Environmental stress destabilizes microbial networks

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(6), P. 1722 - 1734

Published: Jan. 15, 2021

Language: Английский

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Priority effects in microbiome assembly

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 20(2), P. 109 - 121

Published: Aug. 27, 2021

Language: Английский

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Trophic Interactions and the Drivers of Microbial Community Assembly

Current Biology, Journal Year: 2020, Volume and Issue: 30(19), P. R1176 - R1188

Published: Oct. 1, 2020

Despite numerous surveys of gene and species content in heterotrophic microbial communities, such as those found animal guts, oceans, or soils, it is still unclear whether there are generalizable biological ecological processes that control their dynamics function. Here, we review experimental theoretical advances to argue networks trophic interactions, which the metabolic excretions one primary resource for another, constitute central drivers community assembly. Trophic interactions emerge from deconstruction complex forms organic matter into a wealth smaller intermediates, some released environment serve nutritional buffet community. The structure emergent network rate at resources supplied many features assembly, including relative contributions competition cooperation emergence alternative states. Viewing assembly through lens also has important implications spatial communities well functional redundancy taxonomic groups. Given ubiquity across environments, they impart common logic can enable development more quantitative predictive ecology.

Language: Английский

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Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: July 5, 2022

Plant response to drought stress involves fungi and bacteria that live on in plants the rhizosphere, yet stability of these myco- micro-biomes remains poorly understood. We investigate resistance resilience an agricultural system using both community composition microbial associations. Here we show tests fundamental hypotheses fungi, as compared bacteria, are (i) more resistant but (ii) less resilient when rewetting relieves stress, found robust support at level composition. Results were complex all-correlations co-occurrence networks. In general, disrupts networks based significant positive correlations among between fungi. Surprisingly, functional guilds rhizosphere leaf strengthened by drought, same was seen for involving arbuscular mycorrhizal rhizosphere. also gradient hypothesis because increased relative frequency correlations.

Language: Английский

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Bacterial species rarely work together

Science, Journal Year: 2022, Volume and Issue: 376(6593), P. 581 - 582

Published: May 5, 2022

Competition is prevalent and could be harnessed as an alternative to antibiotics.

Language: Английский

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Plastics and the microbiome: impacts and solutions

Environmental Microbiome, Journal Year: 2021, Volume and Issue: 16(1)

Published: Jan. 20, 2021

Abstract Global plastic production has increased exponentially since manufacturing commenced in the 1950’s, including polymer types infused with diverse additives and fillers. While negative impacts of plastics are widely reported, particularly on marine vertebrates, microbial life remain poorly understood. Plastics impact microbiomes directly, exerting toxic effects, providing supplemental carbon sources acting as rafts for colonisation dispersal. Indirect consequences include environmental shading, altered compositions host communities disruption organism or community health, hormone balances immune responses. The isolation application plastic-degrading microbes substantial interest yet little evidence supports biodegradation most high molecular weight synthetic polymers. Over 400 species have been presumptively identified capable degradation, but degradation highly prevalent polymers polypropylene, nylon, polystyrene polyvinyl chloride must be treated caution; studies fail to differentiate losses caused by leaching monomers, Even where is demonstrated, such polyethylene terephthalate, ability microorganisms degrade more crystalline forms used commercial appears limited. Microbiomes frequently work conjunction abiotic factors heat light structural integrity accessibility enzymatic attack. Consequently, there remains much scope extremophile explored a source enzymes microorganisms. We propose best-practice workflow isolating reporting taxa from microbiomes, which should multiple lines supporting changes structure, mass loss, detection presumed products, along confirmation strains (and their associated genes) responsible degradation. Such approaches necessary degraders differentiated organisms only degrading labile within predominantly amorphous plastics,

Language: Английский

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Biodiversity promotes ecosystem functioning despite environmental change

Ecology Letters, Journal Year: 2021, Volume and Issue: 25(2), P. 555 - 569

Published: Dec. 2, 2021

Abstract Three decades of research have demonstrated that biodiversity can promote the functioning ecosystems. Yet, it is unclear whether positive effects on ecosystem will persist under various types global environmental change drivers. We conducted a meta‐analysis 46 factorial experiments manipulating both species richness and environment to test how drivers (i.e. warming, drought, nutrient addition or CO 2 enrichment) modulated effect multiple functions across three taxonomic groups (microbes, phytoplankton plants). found increased in ambient manipulated environments, but often not same degree. In particular, were larger stressful environments induced by drivers, indicating high‐diversity communities more resistant change. Using subset studies, we also mainly driven interspecific complementarity these over time environments. Our findings support conservation as key strategy for sustainable management face

Language: Английский

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From diversity to complexity: Microbial networks in soils

Soil Biology and Biochemistry, Journal Year: 2022, Volume and Issue: 169, P. 108604 - 108604

Published: March 17, 2022

Network analysis has been used for many years in ecological research to analyze organismal associations, example food webs, plant-plant or plant-animal interactions. Although network is widely applied microbial ecology, only recently it entered the realms of soil shown by a rapid rise studies applying co-occurrence communities. While this application offers great potential deeper insights into structure ecosystems, also brings new challenges related specific characteristics datasets and type questions that can be addressed. In Perspectives Paper we assess ecology due small-scale heterogeneity environment nature datasets. We review different approaches construction are commonly discuss their features limitations. Using test dataset communities from two depths forest soil, demonstrate how experimental designs constructing algorithms affect resulting networks, turn may influence conclusions. will reveal assumptions method, methods preparing dataset, definitions thresholds structure. Finally, particular approached analyzing interpreting properties. Targeting these properties meaningful way allow technique not merely descriptive, but hypothesis-driven research. Analysing networks soils opens window better understanding complexity However, approach unfortunately often draw conclusions which far beyond scientific evidence provide, damaged its reputation analysis. Paper, would like sharpen view real soils, at same time raise awareness regarding limitations ways misused misinterpreted.

Language: Английский

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Ecological modelling approaches for predicting emergent properties in microbial communities

Nature Ecology & Evolution, Journal Year: 2022, Volume and Issue: 6(7), P. 855 - 865

Published: May 16, 2022

Language: Английский

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Design of synthetic human gut microbiome assembly and butyrate production

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: May 31, 2021

The capability to design microbiomes with predictable functions would enable new technologies for applications in health, agriculture, and bioprocessing. Towards this goal, we develop a model-guided approach synthetic human gut production of the health-relevant metabolite butyrate. Our data-driven model quantifies microbial interactions impacting growth butyrate separately, providing key insights into ecological mechanisms driving production. We use our explore vast community space using design-test-learn cycle identify high butyrate-producing communities. can accurately predict assembly across wide range species richness. Guided by model, constraints on richness molecular factors production, including hydrogen sulfide, environmental pH, resource competition. In sum, provides flexible generalizable framework understanding predicting metabolic functions.

Language: Английский

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