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Lejzerowicz, Franck ; Gooday, Andrew John ; Angeles, Inés Barrenechea ; Cordier, Tristan ; Morard, Raphaël ; Apothéloz-Perret-Gentil, Laure ; Lins, Lidia ; Menot, Lenaick ; Brandt, Angelika ; Levin, Lisa Ann ; Martínez Arbizu, Pedro ; Smith, Craig Randall ; Pawlowski, Jan
The abyssal seafloor is a mosaic of highly diverse habitats that represent the least known marine ecosystems on Earth. Some regions enriched in natural resources, such as polymetallic nodules in the Clarion-Clipperton Zone (CCZ), attract much interest because of their huge commercial potential. Since nodule mining will be destructive, baseline data are necessary to measure its impact on benthic communities. Hence, we conducted an environmental DNA and RNA metabarcoding survey of CCZ biodiversity targeting microbial and meiofaunal eukaryotes that are the least known component of the deep-sea benthos. We analyzed two 18S rRNA gene regions targeting eukaryotes with a focus on Foraminifera (37F) and metazoans (V1V2), sequenced from 310 surface-sediment samples from the CCZ and other abyssal regions. Our results confirm huge unknown deep-sea biodiversity. Over 60% of benthic foraminiferal and almost a third of eukaryotic operational taxonomic units (OTUs) could not be assigned to a known taxon. Benthic Foraminifera are more common in CCZ samples than metazoans and dominated by clades that are only known from environmental surveys. The most striking results are the uniqueness of CCZ areas, both datasets being characterized by a high number of OTUs exclusive to the CCZ, as well as greater beta diversity compared to other abyssal regions. The alpha diversity in the CCZ is high and correlated with water depth and terrain complexity. Topography was important at a local scale, with communities at CCZ stations located in depressions more diverse and heterogeneous than those located on slopes. This could result from eDNA accumulation, justifying the interim use of eRNA for more accurate biomonitoring surveys. Our descriptions not only support previous findings and consolidate our general understanding of deep-sea ecosystems, but also provide a data resource inviting further taxon-specific and large-scale modeling studies. We foresee that metabarcoding will be useful for deep-sea biomonitoring efforts to consider the diversity of small taxa, but it must be validated based on ground truthing data or experimental studies.
Mishra, Bagdevi ; Ulaszewski, Bartosz ; Meger, Joanna ; Ploch, Sebastian ; Burczyk, Jarosław ; Thines, Marco
Similar to chloroplast loci, mitochondrial markers are frequently used for genotyping, phylogenetic studies, and population genetics, as they are easily amplified due to their multiple copies per cell. In a recent study, it was revealed that the chloroplast offers little variation for this purpose in central European populations of beech. Thus, it was the aim of this study to elucidate, if mitochondrial sequences might offer an alternative, or whether they are similarly conserved in central Europe. For this purpose, a circular mitochondrial genome sequence from the more than 300-year-old beech reference individual Bhaga from the German National Park Kellerwald-Edersee was assembled using long and short reads and compared to an individual from the Jamy Nature Reserve in Poland and a recently published mitochondrial genome from eastern Germany. The mitochondrial genome of Bhaga was 504,730 bp, while the mitochondrial genomes of the other two individuals were 15 bases shorter, due to seven indel locations, with four having more bases in Bhaga and three locations having one base less in Bhaga. In addition, 19 SNP locations were found, none of which were inside genes. In these SNP locations, 17 bases were different in Bhaga, as compared to the other two genomes, while 2 SNP locations had the same base in Bhaga and the Polish individual. While these figures are slightly higher than for the chloroplast genome, the comparison confirms the low degree of genetic divergence in organelle DNA of beech in central Europe, suggesting the colonisation from a common gene pool after the Weichsel Glaciation. The mitochondrial genome might have limited use for population studies in central Europe, but once mitochondrial genomes from glacial refugia become available, it might be suitable to pinpoint the origin of migration for the re-colonising beech population.
Bantis, Filippos ; Graap, Julia ; Früchtenicht, Elena ; Bussotti, Filippo ; Radoglou, Kalliopi ; Brüggemann, Wolfgang
Climate change imposes severe stress on European forests, with forest degradation already visible in several parts of Europe. Thus adaptation of forestry applications in Mediterranean areas and central Europe is necessary. Proactive forestry management may include the planting of Mediter- ranean oak species in oak-bearing Central European regions. Five replicate common gardens of Greek and Italian provenances of Quercus ilex, Q. pubescens and Q. frainetto seedlings (210 each per plantation) were established in Central Italy, NE Greece (two) and Southern Germany (two, including Q. robur) to assess their performance under different climate conditions. Climate and soil data of the plantation sites are given and seedling establishment was monitored for survival and morphological parameters. After 3 years (2019) survival rates were satisfactory in the German and Italian sites, whereas the Greek sites exerted extremely harsh conditions for the seedlings, including extreme frost and drought events. In Germany, seedlings suffered extreme heat and drought periods in 2018 and 2019 but responded well. Provenances were ranked for each country for their performance after plan- tation. In Greece and Italy, Q. pubescens was the best performing species. In Germany, Q. pubescens and Q. robur performed best. We suggest that Greek or Italian provenances of Q. pubescens may be effectively used for future forestation purposes in Central Europe. For the establishment of Quercus plantations in Northern Greece, irrigation appears to be a crucial factor in seedling establishment.
Al Naggar, Yahya ; Brinkmann, Markus ; Sayes, Christie M. ; AL-Kahtani, Saad Naser Saad ; Dar, Showket A. ; El-Seedi, Hesham R. ; Grünewald, Bernd ; Giesy, John P.
Microplastics (MPs) are ubiquitous and persistent pollutants, and have been detected in a wide variety of media, from soils to aquatic systems. MPs, consisting primarily of polyethylene, polypropylene, and polyacrylamide polymers, have recently been found in 12% of samples of honey collected in Ecuador. Recently, MPs have also been identified in honey bees collected from apiaries in Copenhagen, Denmark, as well as nearby semiurban and rural areas. Given these documented exposures, assessment of their effects is critical for understanding the risks of MP exposure to honey bees. Exposure to polystyrene (PS)-MPs decreased diversity of the honey bee gut microbiota, followed by changes in gene expression related to oxidative damage, detoxification, and immunity. As a result, the aim of this perspective was to investigate whether wide-spread prevalence of MPs might have unintended negative effects on health and fitness of honey bees, as well as to draw the scientific community’s attention to the possible risks of MPs to the fitness of honey bees. Several research questions must be answered before MPs can be considered a potential threat to bees.
Photorhabdus and Xenorhabdus are Gram-negative, entomopathogenic bacteria, living in endosymbiosis with the soil-dwelling nematode of the genera Steinernema and Heterorhabditis. The life cycle of these nematodes consists of non-feeding infective juvenile (IJ) stage, which actively searches for insects in the soil. After penetrating the insect prey, Photorhabdus and Xenorhabdus bacteria are released from the nematode gut. The bacteria proliferate and produce toxins to kill the insect. Photorhabdus and Xenorhabdus support nematode development throughout the life cycle and to get rid of food competitors by providing a wide variety of specialized metabolites (SMs). However, little is known about which SMs function as so called “food signals” to trigger the development process.
The IJs develop into adult, self-fertilizing hermaphrodites in a process called recovery, while feeding on cadaver and bacterial biomass. Heterorhabditis and Steinernema proceed to breed until nutrients are exhausted. Next generation IJs (NG-IJs) develop and leave the cadaver to search for another insect prey.
Photorhabdus and Xenorhabdus can be cultivated in defined medium under laboratory conditions. By placing IJs on a plate containing their respective bacterial symbiont, the complete life cycle of the nematodes can be observed in vitro. The in vitro nematode bioassay was used as a tool to investigate the development of the nematode.
The aim of this study was to find the food signals responsible for nematode development. Different Photorhabdus deletion strains unable to produce one or several SMs were co-cultivated with nematodes in the nematode bioassay. Subsequently, two aspects of the life cycle were investigated: recovery and NG-IJ development.
As isopropyl stilbene (IPS) is postulated to function as a food signal to support nematode recovery, it was used as a starting point for investigations. This study was focused on the biosynthetic pathway of IPS, including intermediates, side products and derivatives to investigate which one is in fact responsible for supporting nematode development.
The biosynthesis of IPS requires two precursors, phenylalanine and leucine (Figure 5). The first topic was focused on the phenylalanine derived pathway. Photorhabdus laumondii deletion mutants, defective in intermediate steps of this pathway, were created. The deletion of the genes coding for the phenylalanine ammonium lyase (stlA), converting phenylalanine into cinnamic acid (CA), the coenzyme A (CoA) ligase (stlB) and the operon coding for a ketosynthase and aromatase (stlCDE), were used. These strains were used for nematode bioassay including complementation of mutant phenotypes by feeding experiments. Recovery of nematodes grown on the deletion strains was always lower than recovery of nematodes grown on wild type bacteria. Feeding IPS to a deletion strain did not restore wild type level nematode recovery, thus IPS cannot be the food signal. Instead, the food signal must be another compound derived from this part of biosynthetic pathway. Lumiquinone and 2,5-dihydrostilbene are suggested to function as food signals and need to be investigated in future work.
The second part of this study was focused on the leucine derived pathway, which involved the Bkd complex forming the iso-branched part of IPS. A deletion of bkd was created and phenotypically analysed, subsequently performed with the nematode bioassay. Not only IPS but also other branched SMs, like photopyrones and phurealipids are synthetised by the Bkd complex. Deletions strains defective in producing photopyrones and phurealipids were also performed in nematode bioassays to investigate effects of these SMs individually. Branched SMs did not have an impact on nematode development, but nematodes grown on the ΔbkdABC strain showed a reduced nematode recovery and almost diminished NG-IJs development. As the Bkd complex also produces branched chain fatty acids (BCFAs), feeding experiments were performed with lipid extracts of wild type and mutant strain. All lipid extracts improved recovery, but only wild type lipids could complement NG-IJ development. This strongly indicates that BCFAs play an important role in NG-IJ development, which needs to be proven with purified BCFA feeding. This is an interesting finding, which could improve nematode production for biocontrol agent usage.
The role of IPS derived to epoxy stilbene (EPS) for nematode development, was another focus in the nematode life cycle. Recently it was demonstrated that EPS does not support nematode development. However, EPS forms adducts with amino acids. In my thesis, novel adducts containing the amino acid phenylalanine or a tetrapeptide were characterized. Another adduct, most likely being an EPS dimer, was also characterized. The biological role of such adducts was discussed to be potentially important for insect weakening and the structure of the novel compounds need to be structure elucidated and tested for bioactivity.
Climatic niches describe the climatic conditions in which species can persist. Shifts in climatic niches have been observed to coincide with major climatic change, suggesting that species adapt to new conditions. We test the relationship between rates of climatic niche evolution and paleoclimatic conditions through time for 65 Old-World flycatcher species (Aves: Muscicapidae). We combine niche quantification for all species with dated phylogenies to infer past changes in the rates of niche evolution for temperature and precipitation niches. Paleoclimatic conditions were inferred independently using two datasets: a paleoelevation reconstruction and the mammal fossil record. We find changes in climatic niches through time, but no or weak support for a relationship between niche evolution rates and rates of paleoclimatic change for both temperature and precipitation niche and for both reconstruction methods. In contrast, the inferred relationship between climatic conditions and niche evolution rates depends on paleoclimatic reconstruction method: rates of temperature niche evolution are significantly negatively related to absolute temperatures inferred using the paleoelevation model but not those reconstructed from the fossil record. We suggest that paleoclimatic change might be a weak driver of climatic niche evolution in birds and highlight the need for greater integration of different paleoclimate reconstructions.
The factors that vary the aroma of Tuber magnatum fruiting bodies are poorly understood. The study determined the headspace aroma composition, sensory aroma profiles, maturity and bacterial communities from T. magnatum originating from Italy, Croatia, Hungary, and Serbia, and tested if truffle aroma is dependent on provenance and if fruiting body volatiles are explained by maturity and/or bacterial communities.
Headspace volatile profiles were determined using gas chromatography–mass spectrometry–olfactometry (GC-MS-O) and aroma of fruiting body extracts were sensorially assessed. Fruiting body maturity was estimated through spore melanisation. Bacterial community was determined using 16S rRNA amplicon sequencing.
Main odour active compounds were present in all truffles but varied in concentration. Aroma of truffle extracts were sensorially discriminated by sites. However, volatile profiles of individual fruiting bodies varied more within sites than across geographic area, while maturity level did not play a role. Bacterial communities varied highly and were partially explained by provenance. A few rare bacterial operational taxonomical units associated with a select few nonodour active volatile compounds.
Specificities of the aroma of T. magnatum truffles are more likely to be linked to individual properties than provenance. Some constituents of bacteria may provide biomarkers of provenance and be linked to nonodour active volatiles.
Although macroecology is a well-established field, much remains to be learned about the large-scale variation of fungal traits. We conducted a global analysis of mean fruit body size of 59 geographical regions worldwide, comprising 5340 fungal species exploring the response of fruit body size to latitude, resource availability and temperature. The results showed a hump-shaped relationship between mean fruit body size and distance to the equator. Areas with large fruit bodies were characterised by a high seasonality and an intermediate mean temperature. The responses of mutualistic species and saprotrophs were similar. These findings support the resource availability hypothesis, predicting large fruit bodies due to a seasonal resource surplus, and the thermoregulation hypothesis, according to which small fruit bodies offer a strategy to avoid heat and cold stress and therefore occur at temperature extremes. Fruit body size may thus be an adaptive trait driving the large-scale distribution of fungal species.
Biological and environmental factors as sources of variation in nocturnal behavior of giraffe
(2021)
Upon a drastic decline of the giraffe population in the wild, conservation efforts and therefore the role of zoos have become more important than ever. With their unique opportunities, zoos provide excellent conditions to study animal behavior, expanding the knowledge about the giraffe's behavior repertoire and their ability to adapt. This study therefore examined the nocturnal behavior of 63 giraffe living in 13 different EAZA zoos across Germany and the Netherlands. Giraffe were observed and videos recorded via infrared sensitive cameras during the winter seasons 2015–2018. The observation period spanned nightly from 17:00 to 7:00. Thus, 198 nights, with a total of 2772 h were recorded and analyzed. Linear mixed models were then used to assess potential biological and environmental factors influencing behavior during the dark phase. Results show that individual variables such as age, subspecies and motherhood determined nocturnal activity and sleep behavior most. Among the variables studied, husbandry conditions and environmental factors complying with EAZA standards had no influence on the giraffe's nocturnal behavior. By combining nocturnal activity analyses and an assessment of potential influencing factors, our findings present a holistic approach to a better understanding of captive giraffe behavior and allow for management implications.
Cercosporoid fungi (Mycosphaerellaceae, Mycosphaerellales, Ascomycota) are one of the largest and most diverse groups of hyphomycetes causing a wide range of diseases of economically important plants as well as of plants in the wild. Although more than 6000 species are known for this group, the documentation of this fungal group is far from complete. Especially in the tropics, the diversity of cercosporoid fungi is poorly known. The present study aims to identify and characterise cercosporoid fungi collected on host plants belonging to Fabaceae in Benin, West Africa. Information on their morphology, host species and DNA sequence data (18S rDNA, 28S rDNA, ITS and tef1) is provided. DNA sequence data were obtained by a simple and non-culture-based method for DNA isolation which has been applied for cercosporoid fungi for the first time in the context of the present study. Among the loci used for the phylogenetic analysis, tef1 provided the best resolution together with the multigene dataset. Species delimitation in many cases, however, was only possible by combining molecular sequence data with morphological characteristics. Based on forty specimens recently collected in Benin, 18 species are presented with morphological descriptions, illustrations and sequence data. Among these, six species in the genus Cercospora and two species in Pseudocercospora are proposed as species new to science. The newly described species are Cercospora (C.) beninensis on Crotalaria macrocalyx, C. parakouensis on Desmodium tortuosum, C. rhynchophora on Vigna unguiculata, C. vignae-subterraneae on Vigna subterranea, C. tentaculifera on Vigna unguiculata, C. zorniicola on Zornia glochidiata, Pseudocercospora sennicola on Senna occidentalis and Pseudocercospora tabei on Vigna unguiculata. Eight species of cercosporoid fungi are reported for Benin for the first time, three of them, namely C. cf. canscorina, C. cf. fagopyri and C. phaseoli-lunati are new for West Africa. The presence of two species of cercosporoid fungi on Fabaceae previously reported from Benin, namely Nothopassalora personata and Passalora arachidicola, is confirmed.