Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: June 17, 2020

Biodiversity on the Earth is changing at an unprecedented rate due to a variety of global change factors (GCFs). However, effects GCFs microbial diversity unclear despite that soil microorganisms play critical role in biogeochemical cycling. Here, we synthesize 1235 GCF observations worldwide and show rare species are more sensitive than common species, while do not always lead reduction diversity. GCFs-induced shifts alpha can be predominately explained by changed pH. In addition, impacts functionality community structure biomass rather Altogether, our findings fundamentally different from previous knowledge for well-studied plant animal communities, crucial policy-making conservation hotspots under changes.

Language: Английский

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Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences

Environmental Microbiome, Journal Year: 2020, Volume and Issue: 15(1)

Published: May 18, 2020

Sequencing of 16S rRNA genes has become a powerful technique to study microbial communities and their responses towards changing environmental conditions in various ecosystems. Several tools have been developed for the prediction functional profiles from gene sequencing data, because numerous questions ecosystem ecology require knowledge community functions addition taxonomic composition. However, accuracy these relies on information derived genomes available public databases, which are often not representative microorganisms present studied ecosystem. In addition, there is also lack predict redundancy communities.To address challenges, we Tax4Fun2, an R package redundancies prokaryotic sequences. We demonstrate that predicted by Tax4Fun2 highly correlated metagenomes same samples. further show higher accuracies than PICRUSt Tax4Fun. By incorporating user-defined, habitat-specific genomic information, robustness substantially enhanced. with determined simulated communities.Tax4Fun2 provides researchers unique tool investigate based data. It easy-to-use, platform-independent memory-efficient, thus enabling without extensive bioinformatics or access high-performance clusters profiles. Another feature it allows calculate specific functions, potentially important measure how resilient will be perturbation. implemented freely at https://github.com/bwemheu/Tax4Fun2.

Language: Английский

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Common principles and best practices for engineering microbiomes

Nature Reviews Microbiology, Journal Year: 2019, Volume and Issue: 17(12), P. 725 - 741

Published: Sept. 23, 2019

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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Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Nature Genetics, Journal Year: 2022, Volume and Issue: 54(2), P. 134 - 142

Published: Feb. 1, 2022

Language: Английский

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Applying the core microbiome to understand host–microbe systems

Journal of Animal Ecology, Journal Year: 2020, Volume and Issue: 89(7), P. 1549 - 1558

Published: April 5, 2020

Abstract The host‐associated core microbiome was originally coined to refer common groups of microbes or genes that were likely be particularly important for host biological function. However, the term has evolved encompass variable definitions across studies, often identifying key with respect their spatial distribution, temporal stability ecological influence, as well contribution function and fitness. A major barrier reaching a consensus over how define its relevance biological, evolutionary theory is lack precise terminology associated definitions, persistent association Common, microbiomes can together generate insights into processes act independently function, while functional host‐adapted cores distinguish between facultative near‐obligate symbionts differ in effects on This commentary summarizes five broad have been applied literature, highlighting strengths limitations advancing our understanding host–microbe systems, noting where they are overlap, discussing potential No one definition capture range population. Applied together, reveal different layers microbial organization from which we begin understand govern interactions.

Language: Английский

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Toxicity drives facilitation between 4 bacterial species

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(32), P. 15979 - 15984

Published: July 3, 2019

Competition between microbes is extremely common, with many investing in mechanisms to harm other strains and species. Yet positive interactions species have also been documented. What makes help or each currently unclear. Here, we studied the 4 bacterial capable of degrading metal working fluids (MWF), an industrial coolant lubricant, which contains growth substrates as well toxic biocides. We were surprised find only neutral Using mathematical modeling further experiments, show that this community likely due toxicity MWF, whereby species' detoxification benefited others by facilitating their survival, such they could grow degrade MWF better when together. The addition nutrients, reduction toxicity, more instead resulted competitive behavior. Our work provides support stress gradient hypothesis showing how harsh, environments can strongly favor facilitation microbial mask underlying interactions.

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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Arctic tundra shrubification: a review of mechanisms and impacts on ecosystem carbon balance

Environmental Research Letters, Journal Year: 2021, Volume and Issue: 16(5), P. 053001 - 053001

Published: April 23, 2021

Abstract Vegetation composition shifts, and in particular, shrub expansion across the Arctic tundra are some of most important widely observed responses high-latitude ecosystems to rapid climate warming. These changes vegetation potentially alter ecosystem carbon balances by affecting a complex set soil–plant–atmosphere interactions. In this review, we synthesize literature on (a) expansion, (b) key climatic environmental controls mechanisms that affect (c) impacts balance, (d) research gaps future directions improve process representations land models. A broad range evidence, including in-situ observations, warming experiments, remotely sensed indices have shown increases growth abundance woody plants, particularly tall deciduous shrubs, advancing shrublines circumpolar Arctic. This recent is affected several interacting factors warming, accelerated nutrient cycling, changing disturbance regimes, local variation topography hydrology. Under warmer conditions, shrubs can be more competitive than other plant functional types because their taller maximum canopy heights often dense structure. Competitive abilities vs herbaceous plants also controlled traits investments retention strategies leaves, stems, roots. Overall, may enhancing uptake altering respiration, through feedback snowpack dynamics, permafrost degradation, surface energy litter inputs. Observed projected subsequent effects feedbacks system. Land models, those integrated Earth System Models, need account for differences control interactions accurately predict decadal- centennial-scale dynamics.

Language: Английский

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Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments

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

Published: Nov. 21, 2018

Microbes in Guaymas Basin (Gulf of California) hydrothermal sediments thrive on hydrocarbons and sulfur experience steep, fluctuating temperature chemical gradients. The functional capacities communities inhabiting this dynamic habitat are largely unknown. Here, we reconstructed 551 genomes from hydrothermally influenced, nearby cold belonging to 56 phyla (40 uncultured). These comprise 22 unique lineages, including five new candidate phyla. In contrast findings hydrocarbon seeps, hydrothermal-associated more diverse archaea dominate over bacteria. Genome-based metabolic inferences provide first insights into the ecological niches these uncultured microbes, methane cycling Crenarchaeota alkane utilization ANME-1. shaped by a high biodiversity, partitioning among nitrogen pathways redundancy core carbon-processing pathways. select for distinctive microbial that stand out expansive open up physiological perspectives ecosystem function.

Language: Английский

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