Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood

Tláskal, Vojtěch; Brabcová, Vendula; Větrovský, Tomáš; López-Mondéjar, Rubén; Monteiro, Lummy Maria Oliveira; Saraiva, J.; Rocha, Ulisses Nunes da; Baldrián, Petr

doi:10.1038/s41597-021-00987-8

Cited by 12 publications

(11 citation statements)

References 55 publications

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“…To test the performance of the intron prediction workflow, we used a selection of publicly available metagenomes that represent a wide range of terrestrial, aquatic and host‐associated habitats (Table S4) (Corrêa et al, 2020; Tláskal, Brabcová, Větrovský, López‐Mondéjar, et al, 2021). Assembled contigs from each metagenomic study were analysed by our pipeline SVMmycointron.…”

Section: Methodsmentioning

confidence: 99%

Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns

Větrovský

Baručić

et al. 2023

Molecular Ecology Resources

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Metagenomics provides a tool to assess the functional potential of environmental and host‐associated microbiomes based on the analysis of environmental DNA: assembly, gene prediction and annotation. While gene prediction is straightforward for most bacterial and archaeal taxa, it has limited applicability in the majority of eukaryotic organisms, including fungi that contain introns in gene coding sequences. As a consequence, eukaryotic genes are underrepresented in metagenomics datasets and our understanding of the contribution of fungi and other eukaryotes to microbiome functioning is limited. Here, we developed a machine intelligence‐based algorithm that predicts fungal introns in environmental DNA with reasonable precision and used it to improve the annotation of environmental metagenomes. Intron removal increased the number of predicted genes by up to 9.1% and improved the annotation of several others. The proportion of newly predicted genes increased with the share of eukaryotic genes in the metagenome and—within fungal taxa—increased with the number of introns per gene. Our approach provides a tool named SVMmycointron for improved metagenome annotation, especially of microbiomes with a high proportion of eukaryotes. The scripts described in the paper are made publicly available and can be readily utilized by microbiome researchers analysing metagenomics data.

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Section: Methodsmentioning

confidence: 99%

Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns

Větrovský

Baručić

et al. 2023

Molecular Ecology Resources

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“…A comprehensive screening of temperate forest soil and leaf litter internal transcribed spacer (ITS) barcode sequences deposited in the GlobalFungi database (Větrovský et al, 2020) and analyzed for this review revealed 3,783,412 total yeast sequences belonging to 859 yeast species hypotheses (SHs); yeasts here were categorized in the database as "yeast" or "facultative yeast" as in Põlme et al (2020), with some manual curation (Table S1); and only samples with more than 5,000 fungal sequences were considered. Fungal ITS-targeting primers perform well with all important fungal lineages containing yeasts and with individual yeasts in a mock community (Větrovský et al, 2016(Větrovský et al, , 2019, and no significant polymerase chain reaction (PCR) bias is observed when comparing the yeast share in metagenomic data (without PCR) and ITS amplicon data (Tláskal et al, 2021); nor does there seem to be important DNA extraction bias against selected yeast taxa (Větrovský et al, 2016). This screening showed that the median yeast abundance in soil was significantly higher than in litter (Wilcoxon Rank-Sum test, W = 722,187, p = 2.9 Â 10 À15 ).…”

Section: Yeast Distributions From Environmental Sequencingmentioning

confidence: 99%

Yeasts from temperate forests

Mozzachiodi

Bai

Baldrián

et al. 2022

Yeast

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Yeasts are ubiquitous in temperate forests. While this broad habitat is well‐defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitats and no doubt contribute to broader ecosystem‐wide processes. Researchers have gathered information leading to hypotheses about yeasts' niches and their life cycles based on physiological observations in the laboratory as well as genomic analyses, but the challenge remains to test these hypotheses in the forests themselves. Here, we summarize the habitat and global patterns of yeast diversity, give some information on a handful of well‐studied temperate forest yeast genera, discuss the various strategies to isolate forest yeasts, and explain temperate forest yeasts' contributions to biotechnology. We close with a summary of the many future directions and outstanding questions facing researchers in temperate forest yeast ecology. Yeasts present an exciting opportunity to better understand the hidden world of microbial ecology in this threatened and global habitat.

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“…Although deadwood degradation contributes to release of CO 2 into the atmosphere, its nal degradation products also enrich soils with nutrients and recalcitrant organic matter (OM), assisting nutrient cycling and carbon storage in forest ecosystems (Baldrian et al, 2023). Here, we used deadwood samples from a natural mixed temperate forest in Central Europe, which were previously analyzed through bacterial genomics, metagenomics and metatranscriptomics using second generation high-throughput sequencing (Tláskal et al, 2021a(Tláskal et al, , 2021b(Tláskal et al, , 2017. These studies identi ed fungi and bacteria as the main contributors to deadwood microbiomes.…”

Section: Introductionmentioning

confidence: 99%

Pacbio HiFi sequencing sheds light on key bacteria contributing to deadwood decomposition processes

Richy,

Dobbler,

Tláskal

et al. 2024

Preprint

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Background In forest ecosystems, biological decomposition of deadwood components plays a pivotal role in nutrient cycling and in carbon storage by enriching soils with organic matter. However, deciphering the functional features of deadwood microbiomes is challenging due to their complexity and the limitations of traditional cultivation methods. Our study demonstrates how such limitations can be overcome by describing metagenome composition and function through the analysis of long DNA molecules using the PacBio HiFi platform. Results The accuracy of PacBio HiFi long-read sequencing emerges as a robust tool for reconstructing microbial genomes in deadwood. It outperformed the routine short-read sequencing and genome sequencing of isolates in terms of the numbers of genomes recovered, their completeness, and representation of their functional potential. We successfully assembled 69 bacterial genomes representing seven out of eight predominant bacterial phyla, including 14 high-quality draft MAGs and 7 nearly finished MAGs. Notably, the genomic exploration extends to Myxococcota, unveiling the unique capacity of Polyangiaceae to degrade cellulose. Patescibacteria contributed to deadwood decomposition processes, actively decomposing hemicellulose and recycling fungal-derived compounds. Furthermore, a novel nitrogen-fixing bacteria within the Steroidobacteriaceae family were identified, displaying interesting genomic adaptations to environmental conditions. The discovered diversity of biosynthetic gene clusters highlights the untapped potential of deadwood microorganisms for novel secondary metabolite production. Conclusions Our study emphasizes new contributors to wood decomposition, especially Polyangiaceae and Patescibacteria for complex and easily decomposable organic matter, respectively. The identification of nitrogen-fixing capabilities within the Steroidobacteraceae family introduces novel perspectives on nitrogen cycling in deadwood. The diverse array of observed biosynthetic gene clusters suggests intricate interactions among deadwood bacteria and promises the discovery of bioactive compounds. Long read sequencing not only advances our understanding of deadwood microbial communities but also demonstrates previously undiscovered functional capacities of the deadwood microbiome. Its application opens promising avenues for future ecological and biotechnological exploration of microbiomes.

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Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood

Cited by 12 publications

References 55 publications

Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns

Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns

Yeasts from temperate forests

Pacbio HiFi sequencing sheds light on key bacteria contributing to deadwood decomposition processes

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