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From a global viewpoint, a lot of time is spent within the indoor air compartment of vehicles. A German study on mobility has revealed that, on average, people spend 45 minutes per day inside vehicles. In recent years the number of cars has increased to around 43 million vehicles in private households. This means that more than one car can be used in every household. The ratio has been growing, especially in eastern Germany and rural areas. "Overall and especially outside the cities, the car remains by far number one mode of transport, especially in terms of mileage". Therefore, numerous international studies have addressed different aspects of indoor air hygiene, in the past years. In this paper, meaningful original studies on car indoor air pollution, related to VOCs, COx, PMs, microbials, BFRs, OPFRs, cigarettes, electronic smoking devices, high molecular weight plasticizer, and NOx are summarized in the form of a review. This present review aimed to summarize recently published studies in this important field of environmental medicine and points to the need for further studies with special recommendations for optimizing the interior air hygiene.
Investigating the influence of truffle´s microbiome and genotype on the aroma of truffle fungi
(2019)
Truffles (Tuber spp.) are belowground forming fungi that develop in association with roots of various host trees and shrubs. Their fruiting bodies are renowned for their enticing aromas which vary considerably, even within truffles of the same species. This aroma variability might be attributed to factors such as geographical origin, degree of fruiting body maturation, truffle genotype and microbiome (microbial communities that colonise truffle fruiting bodies) which often co-vary. Although the influence of specific factors is highlighted by several studies, discerning the contribution of each factor remains a challenge since it requires an appropriate experimental design. The primary purpose of this thesis was to gain insight into the influence of truffle’s genotype and microbiome on truffle aroma.
This doctoral thesis is comprised of four chapters. Chapter1 (Vahdatzadeh et al., 2018) aimed to exclusively elucidate the influence of truffle genotype on truffle aroma by investigating the aroma of nine mycelial strains of the white truffle Tuber borchii. We also assessed whether strain selection could be employed to improve the human- perceived truffle aroma. Quantitative differences in aroma profiles among strains could be observed upon feeding of amino acids. Considerable aroma variabilities among strains were attributed to important truffle volatiles, many of which might be derived from amino acid catabolism through the Ehrlich pathway. 13 C-labelling experiments confirmed the existence of the Ehrlich pathway in truffles for leucine, isoleucine, methionine, and phenylalanine. Sensory analyses further demonstrated that the human nose can differentiate among strains. Our results illustrated the influence of truffle genotype on truffle aroma and showed how strain selection could be used to improve the human-perceived truffle aroma.
In chapter 2 the existing knowledge on the composition of bacterial community of four truffle species was compiled using meta-analysis approach (Vahdatzadeh et al., 2015). We highlighted the endemic microbiome of truffle as well as similarities and differences in the composition of microbial community within species at various phases of their life cycle. Furthermore, the potential contribution of truffle microbiome in the formation of truffle odorants was studied. Our findings showed that truffle fruiting bodies harbour complex microbial community composed of bacteria, yeasts, filamentous fungi, and viruses with bacteria being the dominant group. Regardless of truffle species, the composition of endemic microbiome of fruiting bodies appeared very similar and was dominated by α-Proteobacteria class. However, striking differences were observed in the bacterial community composition at various stages of the life cycle of truffle.Our analyses further suggested that odorants common to many truffle species might be produced by both truffle fungi and microbes, whereas specific truffle odorants might be derived from microbes only. Nevertheless, disentangling the origin of truffle odorants is very challenging, since acquiring microbe-free fruiting bodies are currently not possible.
Chapter 3 (Splivallo et al., 2019) further characterises truffle-associated bacterial communities of fruiting bodies of the black truffle T. aestivum from two different orchards. It aimed at defining the native microbiome in this truffle species, evaluating the variability of their microbiome across orchards, and assessing factors that shape assemblages of the bacterial communities. The dominant bacterial communities in T. aestivum revealed to be similar in both orchards: although a large portion of fruiting bodies were dominated by the α-Proteobacteria class (Bradyrhizobium genus) similar to other so far-assessed truffle species, in few cases β-Proteobacteria (Polaromonas genus), or Sphingobacteria (Pedobacter genus) were found to be predominant classes. Moreover, factors shaping bacterial communities influenced the two orchards differently, with spatial location within the orchard being the main driver in Swiss orchard and collection season in the French one. Surprisingly, in contrast to other fungi, truffle genotype and the degree of fruiting body maturity seemed not to contribute in shaping the assembly of truffle microbiome. Altogether, our data highlighted the existence of heterogeneous bacterial communities in T. aestivum fruiting bodies which are dominated by either of the three bacterial classes and mainly by the α-Proteobacteria class, irrespective of geographical origin. They further illustrated that determinants driving the assembly of various bacterial communities within truffle fruiting bodies are site-specific. Truffles are highly perishable delicacies with a short shelf life (1-2 weeks), and their aroma changes profoundly upon storage. Since truffle aroma might be at least partially produced by the truffle microbiome, chapter 4 (Vahdatzadeh et al., 2019) focuses on assessing the influence of the truffle microbiome on aroma deterioration of T.aestivum during post harvest storage. Specifically, volatile profile and bacterial communities of fruiting bodies collected from four different regions (three in France and one in Switzerland) were studied over nine days of storage. Our findings demonstrated the gradual replacement of dominant bacterial classes in fresh truffles (α-Proteobacteria, β-Proteobacteria, and Sphingobacteria) by food spoilage bacteria (members of γ- Proteobacteria and Bacilli classes), regardless of the initial diversity of the bacterial classes. This shift in the bacterial community also correlated with changes in volatile profiles, and markers for truffle freshness and spoilage could be identified. Ultimately, network analysis illustrated possible links among those volatile markers and specific bacterial classes. Our data showed that storage deeply influenced the composition of bacterial community as well as aroma of truffle fruiting bodies. They also illustrated the correlation between the shift in truffle microbiome, from commensal to detrimental, and the change of aroma profile, possibly leading to the loss of fresh truffle aroma. Overall, the work undertaken in this thesis demonstrated that truffle genotype and microbiome had a stronger influence on truffle aroma than previously believed.
Volatile organic compounds are secondary metabolites emitted by all organisms, especially by plants and microbes. Their role as aboveground signals has been established for decades. Recent evidence suggests that they might have a non-negligible role belowground and might be involved in root–root and root–microbial/pest interactions. Our aim here was to make a comprehensive review of belowground volatile diversity using a meta-analysis approach. At first we synthesized current literature knowledge on plant root volatiles and classified them in terms of chemical diversity. In a second step, relying on the mVOC database of microbial volatiles, we classified volatiles based on their emitters (bacteria vs. fungi) and their specific ecological niche (i.e., rhizosphere, soil). Our results highlight similarities and differences among root and microbial volatiles and also suggest that some might be niche specific. We further explored the possibility that volatiles might be involved in intra- and inter-specific root–root communication and discuss the ecological implications of such scenario. Overall this work synthesizes current knowledge on the belowground volatilome and the potential signaling role of its constituents. It also highlights that the total diversity of belowground volatiles might be orders of magnitude larger that the few hundreds of compounds described to date.
Die Kartierung von 25 Arten der Pilzgattung Hygrocybe im Großraum Trier während der Herbstmonate 2010 hat klar gezeigt, dass die meisten sehr eng an mageres altes Grasland gebunden sind. Durch die genaue Kenntnis der Verbreitung solcher Mähwiesen war es möglich, auf 16 Topographischen Karten (1:25.000) einen großen Teil der Vorkommen auf 165 Wiesen zu dokumentieren. Da dieses Magergrasland durch Nutzungsänderungen und N-Eintrag aus der Atmosphäre stark gefährdet ist, sind neben den dort lebenden Pflanzen und Tieren auch eine größere Anzahl von Pilzen akut bedroht. Schon jetzt stehen fast alle diese Arten auf den Roten Listen. Die Auswertung der Funde zeigt, dass im Untersuchungsraum die Mehrzahl der Hygrocybe-Arten einen Verbreitungsschwerpunkt in der collinen bis submontanen Höhenstufe hat. Mit Hilfe der ungewichteten mittleren Zeigerwerte (nach Ellenberg) der von den Wiesen erstellten Pflanzenlisten konnte deutlich gemacht werden, dass diese Pilze überwiegend auf trockenen bis leicht frischen Böden (F-Zahl: 4,5–5,0) mit guter Basenversorgung (R-Zahl: 5,5–6,5) und niedrigen Nährstoffgehalten (N-Zahl: 3,5–4,5) Fruchtkörper bilden. Die mittleren Artenzahlen der zugrunde liegenden Gesamt - artenlisten umfassen Werte von 40 bis 55. Die Flächengrößen waren uneinheitlich, weil jeweils vollständige, einheitlich genutzte Wiesenparzellen für Pflanzenlisten und Pilze als Bezugsgröße dienten. Viele der Pilze haben weite ökologische Amplituden in Bezug auf Wasser- und Basenversorgung. Aber die N-Zahlen überschreiten selten den Wert 5. Unter den selten beobachteten Hygrocybe-Arten sind einige an Extremstandorte gebunden, nämlich an sehr saure, sehr kalkreiche bzw. nasse Böden. Da die Arten der Gattung Hygrocybe durch ihre vielfältigen Farben auffallen, relativ leicht zu bestimmen sind und sehr klare Indikatoreigenschaften für mageres altes Grasland haben, sollten sie überall zur Bewertung von dessen Schutzwürdigkeit mit herangezogen werden. Die heute schon seltenen Pflanzen, Tiere und Pilze werden sich von alleine nach Umbruch, Ackernutzung bzw. intensiver Düngung nur sehr langsam oder gar nicht mehr ansiedeln können, auch wenn versucht wird, die Böden auszuhagern.
Fungi are an important component of every ecosystem but hardly considered in biodiversity monitoring projects. This thesis aims at characterizing fungal diversity, with an emphasis on epigeous fungi, encompassing different biogeographic zones and points in time. A main sampling area was established in the Taunus mountain range in Germany, which was sampled monthly over three years.
For testing species richness on spatial scale, the Taunus transect was compared with four other areas, which were assessed with lower sampling effort. One of these areas was Bulau in Germany, in which four excursions were made. Furthermore, two sampling events were performed in Somiedo in Spain and one sampling event in Kleinwalsertal in Austria. Already existing data of a two-year monitoring project in Panama next to the river Majagua were additionally used for comparison.
All these areas were investigated with a standardized sampling protocol focusing on macroscopically evident fungi and vascular plants using a time-restricted transect design. The transects consisted of strips, which were 500 m long and about 20 m broad, and were sampled for 2 hours at each single sampling event....
Cirsium arvense is one of the worst weeds in agriculture. As herbicides are not very effective and not accepted by organic farming and special habitats, possible biocontrol agents have been investigated since many decades. In particular plant pathogens of C. arvense have received considerable interest and have been promoted as “mycoherbicides” or “bioherbicides”. A total of 10 fungi and one bacterium have been proposed and tested as biocontrol agents against C. arvense. A variety of experiments analysed the noxious influence of spores or other parts of living fungi or bacteria on plants while others used fungal or bacterial products, usually toxins. Also combinations of spores with herbicides and combinations of several pathogens were tested. All approaches turned out to be inappropriate with regard to target plant specificity, effectiveness and application possibilities. As yet, none of the tested species or substances has achieved marketability, despite two patents on the use of Septoria cirsii and Phomopsis cirsii. We conclude that the potential of pathogens for biocontrol of C. arvense has largely been overestimated.
Background: The European beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here, we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany.
Findings: Using a hybrid assembly approach, Illumina reads with short- and long-insert libraries, coupled with long Pacific Biosciences reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation. The largest scaffold was of 1.15 Mb, the N50 length was 145 kb, and the L50 count was 983. The assembly contained 0.12% of Ns. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis retrieved 94% complete BUSCO genes, well in the range of other high-quality draft genomes of trees. A total of 62,012 protein-coding genes were predicted, assisted by transcriptome sequencing. In addition, we are reporting an efficient method for extracting high-molecular-weight DNA from dormant buds, by which contamination by environmental bacteria and fungi was kept at a minimum.
Conclusions: The assembled genome will be a valuable resource and reference for future population genomics studies on the evolution and past climate change adaptation of beech and will be helpful for identifying genes, e.g., involved in drought tolerance, in order to select and breed individuals to adapt forestry to climate change in Europe. A continuously updated genome browser and download page can be accessed from beechgenome.net, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.
Nonmycorrhizal root-colonizing fungi are key determinants of plant growth, driving processes ranging from pathogenesis to stress alleviation. Evidence suggests that they might also facilitate host access to soil nutrients in a mycorrhiza-like manner, but the extent of their direct contribution to plant nutrition is unknown. To study how widespread such capacity is across root-colonizing fungi, we surveyed soils in nutrient-limiting habitats using plant baits to look for fungal community changes in response to nutrient conditions. We established a fungal culture collection and used Arabidopsis thaliana inoculation bioassays to assess the ability of fungi to facilitate host’s growth in the presence of organic nutrients unavailable to plants. Plant baits captured a representation of fungal communities extant in natural habitats and showed that nutrient limitation has little influence on community assembly. Arabidopsis thaliana inoculated with 31 phylogenetically diverse fungi exhibited a consistent fungus-driven growth promotion when supplied with organic nutrients compared to untreated plants. However, direct phosphorus measurement and RNA-seq data did not support enhanced nutrient uptake but rather that growth effects may result from changes in the plant’s immune response to colonization. The widespread and consistent host responses to fungal colonization suggest that distinct, locally adapted nonmycorrhizal fungi affect plant performance across habitats.
IMPORTANCE: Recent studies have shown that root-associated fungi that do not engage in classical mycorrhizal associations can facilitate the hosts’ access to nutrients in a mycorrhiza-like manner. However, the generality of this capacity remains to be tested. Root-associated fungi are frequently deemed major determinants of plant diversity and performance, but in the vast majority of cases their ecological roles in nature remain unknown. Assessing how these plant symbionts affect plant productivity, diversity, and fitness is important to understanding how plant communities function. Recent years have seen important advances in the understanding of the main drivers of the diversity and structure of plant microbiomes, but a major challenge is still linking community properties with function. This study contributes to the understanding of the cryptic function of root-associated fungi by testing their ability to participate in a specific process: nutrient acquisition by plants.
Climate change causes increased tree mortality leading to canopy loss and thus sun-exposed forest floors. Sun exposure creates extreme temperatures and radiation, with potentially more drastic effects on forest organisms than the current increase in mean temperature. Such conditions might potentially negatively affect the maturation of mushrooms of forest fungi. A failure of reaching maturation would mean no sexual spore release and, thus, entail a loss of genetic diversity. However, we currently have a limited understanding of the quality and quantity of mushroom-specific molecular responses caused by sun exposure. Thus, to understand the short-term responses toward enhanced sun exposure, we exposed mushrooms of the wood-inhabiting forest species Lentinula edodes, while still attached to their mycelium and substrate, to artificial solar light (ca. 30°C and 100,000 lux) for 5, 30, and 60 min. We found significant differentially expressed genes at 30 and 60 min. Eukaryotic Orthologous Groups (KOG) class enrichment pointed to defense mechanisms. The 20 most significant differentially expressed genes showed the expression of heat-shock proteins, an important family of proteins under heat stress. Although preliminary, our results suggest mushroom-specific molecular responses to tolerate enhanced sun exposure as expected under climate change. Whether mushroom-specific molecular responses are able to maintain fungal fitness under opening forest canopies remains to be tested.
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.
Gegenstand der vorliegenden Arbeit war es die Hypothese, dass die chronische Rhinosinusitis auf eine immunologische Reaktion auf eingeatmete Pilzelemente zurückgehe, zu prüfen. An der Untersuchung nahmen 26 Patienten (medianes Alter: 47,1) und 6 Kontrollprobanden ohne nasale Entzündung (medianes Alter: 25) teil. Durch serologische Untersuchungen haben wir die CRS-Patienten in 35% Allergiker ohne und 19% mit Eosinophilie sowie 19% nicht-Allergiker ohne und 27% mit Eosinophilie mit eingeteilt. Mit einer verfeinerten Technik gelang es uns Pilze in nur 12% bei CRS-Patienten und in 17% bei der Kontrollgruppe mikrobiologisch nachzuweisen. Des Weiteren haben wir Pilzfragmente in 35% bei CRS-Patienten im Nasen-sekretausstrich gefunden, hingegen in keinem Fall in der Kontrollgruppe. Verteilt auf die CRS-Gruppen ergab sich folgendes Bild, wobei Kulturen und Ausstriche zusammen gezählt wurden: Bei 20% der Allergiker mit und bei 44% ohne Eosinophilie wurden Pilze im Nasenschleim nachgewiesen. In der Gruppe der nicht-Allergiker mit Eosinophilie konnten in 29% der Fälle Pilze gefunden werden. Bei 14% der Fälle wurden Pilze mit Allergic Mucin im Nasenschleim identifiziert. Nicht-Allergiker ohne Eosinophile wiesen in 20% der Fälle Pilze im Nasensekret auf. Folglich konnten wir nicht feststellen, dass bei nahezu jeder Untersuchungsperson Pilze im Nasenschleim sich nachweisen ließen. Bei den CRS-Patienten hatten 4% die Kriterien des EFRS-Krankheitsbildes erfüllt. Betrachtet man die Gruppe der nicht-Allergiker isoliert, so waren es dann 14%. Durch immunologische Serumuntersuchungen konnte ein signifikanter Unterschied (p  0,01) bezüglich der Gesamt-IgE-Werte zwischen der Kontroll- und der CRS-Patientengruppe festgestellt werden, allerdings ohne die übrigen zytologischen und histologischen Kriterien der AFS zu erfüllen. Der Gesamt-IgE-Wert bzw. Gesamt-IgE-Titer war ein hilfreicher Parameter zur Abgrenzung einer allergischen Komponente bei bestehender chronischer Rhinosinusitis, besaß aber keine Aussagfähigkeit über vorliegen einer AFS. Zudem wurde auch der pilzspezifische-IgE-Spiegel gemessen. Insgesamt resultierte bei 12% der CRS-Patienten ein positiver Nachweis von zirkulierenden pilzspezifischen IgEs im Serum. Ein Zusammenhang zwischen pilzspezifischen IgE und Eosinophilie mit Clusterbildung und Pilznachweis konnte in keinem Fall beobachtet werden. Mit Hilfe des biochemischen Entzündungsmarker ECP bestimmten wir die eosinophile Entzündungsaktivität im Nasensekret und im Serum. Die ECP-Konzentration im Nasensekret zeigte einen signifikanten Unterschied (p = 0,02) zwischen CRS- und der Kontrollgruppe auf, hingegen im Serum war der Unterschied geringfügig (p = 0,11). Für das Monitoring von Entzündungs-geschehen im Nasenschleim sind Analysen des Nasensekrets daher gegenüber Blutanalysen zu bevorzugen. Die ECP-Nasensekretwerte der CRS-Patienten ohne Nachweis von Pilzelementen im Ausstrich waren insgesamt ähnlich hoch verteilt wie die der mit Nachweis von Pilzelementen im Ausstrich. Somit bestand kein statistisch signifikanter Unterschied zwischen den ECP-Werten mit und ohne Pilznachweis im Nasensekret-ausstrich (p = 0,87). Das ECP im Nasensekret erscheint zum Screening der pilzassoziierten chronischen Rhinosinusitis ungeeignet. Die These, dass Pilze das ätiologische Agens der Polyposis nasi et sinuum oder gar der chronischen Sinusitis allgemein sind, ist weiterhin sehr kritisch zu werten. Da Pilze über potente Antigene verfügen, kann eine Verstärkung eines bereits bestehenden Entzündungsreizes nicht sicher ausgeschlossen werden. Die Ergebnisse dieser Arbeit weisen darauf hin, dass es möglich ist durch einfache pathomorphologische Verfahren eindeutige Informationen zum Vorkommen von Pilzen und eosinophile Zellen bereits im Ausstrich-Präparat zu erhalten. Bei Problemfällen kann der Hinweis auf ein positiven Pilzbefund in der Histologie wertvoll sein, da differentialdiagnostisch ein zusätzlicher potenzierender Entzündungsfaktor zu berücksichtigen ist. Es liegt dann an der Erfahrung des HNO-Arztes und dem klinischen Verlauf welche therapeutischen Optionen dann nützlich sind. Unklar bleibt weiterhin bis dato was das erste Signal bei der eosinophilen Entzündungsreaktion darstellt. Nach unseren Untersuchungen scheinen Pilze nicht primär in Frage zu kommen.
Tree bark constitutes an 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 focused on agriculturally relevant systems and on single taxonomic groups. Here we implemented a multi-kingdom metabarcoding approach to analyze 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 toward 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.
Auf der Grundlage eines neuen Forschungskonzeptes für die Dauerbeobachtung in 26 bayerischen Naturwaldreservaten wurde in vier gemischten, laubbaumdominierten Reservaten mit der Aufnahme von Waldstrukturdaten und waldökologisch besonders wichtigen Artengruppen begonnen. Die dabei gewonnenen Artdaten zur Bodenvegetation, xylobionten Käfern, Schnecken und Pilzen wurden mit den Strukturdaten des Waldbestandes auf Probekreisebene verschnitten. Alle Artengruppen zeigten ähnliche Muster hinsichtlich ihrer Artenzusammensetzung in Beziehung zu Strukturparametern wie dem Buchenanteil des Bestandes und in zweiter Ebene zu Beteiligung der Hainbuche. Zudem konnten Vögel auf der Basis von Rasterkartierungen über die gesamten Reservatsflächen erfasst werden. Es kann daher abgeleitet werden, dass auch Aufnahmen im Rahmen eines entsprechend einfachen Monitorings Beziehungen zwischen den Arten und Waldstrukturen aufzeigen können. Genauere waldökologische Beziehungen zu naturschutzfachlich interessanten Arten wie Naturnähezeigern und Urwaldreliktarten lassen sich mit den Monitoringansätzen jedoch kaum ableiten.