Enzymatic systems involved in decomposition reflects the ecology and taxonomy of saprotrophic fungi

Eichlerová, Ivana; Homolka, Ladislav; Žifčáková, Lucia; Lisá, Ludmila; Dobiášová, Petra; Baldrián, Petr

doi:10.1016/j.funeco.2014.08.002

Cited by 120 publications

(78 citation statements)

References 66 publications

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“…This information is key in order to estimate the potential for polysaccharide deconstruction in microbial populations dominated by bacteria (49) and to parameterize simulated microbial guilds for ecosystem modeling (50). More broadly, this information will be useful to investigate how fluctuations of environmental bacterial communities, together with fungal populations (9), in response to natural or anthropogenic changes may affect the polysaccharide deconstruction in the environment and, more globally, the carbon cycling.…”

Section: Discussionmentioning

confidence: 99%

Genomic Potential for Polysaccharide Deconstruction in Bacteria

Berlemont

Martiny

2015

Appl Environ Microbiol

147

145

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Glycoside hydrolases are important enzymes that support bacterial growth by enabling the degradation of polysaccharides (e.g., starch, cellulose, xylan, and chitin) in the environment. Presently, little is known about the overall phylogenetic distribution of the genomic potential to degrade these polysaccharides in bacteria. However, knowing the phylogenetic breadth of these traits may help us predict the overall polysaccharide processing in environmental microbial communities. In order to address this, we identified and analyzed the distribution of 392,166 enzyme genes derived from 53 glycoside hydrolase families in 8,133 sequenced bacterial genomes. Enzymes for oligosaccharides and starch/glycogen were observed in most taxonomic groups, whereas glycoside hydrolases for structural polymers (i.e., cellulose, xylan, and chitin) were observed in clusters of relatives at taxonomic levels ranging from species to genus as determined by consenTRAIT. The potential for starch and glycogen processing, as well as oligosaccharide processing, was observed in 85% of the strains, whereas 65% possessed enzymes to degrade some structural polysaccharides (i.e., cellulose, xylan, or chitin). Potential degraders targeting one, two, and three structural polysaccharides accounted for 22.6, 32.9, and 9.3% of genomes analyzed, respectively. Finally, potential degraders targeting multiple structural polysaccharides displayed increased potential for oligosaccharide deconstruction. This study provides a framework for linking the potential for polymer deconstruction with phylogeny in complex microbial assemblages.

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Section: Discussionmentioning

confidence: 99%

Genomic Potential for Polysaccharide Deconstruction in Bacteria

Berlemont

Martiny

2015

Appl Environ Microbiol

147

145

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“…Wood‐associated saprotrophs in the phylum Basidiomycota tend to have more extensive wood‐degrading abilities than Ascomycota (Eichlerová et al. ). Differences in saprotrophic abilities between these phyla do not directly translate to functional differences in an endophyte context, but since many of these taxa are latently present we hypothesized that phyla identity may inform co‐occurrence patterns.…”

Section: Methodsmentioning

confidence: 99%

“…Likewise, the success of fungal taxa in these wood environments may depend on fungal evolutionary history (Eichlerová et al. ). The principle of limiting similarity (Abrams , ) predicts that taxa with similar traits are more likely to engage in negative interactions and lead to competitive exclusion.…”

Section: Introductionmentioning

confidence: 99%

Good neighbors aplenty: fungal endophytes rarely exhibit competitive exclusion patterns across a span of woody habitats

Lee

Powell

Oberle

et al. 2019

Ecology

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Environmental forces and biotic interactions, both positive and negative, structure ecological communities, but their relative roles remain obscure despite strong theory. For instance, ecologically similar species, based on the principle of limiting similarity, are expected to be most competitive and show negative interactions. Specious communities that assemble along broad environmental gradients afford the most power to test theory, but the communities often are difficult to quantify. Microbes, specifically fungal endophytes of wood, are especially suited for testing community assembly theory because they are relatively easy to sample across a comprehensive range of environmental space with clear axes of variation. Moreover, endophytes mediate key forest carbon cycle processes, and although saprophytic fungi from dead wood typically compete, endophytic fungi in living wood may enhance success through cooperative symbioses. To classify interactions within endophyte communities, we analyzed fungal DNA barcode variation across 22 woody plant species growing in woodlands near Richmond, New South Wales, Australia. We estimated the response of endophytes to the measured wood environment (i.e., 11 anatomical and chemical wood traits) and each other using latent‐variable models and identified recurrent communities across wood environments using model‐based classification. We used this information to evaluate whether (1) co‐occurrence patterns are consistent with strong competitive exclusion, and (2) a priori classifications by trophic mode and phylum distinguish taxa that are more likely to have positive vs. negative associations under the principle of limiting similarity. Fungal endophytes were diverse (mean = 140 taxa/sample), with differences in community composition structured by wood traits. Variation in wood water content and carbon concentration were associated with especially large community shifts. Surprisingly, after accounting for wood traits, fungal species were still more than three times more likely to have positive than negative co‐occurrence patterns. That is, patterns consistent with strong competitive exclusion were rare, and positive interactions among fungal endophytes were more common than expected. Confirming the frequency of positive vs. negative interactions among fungal taxa requires experimental tests, and our findings establish clear paths for further study. Evidence to date intriguingly suggests that, across a wide range of wood traits, cooperation may outweigh combat for these fungi.

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“…We identified four genera (Pestalotiopsis, Xylaria, Hansfordia, Seimatosporium) of Xylariales that comprise the most effective group of wood decomposers in the Sordariomycetes (Pointing et al 2003, Eichlerová et al 2015. Furthermore, many of the ascomycotan saproxylic species belonging to the Hypocreales (Trichoderma, Acremonium, Fusarium, Simplicillium, Hypocrea, Villosiclava, Gliocladium, Myrothecium, Chaunopycnis, Clonostachys, Lasionectria), Eurotiales (Aspergillus and Penicillium), Diaporthales (Greeneria and Prosthecium), Chaetosphaeriales (Chloridium) and the Sordariales (Chaetosphaeria, Phiallemonium, Fimetariella, Thielavia) were also retrieved.…”

Section: Discussionmentioning

confidence: 99%

USING Next-Generation Sequencing (NGS) TO UNCOVER DIVERSITY OF WOOD-DECAYING FUNGI IN NEOTROPICAL ATLANTIC FORESTS

et al. 2017

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A targeted amplicon-based metagenomics approach (metabarcoding) provides detailed access to the diversity of the mycobiome in any substrate in distinct environments on Earth. Fungi are the main decomposers of lignocellulosic woody debris in terrestrial forested ecosystems, contributing significantly to the global carbon cycle. The main objectives of this study were to assess the fungal taxonomic diversity in fallen woody debris samples from two Neotropical forest fragments (rainforest and seasonal forest), to analyze the qualitative and quantitative components of the taxonomic diversity, and to investigate the functional diversity of the ecological groups detected. Our study comprised three main methodological steps: (i) sampling in the field; (ii) extraction of DNA, amplification of targeted segments and massively parallel sequencing; and (iii) data analysis and interpretation. A total of 110 molecular operational taxonomic units showing sequence similarity of 95% or more across the two collection sites using two DNA metabarcoding markers (ITS1 and ITS2) were assigned to putative fungal genera in 59 families, 27 orders, and 3 phyla. The number of putative fungal genera and the relative abundance of reads for each genus are higher in the tropical rainforest site than in the tropical seasonal forest site. Most of the identified genera are ligninolytic and cellulolytic and/or hemicellulolytic Basidiomycota (Agaricomycetes) and Ascomycota (Sordariomycetes), but "sugar fungi" and fungi associated with plants and detritivorous insects were also detected. This is the first study using NGS as a rapid and large-scale useful strategy to uncover the diversity of wood-decaying fungi in tropical forests.

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Enzymatic systems involved in decomposition reflects the ecology and taxonomy of saprotrophic fungi

Cited by 120 publications

References 66 publications

Genomic Potential for Polysaccharide Deconstruction in Bacteria

Genomic Potential for Polysaccharide Deconstruction in Bacteria

Good neighbors aplenty: fungal endophytes rarely exhibit competitive exclusion patterns across a span of woody habitats

USING Next-Generation Sequencing (NGS) TO UNCOVER DIVERSITY OF WOOD-DECAYING FUNGI IN NEOTROPICAL ATLANTIC FORESTS

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