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      Fungal Community Development in Decomposing Fine Deadwood Is Largely Affected by Microclimate

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          Abstract

          Fine woody debris (FWD) represents the majority of the deadwood stock in managed forests and serves as an important biodiversity hotspot and refuge for many organisms, including deadwood fungi. Wood decomposition in forests, representing an important input of nutrients into forest soils, is mainly driven by fungal communities that undergo continuous changes during deadwood decomposition. However, while the assembly processes of fungal communities in long-lasting coarse woody debris have been repeatedly explored, similar information for the more ephemeral habitat of fine deadwood is missing. Here, we followed the fate of FWD of Fagus sylvatica and Abies alba in a Central European forest to describe the assembly and diversity patterns of fungal communities over 6 years. Importantly, the effect of microclimate on deadwood properties and fungal communities was addressed by comparing FWD decomposition in closed forests and under open canopies because the large surface-to-volume ratio of FWD makes it highly sensitive to temperature and moisture fluctuations. Indeed, fungal biomass increases and pH decreases were significantly higher in FWD under closed canopy in the initial stages of decomposition indicating higher fungal activity and hence decay processes. The assembly patterns of the fungal community were strongly affected by both tree species and microclimatic conditions. The communities in the open/closed canopies and in each tree species were different throughout the whole succession with only limited convergence in time in terms of both species and ecological guild composition. Decomposition under the open canopy was characterized by high sample-to-sample variability, showing the diversification of fungal resources. Tree species-specific fungi were detected among the abundant species mostly during the initial decomposition, whereas fungi associated with certain canopy cover treatments were present evenly during decomposition. The species diversity of forest stands and the variability in microclimatic conditions both promote the diversity of fine woody debris fungi in a forest.

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          UPARSE: highly accurate OTU sequences from microbial amplicon reads.

          Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.
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            Search and clustering orders of magnitude faster than BLAST.

            Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets. Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch.
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              The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

              Abstract UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode—the nuclear ribosomal internal transcribed spacer (ITS) region—and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustered into ∼459 000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275 000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                13 April 2022
                2022
                : 13
                : 835274
                Affiliations
                [1] 1Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences , Prague, Czechia
                [2] 2Department of Animal Ecology and Tropical Biology, University of Würzburg , Würzburg, Germany
                [3] 3Bavarian Forest National Park , Grafenau, Germany
                [4] 4Animal Ecology, Department of Ecology, Faculty of Biology, Philipps-Universität Marburg , Marburg, Germany
                [5] 5Department of Conservation Biology, Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt , Frankfurt, Germany
                Author notes

                Edited by: Marja Tiirola, University of Jyväskylä, Finland

                Reviewed by: Ari Mikko Hietala, Norwegian Institute of Bioeconomy Research (NIBIO), Norway; Gábor M. Kovács, Eötvös Loránd University, Hungary

                *Correspondence: Vendula Brabcová, brabcova@ 123456biomed.cas.cz

                These authors have contributed equally to this work

                This article was submitted to Terrestrial Microbiology, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2022.835274
                9045801
                35495708
                951f9af9-41cd-4cc5-8103-2bdecd532479
                Copyright © 2022 Brabcová, Tláskal, Lepinay, Zrůstová, Eichlerová, Štursová, Müller, Brandl, Bässler and Baldrian.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 14 December 2021
                : 11 March 2022
                Page count
                Figures: 6, Tables: 0, Equations: 0, References: 93, Pages: 15, Words: 11537
                Funding
                Funded by: Grantová Agentura České Republiky, doi 10.13039/501100001824;
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                decomposition,deadwood,fungal community,succession,canopy cover,microclimate,temperate forest,ecology

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