Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Oct. 24, 2019

Abstract The soil microbiome is highly diverse and comprises up to one quarter of Earth’s diversity. Yet, how such a functionally complex influences ecosystem functioning remains unclear. Here we manipulated the in experimental grassland ecosystems observed that diversity microbial network complexity positively influenced multiple functions related nutrient cycling (e.g. multifunctionality). Grassland microcosms with poorly developed networks reduced richness had lowest multifunctionality due fewer taxa present support same function (redundancy) lower different (reduced functional uniqueness). Moreover, explained pointing significance communities. These findings indicate importance interactions within among fungal bacterial communities for enhancing performance demonstrate extinction ecological associations belowground can impair functioning.

Language: Английский

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Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2019, Volume and Issue: 286(1895), P. 20182448 - 20182448

Published: Jan. 23, 2019

The central aim of conservation biology is to understand and mitigate the effects human activities on biodiversity. To successfully achieve this objective, researchers must take an interdisciplinary approach that fully considers effects, both direct indirect, anthropogenic disturbances wildlife physiology health. A recent surge in research has revealed host-associated microbiota—the archaeal, bacterial, fungal viral communities residing inside organisms—profoundly influence animal health, these microbial can be drastically altered by activities. Therefore, practitioners should consider disruption diversity as a serious threat populations. Despite tremendous potential for microbiome improve outcomes, few efforts have been made truly integrate fields. In review, we call renaissance biology, where biodiversity microbiota recognized essential component management practices. Using evidence from existing literature, will examine known approaches maintaining objectives.

Language: Английский

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Linking bacterial community composition to soil salinity along environmental gradients

The ISME Journal, Journal Year: 2018, Volume and Issue: 13(3), P. 836 - 846

Published: Nov. 16, 2018

Abstract Salinization is recognized as a threat to soil fertility worldwide. A challenge in understanding the effects of salinity on microbial communities fact that it can be difficult disentangle from those other variables may co-vary with salinity. Here we use trait-based approach identify direct bacterial across two gradients. Through dose–response relationships between and growth, quantified distributions trait salt tolerance within communities. Community was closely correlated salinity, indicating strong filtering effect Accompanying increases were consistent shifts community composition. We identified specific taxa increased relative abundances tolerance, which could used bioindicators for high tolerance. also observed pH gradients, pH. propose phenotypic aggregated at level useful study role environmental factors filters

Language: Английский

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Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(12), P. 2128 - 2150

Published: Nov. 28, 2022

Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure function microbial communities multiple habitats on a planetary scale. Here we present multi-omics analysis diverse set 880 community samples collected for Earth Microbiome Project. We include amplicon (16S, 18S, ITS) shotgun metagenomic sequence data, untargeted metabolomics data (liquid chromatography-tandem mass spectrometry gas chromatography spectrometry). used standardized protocols analytical methods to characterize communities, focusing relationships co-occurrences microbially related metabolites taxa environments, thus allowing us explore diversity at extraordinary In addition reference database metabolomic provide framework incorporating additional studies, enabling expansion existing knowledge form an evolving resource. demonstrate utility this by testing hypothesis that every microbe metabolite is everywhere but environment selects. Our results show exhibits turnover nestedness both environment, whereas relative abundances vary co-occur with specific consortia habitat-specific manner. additionally power certain chemistry, particular terpenoids, distinguishing Earth's environments (for example, terrestrial plant surfaces soils, freshwater marine animal stool), as well microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) Pantoea dispersa detritus). This Resource provides insight within from Earth, informing chemical ecology, foundation microbiome hosts environment.

Language: Английский

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Inferring microbiota functions from taxonomic genes: a review

GigaScience, Journal Year: 2022, Volume and Issue: 11

Published: Jan. 1, 2022

Deciphering microbiota functions is crucial to predict ecosystem sustainability in response global change. High-throughput sequencing at the individual or community level has revolutionized our understanding of microbial ecology, leading big data era and improving ability link diversity with functions. Recent advances bioinformatics have been key for developing functional prediction tools based on DNA metabarcoding using taxonomic gene information. This cheaper approach every aspect serves as an alternative shotgun sequencing. Although these are increasingly used by ecologists, objective evaluation their modularity, portability, robustness lacking. Here, we reviewed 100 scientific papers inference ecological trait assignment rank advantages, specificities, drawbacks tools, a benchmarking. To date, mainly devoted bacterial functions, fungal A major limitation lack reference genomes-compared human microbiota-especially complex ecosystems such soils. Finally, explore applied research prospects. These promising already provide relevant information functioning, but standardized indicators corresponding repositories still lacking that would enable them be operational diagnosis.

Language: Английский

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Microbial Growth under Limiting Conditions-Future Perspectives

Microorganisms, Journal Year: 2023, Volume and Issue: 11(7), P. 1641 - 1641

Published: June 23, 2023

Microorganisms rule the functioning of our planet and each one individual macroscopic living creature. Nevertheless, microbial activity growth status have always been challenging tasks to determine both in situ vivo. Microbial is generally related growth, rate a result availability nutrients under adequate or adverse conditions faced by cells changing environment. Most studies on microorganisms carried out optimum near-optimum conditions, but scarce information available about at slow-growing states (i.e., near-zero maintenance metabolism). This study aims better understand growth-limiting conditions. expected provide new perspectives functions relevance world. because (i) nature frequently face severe limitation, (ii) activate singular pathways (mostly genes remaining be functionally annotated), resulting broad range secondary metabolites, (iii) response slow-growth remains understood, including persistence strategies, gene expression, cell differentiation within clonal populations due complexity

Language: Английский

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Unraveling resistance mechanisms in combination therapy: A comprehensive review of recent advances and future directions

Heliyon, Journal Year: 2024, Volume and Issue: 10(6), P. e27984 - e27984

Published: March 1, 2024

Antimicrobial resistance is a global health threat. Misuse and overuse of antimicrobials are the main drivers in developing drug-resistant bacteria. The emergence rapid spread multi-resistant bacteria requires urgent multisectoral action to generate novel treatment alternatives. Combination therapy offers potential exploit synergistic effects for enhanced antibacterial efficacy drugs. Understanding complex dynamics kinetics drug interactions combination crucial. Therefore, this review outlines current advances antibiotic resistance's evolutionary genetic therapies-exposed Moreover, we also discussed four pivotal future research areas comprehend better development treated with strategies.

Language: Английский

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Build your own soil: exploring microfluidics to create microbial habitat structures

The ISME Journal, Journal Year: 2017, Volume and Issue: 12(2), P. 312 - 319

Published: Nov. 14, 2017

Abstract Soil is likely the most complex ecosystem on earth. Despite global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways studying soil microbial ecology by allowing simulation manipulation chemical conditions physical structures at microscale in model habitats.

Language: Английский

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Fundamental research questions in subterranean biology

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2020, Volume and Issue: 95(6), P. 1855 - 1872

Published: Aug. 25, 2020

ABSTRACT Five decades ago, a landmark paper in Science titled The Cave Environment heralded caves as ideal natural experimental laboratories which to develop and address general questions geology, ecology, biogeography, evolutionary biology. Although the ‘caves laboratory’ paradigm has since been advocated by subterranean biologists, there are few examples of studies that successfully translated their results into principles. contemporary era big data, modelling tools, revolutionary advances genetics (meta)genomics provides an opportunity revisit unresolved challenges, well examine promising new avenues research Accordingly, we have developed roadmap guide future endeavours biology adapting well‐established methodology ‘horizon scanning’ identify highest priority across six subject areas. Based on expert opinion 30 scientists from around globe with complementary expertise different academic ages, assembled initial list 258 fundamental concentrating macroecology microbial adaptation, evolution, conservation. Subsequently, through online surveys, 130 biologists various backgrounds assisted us reducing our 50 top‐priority questions. These broad scope ready be addressed next decade. We believe this exercise will stimulate towards deeper understanding foster hypothesis‐driven likely resonate broadly traditional boundaries field.

Language: Английский

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Rare gut microbiota associated with breeding success, hormone metabolites and ovarian cycle phase in the critically endangered eastern black rhino

Microbiome, Journal Year: 2019, Volume and Issue: 7(1)

Published: Feb. 15, 2019

Host microbiomes play a role in hormone production and subsequent fertility humans, but this is less well understood non-model organisms. This of particular relevance to species zoo-based conservation breeding programmes, as relationships between host microbiome composition reproductive output may allow for the development microbial augmentation strategies improve success. Here, we characterise faecal bacterial communities non-breeding eastern black rhino (Diceros bicornis michaeli) using 16S rRNA gene amplicon sequencing quantify progestagen glucocorticoid metabolite concentrations through enzyme immunoassays identify such relationships. We identified significant differences gut according ID, institution, success ovarian cycle phase. In particular, during pregnancy post-parturition was significantly altered. Around third genera showed more than ± 10% correlation with either and/or concentration, general, correlated both hormones same direction. Through combination analyses, four (Aerococcaceae, Atopostipes, Carnobacteriaceae Solobacterium) that were associated success, post-parturition, higher concentrations. These had lower-than-average relative abundance microbiome. Our results indicate many members are some rare microbiota appear be particularly important. Although directionality relationship unclear, variation represents potential biomarker health. multiple indicators output; these could candidate probiotics programmes. Further work required understand efficacy feasibility this, directly (e.g. probiotics) or indirectly via dietary manipulation prebiotics.

Language: Английский

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