Microbial interactions: from networks to models

Nature Reviews Microbiology, Journal Year: 2012, Volume and Issue: 10(8), P. 538 - 550

Published: July 16, 2012

Language: Английский

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Belowground biodiversity and ecosystem functioning

Nature, Journal Year: 2014, Volume and Issue: 515(7528), P. 505 - 511

Published: Nov. 1, 2014

Language: Английский

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Keystone taxa as drivers of microbiome structure and functioning

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 16(9), P. 567 - 576

Published: May 22, 2018

Language: Английский

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A global atlas of the dominant bacteria found in soil

Science, Journal Year: 2018, Volume and Issue: 359(6373), P. 320 - 325

Published: Jan. 18, 2018

The immense diversity of soil bacterial communities has stymied efforts to characterize individual taxa and document their global distributions. We analyzed soils from 237 locations across six continents found that only 2% phylotypes (~500 phylotypes) consistently accounted for almost half the worldwide. Despite overwhelming communities, relatively few are abundant in globally. clustered these dominant into ecological groups build first atlas taxa. Our study narrows down number a "most wanted" list will be fruitful targets genomic cultivation-based aimed at improving our understanding microbes contributions ecosystem functioning.

Language: Английский

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Microbiome definition re-visited: old concepts and new challenges

Microbiome, Journal Year: 2020, Volume and Issue: 8(1)

Published: June 30, 2020

The field of microbiome research has evolved rapidly over the past few decades and become a topic great scientific public interest. As result this rapid growth in interest covering different fields, we are lacking clear commonly agreed definition term "microbiome." Moreover, consensus on best practices is missing. Recently, panel international experts discussed current gaps frame European-funded MicrobiomeSupport project. meeting brought together about 40 leaders from diverse areas, while more than hundred all world took part an online survey accompanying workshop. This article excerpts outcomes workshop corresponding embedded short historical introduction future outlook. We propose based compact, clear, comprehensive description provided by Whipps et al. 1988, amended with set novel recommendations considering latest technological developments findings. clearly separate terms microbiota provide discussion composition microbiota, heterogeneity dynamics microbiomes time space, stability resilience microbial networks, core microbiomes, functionally relevant keystone species as well co-evolutionary principles microbe-host inter-species interactions within microbiome. These broad definitions suggested unifying concepts will help to improve standardization studies future, could be starting point for integrated assessment data resulting transfer knowledge basic science into practice. Furthermore, standards important solving new challenges associated anthropogenic-driven changes planetary health, which understanding might play key role. Video Abstract.

Language: Английский

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Soil bacterial networks are less stable under drought than fungal networks

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: July 27, 2018

Abstract Soil microbial communities play a crucial role in ecosystem functioning, but it is unknown how co-occurrence networks within these respond to disturbances such as climate extremes. This represents an important knowledge gap because changes could have implications for their functioning and vulnerability future disturbances. Here, we show grassland mesocosms that drought promotes destabilising properties soil bacterial, not fungal, networks, bacterial link more strongly during recovery than do fungal communities. Moreover, reveal has prolonged effect on via vegetation composition resultant reductions moisture. Our results provide new insight the mechanisms through which alters with potential long-term consequences, including plant community ability of aboveground belowground withstand

Language: Английский

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Deciphering microbial interactions and detecting keystone species with co-occurrence networks

Frontiers in Microbiology, Journal Year: 2014, Volume and Issue: 5

Published: May 20, 2014

Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential reveal ecological processes, it been insufficiently validated due the technical limitations inherent in studying complex ecosystems. Here, we simulate multi-species communities with known interaction patterns using generalized Lotka-Volterra dynamics, construct co-occurrence networks, and evaluate how well underlying interactions, experimental parameters can affect network inference interpretation. We find that recapitulate under certain conditions, but they lose interpretability when effects of habitat filtering become significant. demonstrate suffer local hot spots spurious correlation neighborhood "hub" species engage many interactions. also topological features associated keystone networks. This study provides a substantiated framework guide environmental microbiologists construction interpretation datasets.

Language: Английский

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Sparse and Compositionally Robust Inference of Microbial Ecological Networks

PLoS Computational Biology, Journal Year: 2015, Volume and Issue: 11(5), P. e1004226 - e1004226

Published: May 7, 2015

16S ribosomal RNA (rRNA) gene and other environmental sequencing techniques provide snapshots of microbial communities, revealing phylogeny the abundances populations across diverse ecosystems. While changes in community structure are demonstrably associated with certain conditions (from metabolic immunological health mammals to ecological stability soils oceans), identification underlying mechanisms requires new statistical tools, as these datasets present several technical challenges. First, operational taxonomic units (OTUs) from amplicon-based compositional. Counts normalized total number counts sample. Thus, not independent, traditional metrics (e.g., correlation) for detection OTU-OTU relationships can lead spurious results. Secondly, sequencing-based studies typically measure hundreds OTUs on only tens samples; thus, inference association networks is severely under-powered, additional information (or assumptions) required accurate inference. Here, we SPIEC-EASI (SParse InversE Covariance Estimation Ecological Association Inference), a method amplicon that addresses both issues. combines data transformations developed compositional analysis graphical model framework assumes network sparse. To reconstruct network, relies algorithms sparse neighborhood inverse covariance selection. synthetic benchmark absence an experimentally validated gold-standard accompanied by set computational tools generate OTU count topologies. outperforms state-of-the-art methods recover edges properties under variety scenarios. also reproducibly predicts previously unknown associations using American Gut project.

Language: Английский

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Fundamentals of Microbial Community Resistance and Resilience

Frontiers in Microbiology, Journal Year: 2012, Volume and Issue: 3

Published: Jan. 1, 2012

Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure predict. Understanding drivers stability, including resistance (insensitivity disturbance) resilience (the rate recovery after is important for predicting response disturbance. Here, we provide an overview concepts stability that relevant communities. First, highlight insights from ecology useful defining measuring stability. To determine whether general disturbance responses exist communities, next examine representative studies literature investigated press (long-term) pulse (short-term) disturbances a variety habitats. Then discuss biological features individual microorganisms, populations, may govern overall We conclude with thoughts about unique systems perspectives - informed by meta-omics data

Language: Английский

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Microbial control over carbon cycling in soil

Frontiers in Microbiology, Journal Year: 2012, Volume and Issue: 3

Published: Jan. 1, 2012

A major thrust of terrestrial microbial ecology is focused on understanding when and how the composition community affects functioning biogeochemical processes at ecosystem scale (meters-to-kilometers days-to-years). While research has demonstrated these linkages for physiologically phylogenetically "narrow" such as trace gas emissions nitrification, there less conclusive evidence that influences "broad" decomposition organic matter turnover in soil. In this paper, we consider soil structure C-cycling. We phylogenetic level which microbes form meaningful guilds, based overall life history strategies, suggest are associated with deep evolutionary divergences, while much species-level diversity probably reflects functional redundancy. then under what conditions it possible differences among to affect process dynamics, argue may be important rate OM breakdown rhizosphere detritus, likely not mineral soil, physical access occluded or sorbed substrates rate-limiting process. Microbial soils organisms allocate C they take up—not only do fates molecules differ, but can system differently well. For example, extracellular enzymes polysaccharides key controls function. How also particularly long-term fate soil—is sequestered not?

Language: Английский

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