Idiosyncratic responses to biotic and environmental filters in wood‐inhabiting fungal communities

Ecology, Journal Year: 2025, Volume and Issue: 106(2)

Published: Feb. 1, 2025

Quantification of different processes affecting the assembly ecological communities remains challenging, especially in species-rich communities. While role environmental filtering has generally been well established, fewer studies have experimentally shown how other processes, such as biotic filtering, structure Here, we studied relative roles and colonization wood-inhabiting fungi, a species-rich, highly interactive, environment-sensitive group species. We conducted field experiment where simulated with inoculations nine fungal species habitat patches (i.e., logs) varying abiotic conditions. characterized local resident before success inoculated after one two years using DNA metabarcoding. asked what determined by comparing predictive performance alternative models. These models included either only predictors physical log properties) or additionally aspects richness, community composition, amount) predictors. all successfully colonized logs, rate factors explaining their varied among The four was explained mostly variables, while three influential from presence individual to collective multiple Finally, for species, showed poor performance. Our results indicate may jointly Overall, show that vary idiosyncratically response factors, highlighting need consider complexity species-level responses when predicting community-level changes.

Language: Английский

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Airborne DNA reveals predictable spatial and seasonal dynamics of fungi

Nature, Journal Year: 2024, Volume and Issue: 631(8022), P. 835 - 842

Published: July 10, 2024

Abstract Fungi are among the most diverse and ecologically important kingdoms in life. However, distributional ranges of fungi remain largely unknown as do ecological mechanisms that shape their distributions 1,2 . To provide an integrated view spatial seasonal dynamics fungi, we implemented a globally distributed standardized aerial sampling fungal spores 3 The vast majority operational taxonomic units were detected within only one climatic zone, spatiotemporal patterns species richness community composition mostly explained by annual mean air temperature. Tropical regions hosted highest diversity except for lichenized, ericoid mycorrhizal ectomycorrhizal which reached peak temperate regions. sensitivity responses was associated with phylogenetic relatedness, suggesting large-scale some groups partially constrained ancestral niche. There strong signal sensitivity, have retained trait sporulating short period. Overall, our results show hyperdiverse kingdom follows highly predictable temporal dynamics, seasonality both increasing latitude. Our study reports resembling those described other major organisms, thus making contribution to long-standing debate on whether organisms microbial lifestyle follow global biodiversity paradigms known macroorganisms 4,5

Language: Английский

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Long- and short-term soil storage methods other than freezing can be useful for DNA-based microbial community analysis

Soil Biology and Biochemistry, Journal Year: 2024, Volume and Issue: 191, P. 109329 - 109329

Published: Feb. 2, 2024

Language: Английский

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Singleton-based species names and fungal rarity: Does the number really matter?

IMA Fungus, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 20, 2024

Fungi are among the least known organisms on earth, with an estimated number of species between 1.5 and 10 million. This is expected to be refined, especially increasing knowledge about microfungi in undersampled habitats amounts data derived from environmental DNA sequencing. A significant proportion newly generated sequences fail match already named species, thus represent what has been referred as fungal "dark taxa". Due challenges associated observing, identifying, preserving sporophores, many macro- microfungal only a single collection, specimen, isolate, and/or sequence-a singleton. Mycologists consequently used working "rare" specimens. However, rarity singleton phenomena lack consideration valorization studies. In particular, practice publishing new names based specimen remains cause debate. Here, we provide some elements reflection this issue light specificities kingdom global change context. If multiple independent sources support existence taxon, encourage mycologists proceed formal description, irrespective specimens at hand. Although description singleton-based may not considered best practice, it does responsible science closing Linnean biodiversity shortfall.

Language: Английский

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Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: May 30, 2024

Novel methods for sampling and characterizing biodiversity hold great promise re-evaluating patterns of life across the planet. The airborne spores with a cyclone sampler, sequencing their DNA, have been suggested as an efficient well-calibrated tool surveying fungal diversity various environments. Here we present data originating from Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations world. Each sample represents DNA extracted 24 m

Language: Английский

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Influence of tree mycorrhizal type, tree species identity, and diversity on forest root‐associated mycobiomes

New Phytologist, Journal Year: 2024, Volume and Issue: 242(4), P. 1691 - 1703

Published: April 24, 2024

Understanding the complex interactions between trees and fungi is crucial for forest ecosystem management, yet influence of tree mycorrhizal types, species identity, diversity on tree-tree their root-associated fungal communities remains poorly understood. Our study addresses this gap by investigating different arbuscular (AM) ectomycorrhizal (EcM) pairs (TSPs) in a subtropical experiment, spanning monospecific, two-species, multi-species mixtures, utilizing Illumina sequencing ITS2 region. The reveals that type significantly impacts alpha monospecific stands. Meanwhile, identity's modulated overall diversity. Tree-related variables spatial distance emerged as major drivers variations community composition. Notably, compositional differences root AM EcM diminish, indicating convergence irrespective type. Interestingly, dual were observed these mixtures. This research underscores pivotal role partnerships interplay biotic abiotic factors shaping communities, particularly varied settings, its implications effective management biodiversity conservation.

Language: Английский

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ASV vs OTUs clustering: Effects on alpha, beta, and gamma diversities in microbiome metabarcoding studies

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(10), P. e0309065 - e0309065

Published: Oct. 3, 2024

In microbial community sequencing, involving bacterial ribosomal 16S rDNA or fungal ITS, the targeted genes are basis for taxonomical assignment. The traditional bioinformatical procedure has decades made use of a clustering protocol by which sequences pooled into packages shared percent identity, typically at 97%, to yield Operational Technical Units (OTUs). Progress in data processing methods however led possibility minimizing technical sequencers errors, were main reason OTU choice, and analyze instead exact Amplicon Sequence Variants (ASV) is choice yielding much less agglomerated reads. We have tested two procedures on same metabarcoded amplicons dataset encompassing series samples from 17 adjacent habitats, taken across 700 meter-long transect different ecological conditions unfolding gradient spanning cropland, through meadows, forest all successional transitions up seashore, within coastal area. This design allowed scan high biodiversity basin measure alpha, beta gamma diversity area, verify effect bioinformatics as concerns values ten indexes other parameters. Two levels progressive OTUs clustering, (99% 97%) compared with ASV data. results showed that proportionally marked underestimation indicators species distorted behaviour dominance evenness respect direct Multivariate ordination analyses resulted also sensitive terms tree topology coherence. Overall, support view reference-based carries several misleading disadvantageous biases, including risk missing novel taxa yet unreferenced databases. Since its alternatives de novo hand drawbacks due heavier computational demand comparability, especially environmental studies contain uncharacterized species, based analysis, least prokaryotes, appears warrant significand advantages comparison every level identity cutoff.

Language: Английский

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The Impact of Oil Palm Plantations and Pastures on Benthic Prokaryotic and Fungal Communities in Tropical Streams

Freshwater Biology, Journal Year: 2025, Volume and Issue: 70(1)

Published: Jan. 1, 2025

ABSTRACT The expansion of oil palm plantations and cattle grazing lands has a detrimental impact on freshwater ecosystems, causing ecological degradation biodiversity loss in the tropics, although little is known about effects aquatic microbial community. We assessed benthic community streams lands, (with without riparian buffers) native vegetation (rainforests) using metabarcoding to analyse prokaryotic amplicon sequence variants (ASVs) fungal operational taxonomic units (OTUs). observed significantly higher richness rainforests than lacking buffers, but not with buffers. Groups commonly found faecal matter were land, buffers showed lower abundance wood decomposers, both land uses had more primary producers. Prokaryote diversity associated positively negatively temperature, light while was proximity forests protected area. negative agriculture stream richness, composition partially mitigated by conservation probably, (a source spores). Our findings demonstrate potential role for benthos monitoring impacts agricultural underlines importance mitigating, some extent, streams.

Language: Английский

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Metabolic Profiling and Substrate Utilization of Hericium erinaceus (Lion’s Mane) Mycelia Isolate Using Biolog Phenotype Microarray

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 16, 2025

Hericium erinaceus, has long been recognized in traditional Chinese medicine for its extensive health benefits. H. erinaceus is notable production of various bioactive compounds. Among these, the terpenoid compounds hericenones and erinacines, derived from fruiting bodies cultured mycelia respectively, have particularly highlighted their ability to stimulate nerve growth factor (NGF) synthesis, contributing mushroom's neuroprotective properties. This study focuses on metabolic characterization mycelium using Biolog Phenotype MicroArray (PM) technology, a high-throughput method analyzing microbial phenotypes. For first time, PMs were applied elucidate comprehensive nutritional utilization profile erinaceus. The involved testing 950 different conditions, including 190 carbon sources, 380 nitrogen 94 biosynthetic pathways, 59 phosphorus 35 sulfur 96 osmotic pressures, pH conditions. results revealed that relatively restricted profile, efficiently utilizing only 23 out mainly simple sugars certain complex carbohydrates like D-Cellobiose, D-Xylose, Arbutin. also demonstrated effective Urea D-glucosamine, was capable growing all sources most with few exceptions. Additionally, exhibited under 65 56 conditions tested. detailed not enhances our understanding erinaceus' requirements capabilities but provides valuable insights into potential applications development functional foods alternative medicines.

Language: Английский

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Exploring Environmental Microfungal Diversity Through Serial Single Cell Screening

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 20, 2025

ABSTRACT Known for its remarkable diversity and ecological importance, the fungal kingdom remains largely unexplored. In fact, number of unknown undescribed fungi is predicted to exceed known species by far. Despite efforts uncover these dark taxa, we still face inherent sampling biases methodological limitations. Here, present a framework that combines taxonomic knowledge, molecular biology data processing explore biodiversity enigmatic aquatic lineages. Our work based on serial screening environmental cells approach taxa. Microscopic documentation followed DNA analysis laser micro‐dissected cells, coupled with ribosomal operon barcoding step realised long‐read sequencing, an optional whole genome sequencing step. We tested this range mostly belonging group hyphomycetes derived from samples. From initial screening, were able identify 60 potentially new taxa in target dataset. By extending methodology other lineages associated different habitats, expect increasingly characterise barcodes diverse This offers promising solution challenges posed unculturable holds potential be applied microeukaryotes.

Language: Английский

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