Journal ArticleDOI
Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes
Jenni Hultman,Jenni Hultman,Mark P. Waldrop,Rachel Mackelprang,Rachel Mackelprang,Maude M. David,Jack W. McFarland,Steven J. Blazewicz,Jennifer W. Harden,Merritt R. Turetsky,A. David McGuire,Manesh B Shah,Manesh B Shah,Nathan C Verberkmoes,Lang Ho Lee,Konstantinos Mavrommatis,Konstantinos Mavrommatis,Janet K. Jansson +17 more
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TLDR
The combination of several molecular ‘omics’ approaches is used to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog.Abstract:
A multi-omics approach, integrating metagenomics, metatranscriptomics and metaproteomics, determines the phylogenetic composition of the microbial community and assesses its functional potential and activity along a thaw transition from intact permafrost to thermokast bog. The application of the various individual 'omics' tools to the study of microbial ecosystems has dramatically altered our view of their constituents and ecology over the past decade. Here Janet Jansson and colleagues develop an multi-omics approach, integrating metagenomics, metatranscriptomics and metaproteomics to analyse microbial gene expression in frozen soils that form part of the Alaska Peatland Experiment. The results show that the community shifts along a natural thaw gradient from permafrost to seasonally thawed active layer to thermokarst bog and the authors find that there is a transition in the potential for several biogeochemical cycles with thaw, including those for denitrification, nitrate reduction, iron reduction and methane oxidation. Over 20% of Earth’s terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere1. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils2,3,4 and a rapid shift in functional gene composition during short-term thaw experiments3. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales5,6. Here we use the combination of several molecular ‘omics’ approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.read more
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2016 update of the PRIDE database and its related tools
Juan Antonio Vizcaíno,Attila Csordas,Noemi del-Toro,José A. Dianes,Johannes Griss,Ilias Lavidas,Gerhard Mayer,Yasset Perez-Riverol,Florian Reisinger,Tobias Ternent,Qing Wei Xu,Rui Wang,Henning Hermjakob +12 more
TL;DR: The developments in PRIDE resources and related tools are summarized and a brief update on the resources under development 'PRIDE Cluster' and 'PRide Proteomes', which provide a complementary view and quality-scored information of the peptide and protein identification data available inPRIDE Archive are given.
Journal ArticleDOI
Embracing the unknown: disentangling the complexities of the soil microbiome.
TL;DR: Although most soil microorganisms remain undescribed, the field is now poised to identify how to manipulate and manage the soil microbiome to increase soil fertility, improve crop production and improve the understanding of how terrestrial ecosystems will respond to environmental change.
Journal ArticleDOI
Best practices for analysing microbiomes.
Rob Knight,Alison Vrbanac,Bryn C. Taylor,Alexander A. Aksenov,Chris Callewaert,Chris Callewaert,Justine W. Debelius,Antonio Gonzalez,Tomasz Kosciolek,Laura-Isobel McCall,Daniel McDonald,Alexey V. Melnik,James T. Morton,Jose Navas,Robert A. Quinn,Jon G. Sanders,Austin D. Swafford,Luke R. Thompson,Luke R. Thompson,Anupriya Tripathi,Zhenjiang Zech Xu,Jesse R. Zaneveld,Qiyun Zhu,J. Gregory Caporaso,Pieter C. Dorrestein,Pieter C. Dorrestein +25 more
TL;DR: This Review focuses on recent findings that suggest that operational taxonomic unit-based analyses should be replaced with new methods that are based on exact sequence variants, methods for integrating metagenomic and metabolomic data, and issues surrounding compositional data analysis.
Journal ArticleDOI
Scientists' Warning to Humanity: Microorganisms and Climate Change
Ricardo Cavicchioli,William J. Ripple,Kenneth N. Timmis,Farooq Azam,Lars R. Bakken,Matthew Baylis,Michael J. Behrenfeld,Antje Boetius,Philip W. Boyd,Aimée T. Classen,Thomas W. Crowther,Roberto Danovaro,Christine M. Foreman,Jef Huisman,David A. Hutchins,Janet K. Jansson,David M. Karl,Britt Koskella,David B. Mark Welch,Jennifer B. H. Martiny,Mary Ann Moran,Victoria J. Orphan,David S. Reay,Justin V. Remais,Virginia I. Rich,Brajesh K. Singh,Lisa Y. Stein,Frank J. Stewart,Matthew B. Sullivan,Madeleine J. H. van Oppen,Madeleine J. H. van Oppen,Scott C. Weaver,Eric A. Webb,Nicole S. Webster,Nicole S. Webster +34 more
TL;DR: This Consensus Statement documents the central role and global importance of microorganisms in climate change biology and puts humanity on notice that the impact of climate change will depend heavily on responses of micro organisms, which are essential for achieving an environmentally sustainable future.
Journal ArticleDOI
Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China.
Bin Ma,Haizhen Wang,Melissa Dsouza,Jun Lou,Yan He,Zhongmin Dai,Philip C. Brookes,Jianming Xu,Jack A. Gilbert,Jack A. Gilbert +9 more
TL;DR: The shifts of topological features in co-occurrence networks inferred from soil microbiota along a continental scale in eastern China provided new insight into studying microbial biogeographic patterns, their organization and impacts on soil-associated function.
References
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QIIME allows analysis of high-throughput community sequencing data.
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