analyses help unlocking the pharmaceutical potential of organisms such as lichens, which are biosynthetically diverse but slow growing, and difficult to cultivate due to their symbiotic nature.
Intraspecific genomic variability affects a species’ adaptive potential towards climatic conditions. Variation in gene content across populations and environments may point at genomic adaptations to specific environments. The lichen symbiosis, a stable association of fungal and photobiont partners, offers an excellent system to study environmentally driven gene content variation. Many species have remarkable environmental tolerances, and often form populations in different climate zones. Here we combine comparative and population genomics to assess the presence and absence of genes in high elevation and low elevation genomes of two lichenized fungi of the genus Umbilicaria. The two species have non-overlapping ranges, but occupy similar climatic niches in North America (U. phaea) and Europe (U. pustulata): high elevation populations are located in the cold temperate zone and low elevation populations in the Mediterranean zone. We assessed gene content variation along replicated elevation gradients in each of the two species, based on a total of 2050 individuals across 26 populations. Specifically, we assessed shared orthologs across species within the same climate zone, and tracked which genes increase or decrease in abundance within populations along elevation. In total, we found 16 orthogroups with shared orthologous genes in genomes at low elevation and 13 at high elevation. Coverage analysis revealed one ortholog that is exclusive to genomes at low elevation. Conserved domain search revealed domains common to the protein kinases (PKs) superfamily. We traced the discovered ortholog in populations along five replicated elevation gradients on both continents. The protein kinase gene linearly declined in abundance with increasing elevation, and was absent in the highest populations. We consider the parallel loss of an ortholog in two species and in two geographic settings a rare find, and a step forward in understanding the genomic underpinnings of climatic tolerances in lichenized fungi. In addition, the tracking of gene content variation provides a widely applicable framework for retrieving biogeographical determinants of gene presence/absence patterns. Our work provides insights into gene content variation of lichenized fungi in relation to climatic gradients, suggesting a new research direction with implications for understanding evolutionary trajectories of complex symbioses in relation to climatic change.
Tree bark constitutes ideal habitat for microbial communities, because it is a stable substrate, rich in micro-niches. Bacteria, fungi, and terrestrial microalgae together form microbial communities, which in turn support more bark-associated organisms, such as mosses, lichens, and invertebrates, thus contributing to forest biodiversity. We have a limited understanding of the diversity and biotic interactions of the bark-associated microbiome, as investigations have mainly focussed on agriculturally relevant systems and on single taxonomic groups. Here we implemented a multi-kingdom metabarcoding approach to analyse diversity and community structure of the green algal, bacterial, and fungal components of the bark-associated microbial communities of beech, the most common broadleaved tree of Central European forests. We identified the most abundant taxa, hub taxa, and co-occurring taxa. We found that tree size (as a proxy for age) is an important driver of community assembly, suggesting that environmental filtering leads to less diverse fungal and algal communities over time. Conversely, forest management intensity had negligible effects on microbial communities on bark. Our study suggests the presence of undescribed, yet ecologically meaningful taxa, especially in the fungi, and highlights the importance of bark surfaces as a reservoir of microbial diversity. Our results constitute a first, essential step towards an integrated framework for understanding microbial community assembly processes on bark surfaces, an understudied habitat and neglected component of terrestrial biodiversity. Finally, we propose a cost-effective sampling strategy to study bark-associated microbial communities across large spatial or environmental scales.
Genome mining as a biotechnological tool for the discovery of novel biosynthetic genes in lichens
(2022)
The ever-increasing demand for novel drugs highlights the need for bioprospecting unexplored taxa for their biosynthetic potential. Lichen-forming fungi (LFF) are a rich source of natural products but their implementation in pharmaceutical industry is limited, mostly because the genes corresponding to a majority of their natural products is unknown. Furthermore, it is not known to what extent these genes encode structurally novel molecules. Advance in next-generation sequencing technologies has expanded the range of organisms that could be exploited for their biosynthetic potential. In this study, we mine the genomes of nine lichen-forming fungal species of the genus Umbilicaria for biosynthetic genes, and categorize the BGCs as “associated product structurally known”, and “associated product putatively novel”. We found that about 25-30% of the biosynthetic genes are divergent when compared to the global database of BGCs comprising of 1,200,000 characterized biosynthetic genes from planta, bacteria and fungi. Out of 217 total BGCs, 43 were only distantly related to known BGCs, suggesting they encode structurally and functionally unknown natural products. Clusters encoding the putatively novel metabolic diversity comprise PKSs (30), NRPSs (12) and terpenes (1). Our study emphasizes the utility of genomic data in bioprospecting microorganisms for their biosynthetic potential and in advancing the industrial application of unexplored taxa. We highlight the untapped structural metabolic diversity encoded in the lichenized fungal genomes. To the best of our knowledge, this is the first investigation identifying genes coding for NPs with potentially novel therapeutic properties in LFF.
Plant communities provide floral resource-landscapes for pollinators. Yet, it is insufficiently understood how these landscapes shape pollinator-mediated interactions among multiple plant species. Here, we study how pollinators and the seed set of plants respond to the distribution of a floral resource (nectar sugar) in space and across plant species, inflorescences and flowering phenologies. In a global biodiversity hotspot, we quantified floral resource-landscapes on 27 sites of 4 ha comprising 127,993 shrubs of 19 species. Visitation rates of key bird pollinators strongly depended on the phenology of site-scale resource amounts. Seed set of focal plants increased with resources of conspecific neighbours and with site-scale resources, notably with heterospecific resources of lower quality (less sugar per inflorescence). Floral resources are thus a common currency determining how multiple plant species interact via pollinators. These interactions may alter conditions for species coexistence in plant communities and cause community-level Allee effects that promote extinction cascades.
Compared to sequence analyses, phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) obtained 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Screening for single nucleotide substitutions in the flanking regions of the TEs show that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, even with strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun and sloth bear form a monophyletic clade. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it easy to confidently extract thousands of TE insertions even from low coverage genomes of non-model organisms, opening new possibilities for biologists to study phylogenies, evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation.
Precise estimates of genome sizes are important parameters for both theoretical and practical biodiversity genomics. We present here a fast, easy-to-implement and precise method to estimate genome size from the number of bases sequenced and the mean sequence coverage. To estimate the latter, we take advantage of the fact that a precise estimation of the Poisson distribution parameter lambda is possible from truncated data, restricted to the part of the coverage distribution representing the true underlying distribution. With simulations we could show that reasonable genome size estimates can be gained even from low-coverage (10X), highly discontinuous genome drafts. Comparison of estimates from a wide range of taxa and sequencing strategies with flow-cytometry estimates of the same individuals showed a very good fit and suggested that both methods yield comparable, interchangeable results.
There is increasing evidence that rapid phenotypic adaptation of quantitative traits is not uncommon in nature. However, the circumstances under which rapid adaptation of polygenic traits occurs are not yet understood. Building on previous concepts of soft selection, i.e. frequency and density dependent selection, I developed and tested the hypothesis that adaptation speed of a polygenic trait depends on the number of offspring per breeding pair in a randomly mating diploid population.
Using individual based modelling on a range of offspring per parent (2–200) in populations of various size (100–10000 individuals), I could show that the by far largest proportion of variance (42%) was explained by the offspring number, regardless of genetic trait architecture (10–50 loci, different locus contribution distributions). In addition, it was possible to identify the majority of the responsible loci and account for even more of the observed phenotypic change with a moderate population size.
The simulation results suggest that offspring numbers may a crucial factor for the adaptation speed of quantitative loci. Moreover, as large offspring numbers translates to a large phenotypic variance in the offspring of each parental pair, this genetic bet hedging strategy increases the chance to contribute to the next generation in unpredictable environments.
Mutations are the ultimate basis of evolution, yet their occurrence rate is known only for few species. We directly estimated the spontaneous mutation rate and the mutational spectrum in the non-biting midge C. riparius with a new approach. Individuals from ten mutation accumulation lines over five generations were deep genome sequenced to count de novo mutations (DNMs) that were not present in a pool of F1 individuals, representing parental genotypes. We identified 51 new single site mutations of which 25 were insertions or deletions and 26 single point mutations. This shift in the mutational spectrum compared to other organisms was explained by the high A/T content of the species. We estimated a haploid mutation rate of 2.1 x 10−9 (95% confidence interval: 1.4 x 10−9 – 3.1 x 10−9) which is in the range of recent estimates for other insects and supports the drift barrier hypothesis. We show that accurate mutation rate estimation from a high number of observed mutations is feasible with moderate effort even for non-model species.
A risk based assessment approach for chemical mixtures from wastewater treatment plant effluents
(2022)
In this study, 56 effluent samples from 52 European wastewater treatment plants (WWTPs) were investigated for the occurrence of 499 emerging chemicals (ECs) and their associated potential risks to the environment. The two main objectives were (i) to extend our knowledge on chemicals occurring in treated wastewater, and (ii) to identify and prioritize compounds of concern based on three different risk assessment approaches for the identification of consensus mixture risk drivers of concern. Approaches include (i) PNEC and EQS-based regulatory risk quotients (RQs), (ii) species sensitivity distribution (SSD)-based hazard units (HUs) and (iii) toxic units (TUs) for three biological quality elements (BQEs) algae, crustacean, and fish.
For this purpose, solid-phase extracts were analysed with wide-scope chemical target screening via liquid chromatography high-resolution mass spectrometry (LC-HRMS), resulting in 366 detected compounds, with concentrations ranging from < 1 ng/L to > 100 µg/L. The detected chemicals were categorized with respect to critical information relevant for risk assessment and management prioritization including: (1) frequency of occurrence, (2) measured concentrations, (3) use groups, (4) persistence & bioaccumulation, and (5) modes of action. A comprehensive assessment using RQ, HU and TU indicated exceedance of risk thresholds for the majority of effluents with RQ being the most sensitive metric. In total, 299 out of the 366 compounds were identified as mixture risk contributors in one of the approaches, while 32 chemicals were established as consensus mixture risk contributors of high concern, including a high percentage (66%) of pesticides and biocides. For samples which have passed an advanced treatment using ozonation or activated carbon (AC), consistently much lower risks were estimated.
Background: The environmental impact of pesticides has been an increasingly discussed issue over the last decades. Constant usage of pesticides presents a burden for soil and causes a decrease in its health, including the negative effects on earthworms which are indicators for soil quality. The objective of this research was the assessment of the effects of two insecticides and two herbicides on the earthworm Eisenia andrei. Namely, the following active ingredients and respective commercial preparations were investigated: esfenvalerate (Sumialfa), thiacloprid (Calypso), dimethenamid-p (Frontier) and prosulfocarb (Filon). Lethal concentrations (48 h) of both active ingredient and commercial preparations were determined using the filter paper contact test. Results: The results showed that Calypso and Frontier were significantly more toxic than the active ingredient. Therefore, all further measurements were performed after exposure of earthworms to the commercial preparations of the pesticides. Specifically, several enzymatic biomarkers and multixenobiotic resistance activity were assessed. Additionally, a fluorescence-based assay for the determination of oxidative stress was established. Significant changes were detected for catalase, carboxylesterase and multixenobiotic activities after 48-h exposures. Also, a significant change in oxidative stress parameters could be observed for both Calypso and Frontier. Conclusions: The obtained results show that commercial preparations can be more toxic than the active ingredients, and the formulations being distributed in the environment can affect earthworms on a molecular level already after short exposures. This emphasizes the importance of a more integrated eco-toxicological assessment of commercial pesticide preparations not to underestimate their effects on the environment.
Background: Studies of parasite communities and patterns in the Antarctic are an important knowledge base with the potential to track shifts in ecological relations and study the effects of climate change on host–parasite systems. Endemic Nototheniinae is the dominant fish group found in Antarctic marine habitats. Through their intermediate position within the food web, Nototheniinae link lower to higher trophic levels and thereby also form an important component of parasite life cycles. The study was set out to gain insight into the parasite fauna of Nototheniops larseni, N. nudifrons and Lepidonotothen squamifrons (Nototheniinae) from Elephant Island (Antarctica).
Methods: Sampling was conducted at three locations around Elephant Island during the ANT-XXVIII/4 expedition of the research vessel Polarstern. The parasite fauna of three Nototheniine species was analysed, and findings were compared to previous parasitological and ecological research collated from a literature review.
Results: All host species shared the parasites Neolebouria antarctica (Digenea), Corynosoma bullosum (Acanthocephala) and Pseudoterranova decipiens E (Nematoda). Other parasite taxa were exclusive to one host species in this study. Nototheniops nudifrons was infected by Ascarophis nototheniae (Nematoda), occasional infections of N. larseni with Echinorhynchus petrotschenkoi (Acanthocephala) and L. squamifrons with Elytrophalloides oatesi (Digenea) and larval tetraphyllidean Cestoda were detected.
Conclusion: All examined fish species’ parasites were predominantly euryxenous regarding their fish hosts. The infection of Lepidonotothen squamifrons with Lepidapedon garrardi (Digenea) and Nototheniops larseni with Echinorhynchus petrotschenkoi represent new host records. Despite the challenges and limited opportunities for fishing in remote areas, future studies should continue sampling on a more regular basis and include a larger number of fish species and sampling sites within different habitats.
Analyses of species functional traits are suitable to better understand the coexistence of species in a given environment. Trait information can be applied to investigate diversity patterns along environmental gradients and subsequently to predict and mitigate threats associated with climate change and land use. Species traits are used to calculate community trait means, which can be related to environmental gradients. However, while species traits can provide insights into the mechanisms underlying community assembly, they can lead to erroneous inferences if mean trait values are used. An alternative is to incorporate intraspecific trait variability (ITV) into calculating the community trait means. This approach gains increasing acceptance in plant studies. For macrofungi, functional traits have recently been applied to examine their community ecology but, to our knowledge, ITV has yet to be incorporated within the framework of community trait means. Here, we present a conceptual summary of the use of ITV to investigate the community ecology of macrofungi, including the underlying ecological theory. Inferences regarding community trait means with or without the inclusion of ITV along environmental gradients are compared. Finally, an existing study is reconsidered to highlight the variety of possible outcomes when ITV is considered. We hope this Opinion will increase awareness of the potential for within-species trait variability and its importance for statistical inferences, interpretations, and predictions of the mechanisms structuring communities of macro- and other fungi.
The UN 2030 Agenda for Sustainable Development stresses the fundamental role science should play in implementing the 17 Sustainable Development Goals endorsed by the global community. But how can and should researchers respond to this societal demand on science? We argue that answering this question requires systematic engagement with the fundamental normative dimensions of the 2030 Agenda and those of the scientific community—and with the implications these dimensions have for research and practice. We suggest that the production of knowledge relevant to sustainable development entails analytic engagement with norms and values through four tasks. First, to unravel and critically reflect on the ethical values involved in sustainability, values should increasingly become an empirical and theoretical object of sustainability research. Second, to ensure that research on social–ecological systems is related to sustainability values, researchers should reflect on and spell out what sustainability values guide their research, taking into account possible interdependencies, synergies, and trade-offs. Third, to find common ground on what sustainability means for specific situations, scientists should engage in deliberative learning processes with societal actors, with a view to jointly reflecting on existing development visions and creating new, contextualized ones. Fourth, this implies that researchers and scientific disciplines must clarify their own ethical and epistemic values, as this defines accountability and shapes identification of problems, research questions, and results. We believe that ignoring these tasks, whether one is in favor or critical of the 2030 Agenda, will undermine the credibility and relevance of scientific contributions for sustainable development.
Competition over land is at the core of many sustainable development challenges in Myanmar: villagers, companies, governments, ethnic minority groups, civil society organisations and non-governmental organisations from local to the international level claim access to and decision-making power over the use of land. Therefore, this article investigates the actor interactions influencing land-use changes and their impacts on the supply of ecosystem services and human well-being. We utilise a transdisciplinary mixed-methods approach and the analytical lens of the social-ecological systems framework. Results reveal that the links between land-use changes, ecosystem services and human well-being are multifaceted; For example ecosystem services can decline, while human well-being increases. We explain this finding through three different pathways to impact (changes in the resource systems, the governance systems or the broader social, economic and political context). We conclude with implications of these results for future sustainable land governance.
Predator-induced plasticity in life-history and antipredator traits during the larval period has been extensively studied in organisms with complex life-histories. However, it is unclear whether different levels of predation could induce warning signals in aposematic organisms. Here, we investigated whether predator-simulated handling affects warning coloration and life-history traits in the aposematic wood tiger moth larva, Arctia plantaginis. As juveniles, a larger orange patch on an otherwise black body signifies a more efficient warning signal against predators but this comes at the costs of conspicuousness and thermoregulation. Given this, one would expect that an increase in predation risk would induce flexible expression of the orange patch. Prior research in this system points to plastic effects being important as a response to environmental changes for life history traits, but we had yet to assess whether this was the case for predation risk, a key driver of this species evolution. Using a full-sib rearing design, in which individuals were reared in the presence and absence of a non-lethal simulated bird attack, we evaluated flexible responses of warning signal size (number of orange segments), growth, molting events, and development time in wood tiger moths. All measured traits except development time showed a significant response to predation. Larvae from the predation treatment developed a more melanized warning signal (smaller orange patch), reached a smaller body size, and molted more often. Our results suggest plasticity is indeed important in aposematic organisms, but in this case may be complicated by the trade-off between costly pigmentation and other life-history traits.
A recent global meta‐analysis reported a decrease in terrestrial but increase in freshwater insect abundance and biomass (van Klink et al., Science 368, p. 417). The authors suggested that water quality has been improving, thereby challenging recent reports documenting drastic global declines in freshwater biodiversity. We raise two major concerns with the meta‐analysis and suggest that these account for the discrepancy with the declines reported elsewhere. First, total abundance and biomass alone are poor indicators of the status of freshwater insect assemblages, and the observed differences may well have been driven by the replacement of sensitive species with tolerant ones. Second, many of the datasets poorly represent global trends and reflect responses to local conditions or nonrandom site selection. We conclude that the results of the meta‐analysis should not be considered indicative of an overall improvement in the condition of freshwater ecosystems.
Primary determinants of communities in deadwood vary among taxa but are regionally consistent
(2020)
The evolutionary split between gymnosperms and angiosperms has far‐reaching implications for the current communities colonizing trees. The inherent characteristics of dead wood include its role as a spatially scattered habitat of plant tissue, transient in time. Thus, local assemblages in deadwood forming a food web in a necrobiome should be affected not only by dispersal ability but also by host tree identity, the decay stage and local abiotic conditions. However, experiments simultaneously manipulating these potential community drivers in deadwood are lacking. To disentangle the importance of spatial distance and microclimate, as well as host identity and decay stage as drivers of local assemblages, we conducted two consecutive experiments, a 2‐tree species and 6‐tree species experiment with 80 and 72 tree logs, respectively, located in canopy openings and under closed canopies of a montane and a lowland forest. We sampled saproxylic beetles, spiders, fungi and bacterial assemblages from logs. Variation partitioning for community metrics based on a unified framework of Hill numbers showed consistent results for both studies: host identity was most important for sporocarp‐detected fungal assemblages, decay stage and host tree for DNA‐detected fungal assemblages, microclimate and decay stage for beetles and spiders and decay stage for bacteria. Spatial distance was of minor importance for most taxa but showed the strongest effects for arthropods. The contrasting patterns among the taxa highlight the need for multi‐taxon analyses in identifying the importance of abiotic and biotic drivers of community composition. Moreover, the consistent finding of microclimate as the primary driver for saproxylic beetles compared to host identity shows, for the first time that existing evolutionary host adaptions can be outcompeted by local climate conditions in deadwood.
Plastid DNA sequence data have been traditionally widely used in plant phylogenetics because of the high copy number of plastids, their uniparental inheritance, and the blend of coding and non-coding regions with divergent substitution rates that allow the reconstruction of phylogenetic relationships at different taxonomic ranks. In the present study, we evaluate the utility of the plastome for the reconstruction of phylogenetic relationships in the pantropical plant family Ochnaceae (Malpighiales). We used the off-target sequence read fraction of a targeted sequencing study (targeting nuclear loci only) to recover more than 100 kb of the plastid genome from the majority of the more than 200 species of Ochnaceae and all but two genera using de novo and reference-based assembly strategies. Most of the recalcitrant nodes in the family’s backbone were resolved by our plastome-based phylogenetic inference, corroborating the most recent classification system of Ochnaceae and findings from a phylogenomic study based on nuclear loci. Nonetheless, the phylogenetic relationships within the major clades of tribe Ochnineae, which comprise about two thirds of the family’s species diversity, received mostly low support. Generally, the phylogenetic resolution was lowest at the infrageneric level. Overall there was little phylogenetic conflict compared to a recent analysis of nuclear loci. Effects of taxon sampling were invoked as the most likely reason for some of the few well-supported discords. Our study demonstrates the utility of the off-target fraction of a target enrichment study for assembling near-complete plastid genomes for a large proportion of samples.
Schistosomiasis is a severe neglected tropical disease caused by trematodes and transmitted by freshwater snails. Snails are known to be highly tolerant to agricultural pesticides. However, little attention has been paid to the ecological consequences of pesticide pollution in areas endemic for schistosomiasis, where people live in close contact with non-sanitized freshwaters. In complementary laboratory and field studies on Kenyan inland areas along Lake Victoria, we show that pesticide pollution is a major driver in increasing the occurrence of host snails and thus the risk of schistosomiasis transmission. In the laboratory, snails showed higher insecticide tolerance to commonly found pesticides than associated invertebrates, in particular to the neonicotinoid Imidacloprid and the organophosphate Diazinon. In the field, we demonstrated at 48 sites that snails were present exclusively in habitats characterized by pesticide pollution and eutrophication. Our analysis revealed that insensitive snails dominated over their less tolerant competitors. The study shows for the first time that in the field, pesticide concentrations considered “safe” in environmental risk assessment have indirect effects on human health. Thus we conclude there is a need for rethinking the environmental risk of low pesticide concentrations and of integrating agricultural mitigation measures in the control of schistosomiasis.
Currently, the genus Polypedates comprises 26 species distributed in South, Southeast, and East Asia. Because of their relatively low dispersal capability and intolerance to seawater, this genus is ideal for the study of terrestrial range evolution that extends into the island archipelagos of southeastern Asia. In this study, based on data compiled for Polypedates from previous studies and partial mitochondrial and nuclear genes collected in this study, we performed systematic biogeographical analysis. We confirmed a Sundaland origin for the extant genus and showed northward dispersal into mainland Southeast Asia and Asia, which coincided with the timing of paleoclimatic change from the Oligocene to Middle Miocene. Climate fluctuations had a profound impact on species diversification within the genus Polypedates. Furthermore, the Red River did not mediate species exchange between Southeast Asia and mainland Asia until the end of the Miocene, with the sudden onset of northward dispersal in several clades independently at that time. Alternatively, the lineage of widespread insular P. leucomystax strongly supports the hypothesis of terrestrial connection between island archipelagos of Southeast Asia during the Mid-Pleistocene paleoclimate fluctuations. Our biogeographical analysis also supports the recent introduction of P. leucomystax to the Philippines and Ryukyus, as previously suggested.
Correction to: The low-copy nuclear gene Agt1 as a novel DNA barcoding marker for Bromeliaceae
(2020)
Correction to: BMC Plant Biol 20, 111 (2020)
https://doi.org/10.1186/s12870-020-2326-5
In the original publication [1] an incorrect version of Additional file 1 was used during typesetting. The incorrect and correct versions of Additional file 1 are available in this correction article. The original article has been updated. The publisher apologizes to the authors and readers for the inconvenience.
Background: The angiosperm family Bromeliaceae comprises over 3.500 species characterized by exceptionally high morphological and ecological diversity, but a very low genetic variation. In many genera, plants are vegetatively very similar which makes determination of non flowering bromeliads difficult. This is particularly problematic with living collections where plants are often cultivated over decades without flowering. DNA barcoding is therefore a very promising approach to provide reliable and convenient assistance in species determination. However, the observed low genetic variation of canonical barcoding markers in bromeliads causes problems.
Result. In this study the low-copy nuclear gene Agt1 is identified as a novel DNA barcoding marker suitable for molecular identification of closely related bromeliad species. Combining a comparatively slowly evolving exon sequence with an adjacent, genetically highly variable intron, correctly matching MegaBLAST based species identification rate was found to be approximately double the highest rate yet reported for bromeliads using other barcode markers.
Conclusion. In the present work, we characterize Agt1 as a novel plant DNA barcoding marker to be used for barcoding of bromeliads, a plant group with low genetic variation. Moreover, we provide a comprehensive marker sequence dataset for further use in the bromeliad research community.
Biominerals fossilisation: fish bone diagenesis in plio–pleistocene african hominid sites of Malawi
(2020)
Fish fossilisation is relatively poorly known, and skeletal element modifications resulting from predation, burial and diagenesis need to be better investigated. In this article, we aim to provide new results about surface, structural and chemical changes in modern and fossil fish bone. Fossil samples come from two distinct localities of roughly the same age in the Pliocene–Pleistocene Chiwondo Beds adjacent to Lake Malawi. Optical and scanning electron microscope (SEM) observations, energy dispersive spectroscopy (EDS) analyses and Fourier transform infrared (FTIR) spectrometry were carried out on three categories of fish bones: (i) fresh modern samples collected in the lake, (ii) extracted from modern fish eagle regurgitation pellets, and (iii) fossils from Malema and Mwenirondo localities. A comparison of these data allowed us to detect various modifications of bone surfaces and structure as well as composition changes. Some differences are observed between fresh bones and modern pellets, and between pellets and fossils. Moreover, fossil fish bone surface modifications, crystallinity, and chemical composition from Malema and Mwenirondo differ despite their chronological and spatial proximities (2.5–2.4 Ma, 500 m). In both sites, the post-predation modifications are strong and may hide alterations due to the predation by bird of prey such as the fish eagle. The combination of the used methods is relevant to analyses of diagenetic alterations in fish bones.
Climate change is influencing some environmental variables in the Southern Ocean (SO) and this will have an effect on the marine biodiversity. Peracarid crustaceans are one of the dominant and most species-rich groups of the SO benthos. To date, our knowledge on the influence of environmental variables in shaping abundance and species composition in the SO’s peracarid assemblages is limited, and with regard to ice coverage it is unknown. The aim of our study was to assess the influence of sea ice coverage, chlorophyll-a, and phytoplankton concentrations on abundance, distribution and assemblage structure of peracarids. In addition, the influence of other physical parameters on peracarid abundance was assessed, including depth, temperature, salinity, sediment type, current velocity, oxygen, iron, nitrate, silicate and phosphate. Peracarids were sampled with an epibenthic sledge (EBS) in different areas of the Atlantic sector of the SO and in the Weddell Sea. Sampling areas were characterized by different regimes of ice coverage (the ice free South Orkney Islands, the seasonally ice-covered Filchner Trough and the Eastern Antarctic Peninsula including the Prince Gustav Channel which was formerly covered by a perennial ice shelf). In total 64766 individuals of peracarids were collected and identified to order level including five orders: Amphipoda, Cumacea, Isopoda, Mysidacea, and Tanaidacea. Amphipoda was the most abundant taxon, representing 32% of the overall abundances, followed by Cumacea (31%), Isopoda (29%), Mysidacea (4%), and Tanaidacea (4%). The Filchner Trough had the highest abundance of peracarids, while the South Orkney Islands showed the lowest abundance compared to other areas. Ice coverage was the main environmental driver shaping the abundance pattern and assemblage structure of peracarids and the latter were positively correlated with ice coverage and chlorophyll-a concentration. We propose that the positive correlation between sea ice and peracarid abundances is likely due to phytoplankton blooms triggered by seasonal sea ice melting, which might increase the food availability for benthos. Variations in ice coverage extent and seasonality due to climate change would strongly influence the abundance and assemblage structure of benthic peracarids.
The species composition of local communities varies in space, and its similarity generally decreases with increasing geographic distance between communities, a phenomenon known as distance decay of similarity. It is, however, not known how changes in local species composition affect ecological processes, that is, whether they lead to differences in the local composition of species' functional roles. We studied eight seed‐dispersal networks along the South American Andes and compared them with regard to their species composition and their composition of functional roles. We tested (1) if changes in bird species composition lead to changes in the composition of bird functional roles, and (2) if the similarity in species composition and functional‐role composition decreased with increasing geographic distance between the networks. We also used cluster analysis to (3) identify bird species with similar roles across all networks based on the similarity in the plants they consume, (i) considering only the species identity of the plants and (ii) considering the functional traits of the plants. Despite strong changes in species composition, the networks along the Andes showed similar composition of functional roles. (1) Changes in species composition generally did not lead to changes in the composition of functional roles. (2) Similarity in species composition, but not functional‐role composition, decreased with increasing geographic distance between the networks. (3) The cluster analysis considering the functional traits of plants identified bird species with similar functional roles across all networks. The similarity in functional roles despite the high species turnover suggests that the ecological process of seed dispersal is organized similarly along the Andes, with similar functional roles fulfilled locally by different sets of species. The high species turnover, relative to functional turnover, also indicates that a large number of bird species are needed to maintain the seed‐dispersal process along the Andes.
Atelopus is a species-rich group of Neotropical bufonids. Present knowledge on bioacoustics in this genus is relatively poor, as vocalisations have been described in only about one fifth of the ca. 100 species known. All studied members of the genus produce vocalisations although, with a few exceptions, most species lack a middle ear. Nonetheless, hearing has been demonstrated even in earless Atelopus making bioacoustics in these toads an inspiring research field. So far, three structural call types have been identified in the genus. As sympatry is uncommon in Atelopus, calls of the same type often vary little between species. Based on recordings from the 1980s, we describe vocalisations of three Venezuelan species (A. carbonerensis, A. mucubajiensis, A. tamaense) from the Cordillera de Mérida, commonly known as the Andes of Venezuela and the Tamá Massif, a Venezuelan spur of the Colombian Cordillera Oriental. Vocalisations correspond, in part, to the previously identified call types in Atelopus. Evaluation of the vocalisations of the three species presented in this study leads us to recognise a fourth structural call type for the genus. With this new addition, the Atelopus acoustic repertoire now includes (1) pulsed calls, (2) pure tone calls, (3) pulsed short calls and (4) pure tone short calls. The call descriptions provided here are valuable contributions to the bioacoustics of these Venezuelan Atelopus species, since all of them have experienced dramatic population declines that limit possibilities of further studies.
Climate change forces many species to move their ranges to higher latitudes or elevations. Resulting immigration or emigration of species might lead to functional changes, e.g., in the trait distribution and composition of ecological assemblages. Here, we combined approaches from biogeography (species distribution models; SDMs) and community ecology (functional diversity) to investigate potential effects of climate-driven range changes on frugivorous bird assemblages along a 3000 m elevational gradient in the tropical Andes. We used SDMs to model current and projected future occurrence probabilities of frugivorous bird species from the lowlands to the tree line. SDM-derived probabilities of occurrence were combined with traits relevant for seed dispersal of fleshy-fruited plants to calculate functional dispersion (FDis; a measure of functional diversity) for current and future bird assemblages. Comparisons of FDis between current and projected future assemblages showed consistent results across four dispersal scenarios, five climate models and two representative concentration pathways. Projections indicated a decrease of FDis in the lowlands, an increase of FDis at lower mid-elevations and little changes at high elevations. This suggests that functional dispersion responds differently to global warming at different elevational levels, likely modifying avian seed dispersal functions and plant regeneration in forest ecosystems along tropical mountains.
The ongoing biodiversity crisis becomes evident in the widely observed decline in abundance and diversity of species, profound changes in community structure, and shifts in species’ phenology. Insects are among the most affected groups, with documented decreases in abundance up to 76% in the last 25–30 years in some terrestrial ecosystems. Identifying the underlying drivers is a major obstacle as most ecosystems are affected by multiple stressors simultaneously and in situ measurements of environmental variables are often missing. In our study, we investigated a headwater stream belonging to the most common stream type in Germany located in a nature reserve with no major anthropogenic impacts except climate change. We used the most comprehensive quantitative long‐term data set on aquatic insects available, which includes weekly measurements of species‐level insect abundance, daily water temperature and stream discharge as well as measurements of additional physicochemical variables for a 42‐year period (1969–2010). Overall, water temperature increased by 1.88 °C and discharge patterns changed significantly. These changes were accompanied by an 81.6% decline in insect abundance, but an increase in richness (+8.5%), Shannon diversity (+22.7%), evenness (+22.4%), and interannual turnover (+34%). Moreover, the community's trophic structure and phenology changed: the duration of emergence increased by 15.2 days, whereas the peak of emergence moved 13.4 days earlier. Additionally, we observed short‐term fluctuations (<5 years) in almost all metrics as well as complex and nonlinear responses of the community toward climate change that would have been missed by simply using snapshot data or shorter time series. Our results indicate that climate change has already altered biotic communities severely even in protected areas, where no other interacting stressors (pollution, habitat fragmentation, etc.) are present. This is a striking example of the scientific value of comprehensive long‐term data in capturing the complex responses of communities toward climate change.
Peronospora salviae‐officinalis, the causal agent of downy mildew on common sage, is an obligate biotrophic pathogen. It grows in the intercellular spaces of the leaf tissue of sage and forms intracellular haustoria to interface with host cells. Although P. salviae‐officinalis was described as a species of its own 10 years ago, the infection process remains obscure. To address this, a histological study of various infection events, from the adhesion of conidia on the leaf surface to de novo sporulation is presented here. As histological studies of oomycetes are challenging due to the lack of chitin in their cell wall, we also present an improved method for staining downy mildews for confocal laser scanning microscopy as well as evaluating the potential of autofluorescence of fixed nonstained samples. For staining, a 1:1 mixture of aniline blue and trypan blue was found most suitable and was used for staining of oomycete and plant structures, allowing discrimination between them as well as the visualization of plant immune responses. The method was also used to examine samples of Peronospora lamii on Lamium purpureum and Peronospora belbahrii on Ocimum basilicum, demonstrating the potential of the presented histological method for studying the infection processes of downy mildews in general.
Active species reintroduction is an important conservation tool when aiming for the restoration of biological communities and ecosystems. The effective monitoring of reintroduction success is a crucial factor in this process. Here, we used a combination of environmental DNA (eDNA) techniques and species distribution models (SDMs) to evaluate the success of recent reintroductions of the freshwater fish Alburnoides bipunctatus in central Germany. We built SDMs without and with eDNA presence data to locate further suitable reintroduction sites and potentially overlooked populations of the species. We successfully detected eDNA of A. bipunctatus at all reintroduction sites, as well as several adjacent sites mostly in downstream direction, which supports the success of reintroduction efforts. eDNA‐based species detection considerably improved SDMs for A. bipunctatus, which allowed to identify species presence in previously unknown localities. Our results confirm the usefulness of eDNA techniques as standard tool to monitor reintroduced fish populations. We propose that combining eDNA with SDMs is a highly effective approach for long‐term monitoring of reintroduction success in aquatic species.
Morphological malformations induced by tributyltin (TBT) exposure during embryonic development have already been characterized in various taxonomic groups, but, nonetheless, the molecular processes underlying these changes remain obscure. The present study provides the first genome-wide screening for differentially expressed genes that are linked to morphological alterations of gonadal tissue from chicken embryos after exposure to TBT. We applied a single injection of TBT (between 0.5 and 30 pg as Sn/g egg) into incubated fertile eggs to simulate maternal transfer of the endocrine disruptive compound. Methyltestosterone (MT) served as a positive control (30 pg/g egg). After 19 days of incubation, structural features of the gonads as well as genome-wide gene expression profiles were assessed simultaneously. TBT induced significant morphological and histological malformations of gonadal tissue from female embryos that show a virilization of the ovaries. This phenotypical virilization was mirrored by altered expression profiles of sex-dependent genes. Among these are several transcription and growth factors (e.g. FGF12, CTCF, NFIB), whose altered expression might serve as a set of markers for early identification of endocrine active chemicals that affect embryonic development by transcriptome profiling without the need of elaborate histological analyses.
Aim: To provide distribution information and preliminary conservation assessments for all species of the pineapple family (Bromeliaceae), one of the most diverse and ecologically important plant groups of the American tropics—a global biodiversity hotspot. Furthermore, we aim to analyse patterns of diversity, endemism and the conservation status of the Bromeliaceae on the continental level in the light of their evolutionary history.
Location: The Americas.
Methods: We compiled a dataset of occurrence records for 3,272 bromeliad species (93.4% of the family) and modelled their geographic distribution using either climate‐based species distribution models, convex hulls or geographic buffers dependent on the number of occurrences available. We then combined this data with information on taxonomy and used the ConR software for a preliminary assessment of the conservation status of all species following Criterion B of the International Union for the Conservation of Nature (IUCN).
Results: Our results stress the Atlantic Forest in eastern Brazil, the Andean slopes, Central America and the Guiana Highlands as centres of bromeliad diversity and endemism. Phylogenetically ancient subfamilies of bromeliads are centred in the Guiana highlands whereas the large radiations of the group spread across different habitats and large geographic area. A total of 81% of the evaluated bromeliad species are Possibly Threatened with extinction. We provide range polygons for 3,272 species, as well as newly georeferenced point localities for 911 species in the novel “bromeliad” r package, together with functions to generate diversity maps for individual taxonomic or functional groups.
Main conclusions: Diversity centres of the Bromeliaceae agreed with macroecological patterns of other plant and animal groups, but show some particular patterns related to the evolutionary origin of the family, especially ancient dispersal corridors. A staggering 2/3rds of Bromeliaceae species might be threatened with extinction, especially so in tropical rain forests, raising concerns about the conservation of the family and bromeliad‐dependent animal species.
In 2010, the Conference of the Parties of the Convention on Biological Diversity agreedon the Strategic Plan for Biodiversity 2011–2020 in Aichi Prefecture, Japan. As this planapproaches its end, we discussed whether marine biodiversity and prediction studieswere nearing the Aichi Targets during the 4th World Conference on Marine Biodiversityheld in Montreal, Canada in June 2018. This article summarises the outcome of a five-day group discussion on how global marine biodiversity studies should be focusedfurther to better understand the patterns of biodiversity. We discussed and reviewedseven fundamental biodiversity priorities related to nine Aichi Targets focusing onglobal biodiversity discovery and predictions to improve and enhance biodiversitydata standards (quantity and quality), tools and techniques, spatial and temporal scaleframing, and stewardship and dissemination. We discuss how identifying biodiversityknowledge gaps and promoting efforts have and will reduce such gaps, including via theuse of new databases, tools and technology, and how these resources could be improvedin the future. The group recognised significant progress toward Target 19 in relationto scientific knowledge, but negligible progress with regard to Targets 6 to 13 whichaimed to safeguard and reduce human impacts on biodiversity.
The subfamily Bromelioideae is one of the most diverse groups among the neotropical Bromeliaceae. Previously, key innovations have been identified which account for the extraordinary radiation and species richness of this subfamily, especially in the so-called core Bromelioideae. However, in order to extend our understanding of the evolutionary mechanisms, the genomic mechanisms (e.g. polyploidy, dysploidy) that potentially underlie this accelerated speciation also need to be tested. Here, using PI and DAPI staining and flow cytometry we estimated genome size and GC content of 231 plants covering 30 genera and 165 species and combined it with published data. The evolutionary and ecological significance of all three genomic characters was tested within a previously generated dated phylogenetic framework using ancestral state reconstructions, comparative phylogenetic methods, and multiple regressions with climatic variables. The absolute genome size (2C) of Bromelioideae varied between 0.59 and 4.11 pg, and the GC content ranged between 36.73 and 41.43%. The monoploid genome sizes (Cx) differed significantly between core and early diverging lineages. The occurrence of dysploidy and polyploidy was, with few exceptions, limited to the phylogenetically isolated early diverging tank-less lineages. For Cx and GC content Ornstein–Uhlenbeck models outperformed the Brownian motion models suggesting adaptive potential linked to the temperature conditions. 2C-values revealed different rates of evolution in core and early diverging lineages also related to climatic conditions. Our results suggest that polyploidy is not associated with higher net diversification and fast radiation in core bromelioids. On the other hand, although coupled with higher extinction rates, dysploidy, polyploidy, and resulting genomic reorganizations might have played a role in the survival of the early diverging bromelioids in hot and arid environments.
Our knowledge of early evolution of snakes is improving, but all that we can infer about the evolution of modern clades of snakes such as boas (Booidea) is still based on isolated bones. Here, we resolve the phylogenetic relationships of Eoconstrictor fischeri comb. nov. and other booids from the early-middle Eocene of Messel (Germany), the best-known fossil snake assemblage yet discovered. Our combined analyses demonstrate an affinity of Eoconstrictor with Neotropical boas, thus entailing a South America-to-Europe dispersal event. Other booid species from Messel are related to different New World clades, reinforcing the cosmopolitan nature of the Messel booid fauna. Our analyses indicate that Eoconstrictor was a terrestrial, medium- to large-bodied snake that bore labial pit organs in the upper jaw, the earliest evidence that the visual system in snakes incorporated the infrared spectrum. Evaluation of the known palaeobiology of Eoconstrictor provides no evidence that pit organs played a role in the predator–prey relations of this stem boid. At the same time, the morphological diversity of Messel booids reflects the occupation of several terrestrial macrohabitats, and even in the earliest booid community the relation between pit organs and body size is similar to that seen in booids today.
Animal tracking and biologging devices record large amounts of data on individual movement behaviors in natural environments. In these data, movement ecologists often view unexplained variation around the mean as “noise” when studying patterns at the population level. In the field of behavioral ecology, however, focus has shifted from population means to the biological underpinnings of variation around means. Specifically, behavioral ecologists use repeated measures of individual behavior to partition behavioral variability into intrinsic among-individual variation and reversible behavioral plasticity and to quantify: a) individual variation in behavioral types (i.e. different average behavioral expression), b) individual variation in behavioral plasticity (i.e. different responsiveness of individuals to environmental gradients), c) individual variation in behavioral predictability (i.e. different residual within-individual variability of behavior around the mean), and d) correlations among these components and correlations in suites of behaviors, called ‘behavioral syndromes’. We here suggest that partitioning behavioral variability in animal movements will further the integration of movement ecology with other fields of behavioral ecology. We provide a literature review illustrating that individual differences in movement behaviors are insightful for wildlife and conservation studies and give recommendations regarding the data required for addressing such questions. In the accompanying R tutorial we provide a guide to the statistical approaches quantifying the different aspects of among-individual variation. We use movement data from 35 African elephants and show that elephants differ in a) their average behavior for three common movement behaviors, b) the rate at which they adjusted movement over a temporal gradient, and c) their behavioral predictability (ranging from more to less predictable individuals). Finally, two of the three movement behaviors were correlated into a behavioral syndrome (d), with farther moving individuals having shorter mean residence times. Though not explicitly tested here, individual differences in movement and predictability can affect an individual’s risk to be hunted or poached and could therefore open new avenues for conservation biologists to assess population viability. We hope that this review, tutorial, and worked example will encourage movement ecologists to examine the biology of individual variation in animal movements hidden behind the population mean.
Soil degradation can have an impact on the soil microbiota, but its specific effects on soil fungal communities are poorly understood. In this work, we studied the impact of soil degradation on the richness and diversity of communities of soil fungi, including three different degrees of degradation in Germany and Panama. Soil fungi were isolated monthly using the soil-sprinkling method for 8 months in Germany and 3 months in Panama, and characterized by morphological and molecular data. Soil physico-chemical properties were measured and correlated with the observed values of fungal diversity. We isolated a total of 71 fungal species, 47 from Germany, and 32 from Panama. Soil properties were not associated with fungal richness, diversity, or composition in soils, with the exception of soil compaction in Germany. The geographic location was a strong determinant of the soil fungal species composition although in both countries there was dominance by members of the orders Eurotiales and Hypocreales. In conclusion, the results of this work do not show any evident influence of soil degradation on communities of soil fungi in Germany or Panama.
The Culex pipiens complex encompasses five species and subspecies of the genus Culex. Over time, a multitude of morphologically indistinguishable species has been assigned to this complex with several species being classified as important vectors for different diseases. Some species of this complex hibernate in subterranean habitats, and it has been proven that viruses can survive this phase of hibernation. However, studies focusing on the environmental requirements, ecology and spatial and temporal distribution patterns of mosquitos in underground habitats are sparse. Here, we investigate the main environmental factors and dependencies of Culex, considering the number of individuals and survival probabilities in underground habitats during the winter months. Methods. Since the State of Hesse, Germany harbors about 3500 to 4000 subterranean shelters ample availability of subterranean habitats there provides a good opportunity to conduct detailed investigations of the Culex pipiens complex. In this study, we identified a sample of 727 specimens of overwintering females within the Culex pipiens complex from 52 different underground sites collected over a period of 23 years using qPCR. A complete data set of samplings of hibernating mosquitos from 698 subterranean habitats in Central Germany over the same period was available to study the spatial and temporal patterns and the effect of temperature and precipitation conditions on these hibernating populations using a generalized linear model (GLM). Results. Our qPCR-results show, similar to aboveground studies of mosquitos, that Culex pipiens pipiens and Culex torrentium occur sympatrically. On the other hand, Culex pipiens molestus occurred very rarely. The GLM revealed no shifts in species composition over time, but different preferences for subterranean hibernacula, chemical effects on overwintering populations as well as effects of annual and seasonal mean temperature and precipitation during the active phase from March to November. Cx. p. pipiens and Cx. torrentium are the most common species within Hessian caves and other underground habitats during winter. They co-occur with different frequency without any patterns in species composition. Weather conditions influence the number of overwintering mosquitos during the activity phase. Depending on cave parameters, the number of mosquitos decreases during the winter months.
Diatoms are thought to provide about 40% of total global photosynthesis and diatoms of the genus Coscinodiscus are an important, sometimes dominant, cosmopolitan component of the marine diatom community. The oomycete parasitoid Lagenisma coscinodisci is widespread in the northern hemisphere on its hosts in the genus Coscinodiscus. Because of its potential ecological importance, it would be a suitable pathogen model to investigate plankton/parasite interactions, but the species cannot be cultivated on media without its host, so far. Thus, it was the aim of this study to explore the potential of dual culture of host and pathogen in the laboratory and to optimise cultivation to ensure a long-term cultivation of the pathogen. Here, we report successful cultivation of a single spore strain of L. coscinodisci (Isla), on several Coscinodiscus species and strains, as well as the establishment of a cultivation routine with Coscinodiscus granii (CGS1 and CG36), which enabled us to maintain the single spore strain for more than 3 years in 6 cm Petri dishes and 10 ml tissue culture flasks. This opens up the opportunity to study the processes and mechanism in plankton/parasitoid interactions under controlled conditions.
The oomycete genus Ectrogella currently comprises a rather heterogeneous group of obligate endoparasitoids, mostly of diatoms and algae. Despite their widespread occurrence, little is known regarding the phylogenetic affinities of these bizarre organisms. Traditionally, the genus was included within the Saprolegniales, based on zoospore diplanetism and a saprolegnia/achlya-like zoospore discharge. The genus has undergone multiple re-definitions in the past, and has often been used largely indiscriminately for oomycetes forming sausage-like thalli in diatoms. While the phylogenetic affinity of the polyphyletic genus Olpidiopsis has recently been partially resolved, taxonomic placement of the genus Ectrogella remained unresolved, as no sequence data were available for species of this genus. In this study, we report the phylogenetic placement of Ectrogella bacillariacearum infecting the freshwater diatom Nitzschia sigmoidea. The phylogenetic reconstruction shows that Ectrogella bacillariacearum is grouped among the early diverging lineages of the Saprolegniomycetes with high support, and is unrelated to the monophyletic diatom-infecting olpidiopsis-like species. As these species are neither related to Ectrogella, nor to the early diverging lineages of Olpidiopsis s. str. and Miracula, they are placed in a new genus, Diatomophthora, in the present study.
Holocarpic oomycetes are poorly known but widespread parasites in freshwater and marine ecosystems. Most of the holocarpic species seem to belong to clades that diverge before the two crown lineages of the oomycetes, the Saprolegniomycetes and the Peronosporomycetes. Recently, the genus Miracula was described to accommodate Miracula helgolandica, a holocarpic parasitoid of Pseudo-nitzschia diatoms, which received varying support for its placement as the earliest-diverging oomycete lineage. In the same phylogenetic reconstruction, Miracula helgolandica was grouped with some somewhat divergent sequences derived from environmental sequencing, indicating that Miracula would not remain monotypic. Here, a second species of Miracula is reported, which was found as a parasitoid in the limnic centric diatom Pleurosira leavis. Its life-cycle stages are described and depicted in this study and its phylogenetic placement in the genus Miracula revealed. As a consequence, the newly discovered species is introduced as Miracula moenusica.
Olpidiopsis is a genus of obligate holocarpic endobiotic oomycetes. Most of the species classified in the genus are known only from their morphology and life cycle, and a few have been examined for their ultrastructure or molecular phylogeny. However, the taxonomic placement of all sequenced species is provisional, as no sequence data are available for the type species, O. saprolegniae, to consolidate the taxonomy of species currently placed in the genus. Thus, efforts were undertaken to isolate O. saprolegniae from its type host, Saprolegnia parasitica and to infer its phylogenetic placement based on 18S rDNA sequences. As most species of Olpidiopsis for which sequence data are available are from rhodophyte hosts, we have also isolated the type species of the rhodophyte-parasitic genus Pontisma, P. lagenidioides and obtained partial 18S rDNA sequences. Phylogenetic reconstructions in the current study revealed that O. saprolegniae from Saprolegnia parasitica forms a monophyletic group with a morphologically similar isolate from S. ferax, and a morphologically and phylogenetically more divergent species from S. terrestris. However, they were widely separated from a monophyletic, yet unsupported clade containing P. lagenidioides and red algal parasites previously classified in Olpidiopsis. Consequently, all holocarpic parasites in red algae should be considered to be members of the genus Pontisma as previously suggested by some researchers. In addition, a new species of Olpidiopsis, O. parthenogenetica is introduced to accommodate the pathogen of S. terrestris.
Genotoxicity assessment is of high relevance for crude and refined petroleum products, since oil compounds are known to cause DNA damage with severe consequences for aquatic biota as demonstrated in long-term monitoring studies. This study aimed at the optimization and evaluation of small-scale higher-throughput assays (Ames fluctuation, micronucleus, Nrf2-CALUX®) covering different mechanistic endpoints as first screening tools for genotoxicity assessment of oils. Cells were exposed to native and chemically dispersed water-accommodated fractions (WAFs) of three oil types varying in their processing degree. Independent of an exogenous metabolic activation system, WAF compounds induced neither base exchange nor frame shift mutations in bacterial strains. However, significantly increased chromosomal aberrations in zebrafish liver (ZF-L) cells were observed. Oxidative stress was indicated for some treatments and was not correlated with observed DNA damage. Application of a chemical dispersant increased the genotoxic potential rather by the increased bioavailability of dissolved and particulate oil compounds. Nonetheless, the dispersant induced a clear oxidative stress response, indicating a relevance for general toxic stress. Results showed that the combination of different in vitro assays is important for a reliable genotoxicity assessment. Especially, the ZF-L capable of active metabolism and DNA repair seems to be a promising model for WAF testing.
Solenogastres (Aplacophora) is a small clade of marine, shell-less worm-molluscs with close to 300 valid species. Their distribution ranges across all oceans, and whereas the vast majority of species has been collected and described from the continental shelf and slope, only few species are known from depths below 4,000 m. Following traditional taxonomy, identification of specimens to species level is complex and time-consuming and requires detailed investigations of morphology and anatomy—often resulting in the exclusion of the clade in biodiversity or biogeographic studies. During the KuramBio expedition (Kuril-Kamchatka Biodiversity Studies) to the abyssal plain of the Northwest Pacific and the Kuril-Kamchatka Trench, 33 solenogaster specimens were sampled from 4,830 m to 5,397 m. Within this study we present an efficient workflow to address solenogaster diversity, even when confronted with a high degree of singletons and minute body sizes, hampering the use of single individuals for multiple morphological and molecular approaches. We combine analyses of external characters and scleritome with molecular barcoding based on a self-designed solenogaster specific set of mitochondrial primers. Overall we were able to delineate at least 19 solenogaster lineages and identify 15 species to family level and beyond. Based on our approach we identified three key lineages from the two regionally most species-rich families (Acanthomeniidae and Pruvotinidae) for deeper taxonomic investigations and describe the novel abyssal species Amboherpia abyssokurilensis sp. nov. (Cavibelonia, Acanthomeniidae) using microanatomical 3D-reconstructions. Our study more than doubles the previous records of solenogaster species from the Northwest Pacific and its marginal seas. Almost all lineages are reported for the first time from the region of the (Northwest) Pacific, vastly expanding distribution ranges of the respective clades. Moreover it doubles the number of Solenogastres collected from abyssal depths on a global scale and underlines the lack of exploratory α-diversity work in the abyssal zone for reliable species estimates in marine biodiversity.
Blow flies are the first insect group to colonize on a dead body and thus correct species identification is a crucial step in forensic investigations for estimating the minimum postmortem interval, as developmental times are species-specific. Due to the difficulty of traditional morphology-based identification such as the morphological similarity of closely related species and uncovered taxonomic keys for all developmental stages, DNA-based identification has been increasing in interest, especially in high biodiversity areas such as Thailand. In this study, the effectiveness of long mitochondrial cytochrome c oxidase subunit I and II (COI and COII) sequences (1247 and 635 bp, respectively) in identifying 16 species of forensically relevant blow flies in Thailand (Chrysomya bezziana, Chrysomya chani, Chrysomya megacephala, Chrysomya nigripes, Chrysomya pinguis, Chrysomya rufifacies, Chrysomya thanomthini, Chrysomya villeneuvi, Lucilia cuprina, Lucilia papuensis, Lucilia porphyrina, Lucilia sinensis, Hemipyrellia ligurriens, Hemipyrellia pulchra, Hypopygiopsis infumata, and Hypopygiopsis tumrasvini) was assessed using distance-based (Kimura two-parameter distances based on Best Match, Best Close Match, and All Species Barcodes criteria) and tree-based (grouping taxa by sequence similarity in the neighbor-joining tree) methods. Analyses of the obtained sequence data demonstrated that COI and COII genes were effective markers for accurate species identification of the Thai blow flies. This study has not only demonstrated the genetic diversity of Thai blow flies, but also provided a reliable DNA reference database for further use in forensic entomology within the country and other regions where these species exist.
Understanding land cover degradation patterns and the effects of geomorphological units on phytodiversity is important for guiding management decisions and restoration strategies in the Sahelian vulnerables zones. This paper describes land cover degradation by combining Landsat TM image analysis and field data measurements in the Gourouol catchment of the Sahelian zone of Burkina Faso. Erdas Imagine 9.2 and Arc-GIS.10 were applied. The change patterns were obtained by superposing land cover maps for 1992 and 2010. The field data were collected by the mean of inventories according to the Braun-Blanquet phytosociological relevés methods. Plot sizes were 50 m x 20 m for woody species and 10 m x 10 m for herbaceous species. Six land cover types were identified and mapped: cultivated lands, bared lands, lowlands, which all spatially increased; and shrub-steppes, grasslands and water bodies, which all spatially decreased. The dynamic patterns based on the geomorphological units were non-degraded lowlands, stable sand dunes and degraded glacis. High plant diversity was found in lowlands, whereas low diversity occurred in glacis. A significant dissimilarity was observed between communities. The Shannon diversity indices in plant communities were approximately close to ln(species richness). The Pielou indices were close to 1, indicating a species fairly good distribution. Our results showed a variation of land cover over time and the effects of geomorphological units on phytodiversity. Furthermore, this variation helps oppose land degradation in the Sahel.
Microthlaspi erraticum is widely distributed in temperate Eurasia, but restricted to Ca2+-rich habitats, predominantly on white Jurassic limestone, which is made up by calcium carbonate, with little other minerals. Thus, naturally occurring Microthlaspi erraticum individuals are confronted with a high concentration of Ca2+ ions while Mg2+ ion concentration is relatively low. As there is a competitive uptake between these two ions, adaptation to the soil condition can be expected. In this study, it was the aim to explore the genomic consequences of this adaptation by sequencing and analysing the genome of Microthlaspi erraticum. Its genome size is comparable with other diploid Brassicaceae, while more genes were predicted. Two Mg2+ transporters known to be expressed in roots were duplicated and one showed a significant degree of positive selection. It is speculated that this evolved due to the pressure to take up Mg2+ ions efficiently in the presence of an overwhelming amount of Ca2+ ions. Future studies on plants specialized on similar soils and affinity tests of the transporters are needed to provide unequivocal evidence for this hypothesis. If verified, the transporters found in this study might be useful for breeding Brassicaceae crops for higher yield on Ca2+-rich and Mg2+ -poor soils.
In the light of emerging resistances against common drugs, new drug leads are required. In the past natural sources have been more yielding in this respect than synthetic strategies. Fungi synthesize many natural products with biological activities and pharmacological relevance. However, only a fraction of the estimated fungal diversity has been evaluated for biological activity, and much of the Fungi’s natural chemical diversity awaits discovery. Especially promising in this context are lichenized fungi. Lichens are well known for their particularly rich and characteristic secondary chemistry which allows them to withstand intense UV radiation, protects them against herbivory, and prevents them from being overgrown. The slow growth rates of lichens and difficulties and infeasibility of large scale cultivations in the laboratory render lichens inaccessible for applied purposes. These experimental challenges have led to a poor understanding of the molecular mechanisms underlying the biosynthesis of characteristic lichen secondary metabolites. The recent development of improved sequencing techniques has enabled new strategies to address multi-species assemblages directly through metagenome sequencing and survey their biosynthetic potential through genome mining. However, whole genome sequencing of entire lichen thalli to metagenomically assess the lichen-forming fungus without the need of cultivation has not been evaluated for lichens before. This approach will enable the reconstruction of fungal genomes from mixed DNA from lichen thalli and allow the exploration of biosynthetic gene content.
My thesis was conducted in two parts: a methodological evaluation of a metagenomic strategy to reconstruct genomes and gene sets of lichen-forming fungi, and the exploration of biosynthetic gene content with the help of comparative genomics and phylogenetics. For the first part, I evaluated the quality of metagenome-derived genome assemblies and gene sets by direct comparison to culture-derived reference assemblies and gene sets of the same species. I showed that metagenome-derived fungal assemblies are comparable to culture-derived references genomes and have a similar total genome size and fungal genome completeness. The quality of assemblies was affected strongly by the choice of assembler, but not by the method of taxonomic assignment or inference of non-mycobiont DNA sequences. The fungal gene space is well covered in metagenome-derived and culture-derived fungal gene sets and overlaps to 88-90 %. Finally, the metagenome-derived assemblies reliably recover gene families of secondary metabolism. This shows the suitability of metagenomically derived genomes for mining biosynthetic genes, and potentially also other gene families. Overall, the method validation showed a high similarity between metagenome- and culture-derived genome assemblies.
For the second part of my thesis, I explored the biosynthetic gene content in two different systems: Between two sister-species with different ecological requirements but similar chemical profile, and between two species which are metabolite-rich and economically relevant in the perfume industry. I compared the diversity of biosynthetic gene clusters between the species and in the broader context of other lichenized and non-lichenized fungi. Overall, the whole genome mining revealed a large number of uncharacterised secondary metabolite gene clusters in fifteen genomes of lichen-forming fungi compared to other fungal classes. Their number highly outweighs the number of known synthesized metabolites and highlights the hidden biosynthetic potential in lichen-forming fungi. Many biosynthetic gene clusters in the ecological distinct sister-species showed a high homology in accordance with the high synteny in gene content and order in both genomes. These clusters represent ideal candidates for secondary metabolites synthesized by both species, while the remaining clusters may encode for metabolites relevant for the different ecological requirements of both species. The metabolite-rich species used in the perfume industry showed a particularly high number of biosynthetic gene clusters. An in-depth characterization of architecture and gene content of homologous gene clusters together with hints from phylogenetic relatedness to functional characterized metabolites provides promising insights into the biosynthetic gene content of these lichen-forming fungi.
In conclusion, I showed that metagenome sequencing of natural lichen thalli is a feasible approach to reconstruct the fungal mycobiont genome of lichens and circumvent time-consuming and in some cases impossible cultivation of individuals. The genome mining for secondary metabolite gene clusters in lichen-forming fungi revealed a high biosynthetic potential for the discovery of new natural products. One of the focal species, Evernia prunastri, contained the highest ever reported number (80) of biosynthetic clusters in lichenized fungi. The comprehensive cluster characterizations through annotation, comparative mapping and phylogenetics provide first valuable hints for linking metabolites to genes in these lichen-forming fungi. My results pave the way for biotechnological strategies to unlock the vast richness of natural products from lichens for applied purposes.
Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the extent to which stochastic or deterministic processes influenced the composition of local communities. A combination of phylogenetic turnover analysis and null modeling demonstrated that either homogenization by unlimited stochastic dispersal or scenarios, in which neither stochastic processes nor deterministic forces dominated, explained local assembly processes. Thus, the majority of all sampled communities (82%) was rather homogeneous with no significant changes in abundance-weighted composition. However, we detected strong and uniform taxonomic shifts within just nine samples in early summer. Thus, community snapshots sampled from single points in time or space do not necessarily reflect a representative community state. The potential for change despite the overall homogeneity was further demonstrated when the focus shifted to the rare biosphere. Rare OTU turnover, rather than nestedness, characterized abundance-independent β-diversity. Accordingly, boosted generalized additive models encompassing spatial, temporal and environmental variables revealed strong and highly diverse effects of space on OTU abundance, even within the same genus. This pure spatial effect increased with decreasing OTU abundance and frequency, whereas soil moisture – the most important environmental variable – had an opposite effect by impacting abundant OTUs more than the rare ones. These results indicate that – despite considerable oscillation in space and time – the abundant and resident OTUs provide a community backbone that supports much higher β-diversity of a dynamic rare biosphere. Our findings reveal complex interactions among space, time, and environmental filters within bacterial communities in a long-established temperate grassland.