Ecology and evolution of antimicrobial resistance in bacterial communities

The ISME Journal, Journal Year: 2020, Volume and Issue: 15(4), P. 939 - 948

Published: Nov. 20, 2020

Abstract Accumulating evidence suggests that the response of bacteria to antibiotics is significantly affected by presence other interacting microbes. These interactions are not typically accounted for when determining pathogen sensitivity antibiotics. In this perspective, we argue resistance and evolutionary responses antibiotic treatments should be considered only a trait an individual species but also emergent property microbial community in which pathogens embedded. We outline how interspecies can affect communities treatment, these could strength selection, potentially changing trajectory evolution. Finally, identify key areas future research will allow more complete understanding bacterial communities. emphasise acknowledging ecological context, i.e. occur between within communities, help development efficient effective treatments.

Language: Английский

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Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

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

Published: Jan. 10, 2022

Abstract Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how abundances shaped by biotic abiotic factors. Here we show that the ribosomal RNA gene operon ( rrn ) copy number, a genomic trait related to bacterial growth rate nutrient demand, decreases from abundant rare biosphere in nutrient-rich coastal sediment but exhibits opposite pattern nutrient-scarce pelagic zone global ocean. Both patterns underlain positive correlations between community-level number nutrients. Furthermore, inter-species co-exclusion inferred negative network associations observed more than ocean water samples. manipulation experiments yield effects availability on numbers consistent with our field observations. Based these results, propose “hunger games” hypothesis define abundance using ecological interaction, availability.

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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Agricultural subsoil microbiomes and functions exhibit lower resistance to global change than topsoils in Chinese agroecosystems

Nature Food, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 3, 2025

Language: Английский

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Vertical diversity and association pattern of total, abundant and rare microbial communities in deep‐sea sediments

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(12), P. 2800 - 2816

Published: May 8, 2021

Microbial abundance and community composition in marine sediments have been widely explored. However, high-resolution vertical changes of benthic microbial diversity co-occurrence patterns are poorly described. The ecological contributions abundant rare species also remain largely unknown. Here, by analysing populations at 14 depth layers 10 subseafloor sediment cores (water 1,250-3,530 m) obtained the South China Sea, we provided profiles β-diversity influenced subcommunities different abundance. These 134 samples were clustered into four groups according to (1-2, 6-10, 30-90 190-790 cm) with obvious shifts compositions. succession microorganisms was consistent redox zonation terrestrial inputs. Partitioning showed extremely high replacement between deep surface layer, indicating selection-induced loss dispersal dormant cells spores. By contrast, for horizontal β-diversity, richness became increasingly significant sediments. Accompanying this profile clear association pattern, being less connected deeper layers, probably reflecting reduced syntrophic interactions. Rare accounted an indispensable proportion network, tended form complex "small worlds." subcommunity responded differently various environmental factors compared subcommunity. Our findings expand current knowledge on their patterns, emphasizing potential roles species.

Language: Английский

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Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community

The ISME Journal, Journal Year: 2022, Volume and Issue: 16(5), P. 1442 - 1452

Published: Jan. 22, 2022

Abstract Species loss within a microbial community can increase resource availability and spur adaptive evolution. Environmental shifts that cause species or fluctuations in composition are expected to become more common, so it is important understand the evolutionary forces shape stability function of emergent community. Here we study experimental cultures simple, ecologically stable Saccharomyces cerevisiae Lactobacillus plantarum, order how presence absence impacts coexistence over timescales. We found evolution coculture led drastically altered outcomes for L. but not S. cerevisiae. Both monoculture- co-culture-evolved plantarum evolved dozens mutations 925 generations evolution, only had isolation from lost capacity coexist with find ecological corresponds fitness differences between monoculture-evolved genetic changes repeatedly evolve across replicate populations plantarum. This work shows coevolution prevent destabilising individual species, thereby preserving diversity stability, despite rapid adaptation.

Language: Английский

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Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions

Microbial Ecology, Journal Year: 2024, Volume and Issue: 87(1)

Published: April 8, 2024

Abstract Microbial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring these dynamic systems, one can begin to unravel role played by microbial species. Towards this, various methods have been developed decipher communities. The current review focuses on qualitative and quantitative that currently exist study interactions. Qualitative such co-culturing experiments are visualized using microscopy-based techniques combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics). Quantitative include construction networks network inference, computational models, development synthetic consortia. These provide valuable clue roles interacting partners, well possible solutions overcome pathogenic microbes cause life-threatening infections susceptible hosts. Studying will further our understanding less-studied ecosystems enable design effective frameworks for treatment infectious diseases.

Language: Английский

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Simulations reveal challenges to artificial community selection and possible strategies for success

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(6), P. e3000295 - e3000295

Published: June 25, 2019

Multispecies microbial communities often display "community functions" arising from interactions of member species. Interactions are difficult to decipher, making it challenging design with desired functions. Alternatively, similar artificial selection for individuals in agriculture and industry, one could repeatedly choose the highest community functions reproduce by randomly partitioning each into multiple "Newborn" next cycle. However, previous efforts selecting complex have generated mixed outcomes that interpret. To understand how effectively enact selection, we simulated improve a function requires 2 species imposes fitness cost on or both Our simulations predict improvement be easily stalled unless various aspects carefully considered. These include promoting coexistence, suppressing noncontributors, choosing additional besides functioning ones reproduce, reducing stochastic fluctuations biomass Newborn communities. considerations can addressed experimentally. When executed effectively, is predicted costly function, may even force evolve slow growth achieve coexistence. conclusions hold under alternative model assumptions therefore applicable variety

Language: Английский

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Community composition of microbial microcosms follows simple assembly rules at evolutionary timescales

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

Published: May 11, 2021

Managing and engineering microbial communities relies on the ability to predict their composition. While progress has been made predicting compositions short, ecological timescales, there is still little work aimed at evolutionary timescales. Therefore, it unknown for how long typically remain stable after reaching equilibrium, repeatable predictable are changes when they occur. Here, we address this knowledge gap by tracking composition of 87 two- three-species bacterial communities, with 3-18 replicates each, ~400 generations. We find that community changed during evolution, but replicate remained similar. Furthermore, these were in a bottom-up approach-changes trios consistent those occurred pairs coevolution. Our results demonstrate simple assembly rules can hold even suggesting may be possible forecast evolution communities.

Language: Английский

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Experimental Evolution in Plant-Microbe Systems: A Tool for Deciphering the Functioning and Evolution of Plant-Associated Microbial Communities

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 12

Published: May 7, 2021

In natural environments, microbial communities must constantly adapt to stressful environmental conditions. The genetic and phenotypic mechanisms underlying the adaptive response of new (and often complex) environments can be tackled with a combination experimental evolution next generation sequencing. This allows analyse real-time populations in imposed factors or during interaction host, by screening for genotypic changes over multitude identical cycles. Experimental (EE) coupled comparative genomics has indeed facilitated monitoring bacterial understanding processes. Basically, EE studies had long been done on single strains, allowing reveal dynamics targets selection uncover correlation between changes. However, species are always evolving relation other have not only environment itself but also biotic dynamically shaped species. Nowadays, there is growing interest apply under environments. this paper, we provide non-exhaustive review systems increasing complexity (from species, synthetic communities) particular focus plants plant-associated microorganisms. We highlight some controlling functioning their responses emphasize importance considering complex studies.

Language: Английский

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