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Baldrian, P.

Publications and source records attributed to Baldrian, P..

14 recordsLinked to original sources

Forest biodiversity benefits from warmer microclimate, but only in colder regions

The diversity of many forest-dwelling organisms depends on forest structure, but it remains unknown to which degree this is mediated by microclimatic temperature, and whether microclimatic buffering is universally beneficial for forest biodiversity. In 234 broad-leaved forest plots across nine climatically differing regions in Germany, we measured micro- and macroclimatic temperatures, canopy cover, and deadwood volume after experimental manipulations of forest structure through thinning operations and gap cuts. We surveyed 21 taxonomic groups, representing plants, bacteria, fungi, and animals, to assess how their diversity depended on the predictors. Multi-taxon diversity, and diversity of ten separate taxonomic groups, increased from closed to open canopies. Only necrophagous beetles were more diverse in closed stands. These effects of canopy cover on diversity were partly mediated by microclimatic temperatures. Thereby, diversity responses to microclimatic temperature depended on the macroclimatic context. In regions with colder summers, locally warmer microclimates in canopy gaps had strong positive effects on biodiversity, while these effects were not found in regions with warmer summers. Consequently, management strategies aimed at multi-taxon forest diversity conservation should be chosen based on the regional climate, favoring canopy gaps primarily in colder regions, and taking future climate warming into consideration.

ecology↗

Niche constraints drive differences between mycorrhizal fungal guilds in future range shifts

Mycorrhizal fungi are a diverse and ubiquitous group of plant symbionts whose distribution strongly influences ecosystem function across the globe. Yet, until now, we do not have quantitative data on the range sizes of different mycorrhizal fungal taxa, limiting our capacity to forecast future shifts in community composition and function. Here, we use 115,924 DNA sequence-derived observations to map the distribution of 651 common mycorrhizal fungal taxa and forecast future changes to their range sizes. We demonstrate that climate, plant cover, and soil factors, particularly mean annual temperature, net primary productivity, and soil organic carbon, exert major control over mycorrhizal fungal distributions. Based on these drivers, the ecological niches of mycorrhizal fungi consistently differ between arbuscular and ectomycorrhizal functional guilds. Arbuscular mycorrhizal fungal taxa generally occupy a wider niche breadth than ectomycorrhizal fungi, occurring across larger ranges of climate, soil, plant cover, topography, and disturbance conditions. Our models also predict widespread decreases in the suitable range size of mycorrhizal fungal taxa under projected future global climates, with average ranges decreasing by 13.8% or ~2.2 million km2 under high emissions scenarios (ssp5-8.5). This decrease in projected range size will be most pronounced for ectomycorrhizal fungi, strongly linked to constraints from their smaller overall niches. By generating a global atlas of common mycorrhizal fungi and their associated environmental niche, we establish a critical baseline for widely suspected declines in global fungal biodiversity.

ecology↗

Experimentally manipulating forest structure to mimic management strategies: effects on deadwood fungal diversity and related ecosystem processes

Understanding the relationships between forest management, biodiversity, and ecosystem processes is necessary for achieving multifunctionality. Deadwood fungi are extremely diverse and important for carbon turnover in forests. However, how forest structure, resulting from management, affects deadwood fungal diversity and decomposition is not well known. We experimentally tested the effects of microclimate (via canopy cover) and deadwood enrichment (snags, logs, tree crowns, and habitat trees) on fungal diversity. Further, we assessed the effects of the treatments and fungal diversity on wood mass loss. We characterized the fungal communities of Fagus sylvatica (European beech) and Pinus sylvestris (Scots pine) deadwood via metabarcoding and measured wood mass loss after 3 years. We found that the host tree species was more important than canopy cover or deadwood enrichment for fungal alpha and beta diversity. Fungal alpha diversity of beech was mainly related to canopy cover; diversity of beech was higher under closed canopies. While alpha diversity of pine was related only to deadwood enrichment as diversity increased where habitat trees and crowns remained. Furthermore, while mass loss of beech was significantly higher in patches where trees were removed and patches where crowns remained, pine mass loss was neither affected by canopy cover nor deadwood enrichment. Host tree diversity is more important than environmental variability as a determinant of fungal diversity, underpinning the importance of maintaining diverse hosts in forests. However, contrasting diversity and decomposition effects between beech and pine suggest the need for forest management strategies tailored to tree species to maintain fungal diversity and ecosystem processes.

ecology↗

Enhancing experimentally the structural heterogeneity of forests increase soil fungal diversity but functional lifestyles in contrasting ways

Fungal communities in soils are highly diverse both in species and functions forming a major backbone of forest ecosystems. Recent observational high-throughput-sequencing studies have shown that fungal diversity is correlated with resource availability and climate across different spatial scales. However, the underlying mechanisms remain poorly understood. Across Germany, we experimentally manipulated 11 typically homogeneous, broadleaf production forests to increase their between-patch-heterogeneity (ESBC) and compared them with a control forest. In specific, we enhanced light availability via canopy openness and deadwood resources in the ESBC treatments. Fungal communities were determined by metabarcoding at 234 patches and analysed using a novel meta-analytical approach for pairwise comparisons of taxonomic and phylogenetic diversity along Hill numbers. We hypothesized that {gamma}-diversity is primarily driven by {beta}-diversity increasing with canopy mediated microclimate variability and secondarily by -diversity increasing with resource availability. Furthermore, we expected an increase in {gamma}-diversity by unique phylogenetic lineages supporting the insurance hypothesis. Our results showed a significant increase in {gamma}-diversity in ESBC forests, first by - and second by {beta}-diversity, both of which were influenced mainly by microclimate and not resource availability. The increase of phylogenetic diversity with ESBC was weak indicating functional similarity of species. Analysis of symbiotic, saprotrophic and parasitic fungal assemblages revealed contrasting effects of resource availability and microclimate across the scales. As in the UN Decade of Ecosystem Restoration many forest managers aim to increase the heterogeneity of forests and are simultaneously face rising tree mortality, our study provides first robust empirical evidence for the varying effects of forest gaps and deadwood on fungal diversity across -, {beta}-, {gamma}-scales for this major kingdom.

ecology↗

Long-term evolution of prokaryotic genomes in a chemolithotrophic cave over 5.5 million years of isolation

Fluctuating conditions drive adaptive evolution, yet understanding how genomes evolve under stable conditions over extended periods remains a major challenge, since most research on microbial evolution relies on short-term experiments or phylogenetic comparisons. The Movile Cave, isolated from external influences 5.5 million years, offers a unique opportunity to explore microbial evolution under prolonged environmental stability. Here, we analyzed metagenome-assembled genomes from this cave, revealing that prokaryotes exhibit lower gene diversity and higher levels of pseudogenization compared to those from non-isolated environments, mainly affecting housekeeping functions involved in translation. Functional redundancy across genomes remained comparable to related habitats. Our results suggest that pseudogenization may serve as a fine-tuning mechanism to reduce excess redundancy. Although horizontal gene transfer is limited overall, the cave virome seems to contribute to microbial adaptation through the transfer of auxiliary metabolic genes. Movile microorganisms harbor fewer phage-defense systems than counterparts in related environments, suggesting a long-term adaptation to a relatively stable virosphere. Our findings indicate that prolonged isolation under stable selective pressures does not necessarily lead to major genomic divergence, but rather promotes adaptive gene loss. This study provides key insights into how long-term stability shapes microbial genome evolution and ecosystem function.

microbiology↗

Closing the gap: Examining the impact of source habitat proximity on plant and soil microbial communities in post-mining spoil heap primary succession

Revegetation of barren substrates is often determined by the composition and distance of the nearest plant community, serving as a source of colonising propagules. Whether such dispersal effect can be observed during the development of soil microbial communities, is not clear. In this study, we aimed to elucidate which factors structure plant and soil bacterial and fungal communities during primary succession on a limestone quarry spoil heap, focusing on the effect of distance to the adjoining xerophilous grassland. We established a grid of 35 plots covering three successional stages - initial barren substrate, early successional community and late successional grassland ecosystem, the latter serving as the primary source of soil colonization. On these plots, we performed vegetation surveys of plant community composition and collected soil cores to analyse soil chemical properties and bacterial and fungal community composition. The composition of early successional plant community was significantly affected by the proximity of the source late successional community, however, the effect weakened when the distance exceeded 20 m. Early successional microbial communities were structured mainly by the local plant community composition and soil chemical properties, with minimal contribution of the source community proximity. These results show that on small spatial scales, species migration is an important determinant of plant community composition during primary succession while the establishment of soil microbial communities is not limited by dispersal and is primarily driven by local biotic and abiotic conditions.

microbiology↗

Variation of carbon, nitrogen and phosphorus content in fungi reflects their ecology and phylogeny

Fungi are an integral part of the nitrogen and phosphorus cycling in trophic networks, as they participate in biomass decomposition and facilitate plant nutrition through root symbioses. Nutrient content varies considerably between the main fungal habitats, such as soil, plant litter or decomposing dead wood, but there are also large differences within habitats. While some soils are heavily loaded with N, others are limited by N or P. One way in which nutrient availability can be reflected in fungi is their content in biomass. In this study, we determined the C, N, and P content (in dry mass) of sporocarps of 214 fungal species to inspect how phylogeny and membership in ecological guilds (soil saprotrophs, wood saprotrophs, and ectomycorrhizal fungi) affect the nutrient content of fungal biomass. The C content of sporocarps (415 {+/-} 25 mg g-1) showed little variation (324-494 mg g-1), while the range of N (46 {+/-} 20 mg g-1) and P (5.5 {+/-} 3.0 mg g-1) contents was within one order of magnitude (8-103 mg g-1 and 1.0-18.9 mg g-1, respectively). Importantly, the N and P contents were significantly higher in the biomass of soil saprotrophic fungi compared to wood saprotrophic and ectomycorrhizal fungi. While the average C/N ratio in fungal biomass was 11.2, values exceeding 40 were recorded for some fungi living on dead wood, typically characterized by low N content. The N and P content of fungal mycelium also showed a significant phylogenetic signal, with differences in nutrient content being relatively low within species and genera of fungi. A strong correlation was found between N and P content in fungal biomass, while the correlation of N content and the N-containing fungal cell wall biopolymer - chitin showed only weak significance. The content of macronutrients in fungal biomass is influenced by the fungal life style and nutrient availability and is also limited by phylogeny.

microbiology↗

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A global genome database of all of Earths species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all [~]1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.

genomics↗

MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy

Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes, and viruses from metagenomes exist. However, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool accessible for non-bioinformaticians that make it easy to recover genomes of prokaryotes, eukaryotes, and viruses from metagenomes, either alone or in combination. We tested MuDoGer using 24 individual-isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR.

bioinformatics↗

Recovery of 447 Eukaryotic bins reveals major challenges for Eukaryote genome reconstruction from metagenomes.

An estimated 8.7 million eukaryotic species exist on our planet. However, recent tools for taxonomic classification of eukaryotes only dispose of 734 reference genomes. As most Eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recover Prokaryotic genomes have become common in genome biology, few studies have tackled the recovery of Eukaryotic genomes from metagenomes. This study assessed the reconstruction of Eukaryotic genomes using 215 metagenomes from diverse environments using the EukRep pipeline. We obtained 447 eukaryotic bins from 15 classes (e.g., Saccharomycetes, Sordariomycetes, and Mamiellophyceae) and 16 orders (e.g., Mamiellales, Saccharomycetales, and Hypocreales). More than 73% of the obtained eukaryotic bins were recovered from samples whose biomes were classified as host-associated, aquatic and anthropogenic terrestrial. However, only 93 bins showed taxonomic classification to (9 unique) genera and 17 bins to (6 unique) species. A total of 193 bins contained completeness and contamination measures. Average completeness and contamination were 44.64% ({sigma}=27.41%) and 3.97% ({sigma}=6.53%), respectively. Micromonas commoda was the most frequent taxa found while Saccharomyces cerevisiae presented the highest completeness, possibly resulting from a more significant number of reference genomes. However, mapping eukaryotic bins to the chromosomes of the reference genomes suggests that completeness measures should consider both single-copy genes and chromosome coverage. Recovering eukaryotic genomes will benefit significantly from long-read sequencing, intron removal after assembly, and improved reference genomes databases.

bioinformatics↗

Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities

Development of soil microbial communities along ecological succession is crucial for ecosystem recovery and maintenance. However, mechanisms mediating microbial community dynamics and co-occurrence patterns along ecological succession remain unclear. Here, we explored community dynamics and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Meanwhile, by synthesizing previous studies and ecological theories, we devised two conceptual models that integrate microbial phylogeny with patterns in community dynamics and in taxa co-occurrence. We further tested these models by using empirical data. At early successional stages, bacterial community structures became increasingly phylogenetically clustered with soil age, which was co-determined by the environmental selection from soil vegetation cover and by heterogeneous responses of less phylogenetically similar bacteria to the increasing resource availability along succession. At later successional stages, bacterial community phylogenetic structures displayed progressively lower variability. The fungal community phylogenetic structures varied relatively less and were independent of soil age, soil properties and vegetation cover, which was attributed to the dominance of stochastic processes in community turnover along succession. Network analysis revealed a decrease in bacterial co-occurrence complexity along succession, which aligned with a decrease in average pairwise phylogenetic distances between co-occurring bacteria. These patterns together implied a decrease in potential bacterial cooperation that was probably mediated by increasing resource availability along succession. The increased complexity of fungal co-occurrence along succession was independent of phylogenetic distances between co-occurring fungi. This study provides new sights into ecological mechanisms underlying bacterial and fungal community succession.

microbiology↗

Explorative meta-analysis of 417 extant archaeal genomes to predict their contribution to the total microbiome functionality

Unveiling the relationship between taxonomy and function in microbiomes is crucial to determine their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi was reported, this is not the case for archaea. Here, we used a meta-analysis of completely annotated extant genomes of 417 taxonomically unique archaeal species to describe intergenome and intragenome redundancy of functions and to predict the extent of microbiome functionality on Earth contained within archaeal genomes using accumulation curves of all known functions from the level 3 of KEGG Orthology. We found that intergenome redundancy as functions present in multiple genomes was inversely related to intragenome redundancy as multiple copies of a gene in one genome, implying the trade of between additional copies of functionally important genes or a higher number of different genes. A logarithmic model described the relationship between functional diversity and species richness better than both the unsaturated and the saturated model, which suggests a limited total number of archaeal functions in contrast to the potential of bacteria and fungi. Using a global archaeal species richness estimate of 13,159, the logarithmic model predicts a total of 4,164.1 {+/-}2.9 KEGG level 3 functions while the non-parametric bootstrap estimate yields a lower bound of 2,994 {+/-}57 KEGG level 3 functions. Our approach not only highlights similarities in functional redundancy but also the difference in functional potential of archaea compared to other domains of life.

ecology↗

GlobalFungi: Global database of fungal records from high-throughput-sequencing metabarcoding studies

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultural and wild plants and pathogenicity. The high importance of fungi in the ecosystem processes contrasts with the incompleteness of understanding of the patterns of fungal biogeography and the environmental factors that drive it. To close this gap of knowledge, we have here collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at http://globalfungi.com. The GlobalFungi database contains over 650 million observations of fungal sequences across >20 000 samples with geographical locations and additional metadata contained in 207 original studies with millions of unique sequence variants of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. As it is, the study represents the most comprehensive atlas of fungal distribution on the global scale open to further additions.

ecology↗

The total fungal microbiome functionality

Unveiling the relationship between taxonomy and function of the microbiome is crucial to determine its contribution to ecosystem functioning. However, while there is a considerable amount of information on microbial taxonomic diversity, our understanding of its relationship to functional diversity is still scarce. Here we used a meta-analysis of 377 completely annotated and taxonomically different fungal genomes to predict the total fungal microbiome functionality on Earth with all known functions from level 3 of KEGG Orthology using both parametric and non-parametric estimations. The unsaturated model described the accumulation of functions with increasing species richness significantly better (P-value < 2.2e-16) than the saturated model suggesting the presence of widespread and rare functions. Consistent with the parametric approach, the non-parametric Chao-1 estimator that assumes a maximum functional richness did not reach a plateau. Based on previous estimates of fungal species richness on Earth, we propagated the unsaturated model to predict a total fungal microbiome functionality of 42.4 million. Of those, only 0.06% are known today since the vast majority belongs to yet unknown rare functions. Logically, our approach not only highlighted the presence of two types of functions but pointed towards the necessity of novel and more sophisticated methods to unveil the entirety of functions to fully understand the involvement of the fungal microbiome in ecosystem functioning.

ecology↗