Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model

Nature Microbiology, Год журнала: 2024, Номер 9(2), С. 421 - 433

Опубликована: Фев. 5, 2024

Abstract Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual predicted. Here we combine theory-driven predictions substrate uptake kinetics with genome-informed trait-based dynamic energy budget model predict life-history trade-offs soil bacteria. When applied plant microbiome system, the accurately predicted distinct substrate-acquisition strategies that aligned observations, uncovering resource-dependent between growth rate efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later stages, exhibited enhanced carbon use efficiency (yield) without sacrificing (power). This insight has implications for retaining root-derived soils highlights power data-driven, approaches improving models.

Язык: Английский

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Emerging multiscale insights on microbial carbon use efficiency in the land carbon cycle

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Сен. 13, 2024

Microbial carbon use efficiency (CUE) affects the fate and storage of in terrestrial ecosystems, but its global importance remains uncertain. Accurately modeling predicting CUE on a scale is challenging due to inconsistencies measurement techniques complex interactions climatic, edaphic, biological factors across scales. The link between microbial soil organic relies stabilization necromass within aggregates or association with minerals, necessitating an integration processes approaches. In this perspective, we propose comprehensive framework that integrates diverse data sources, ranging from genomic information traditional assessments, refine cycle models by incorporating variations CUE, thereby enhancing our understanding contribution cycling.

Язык: Английский

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Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome

Nature Microbiology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 2, 2025

Язык: Английский

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Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits

Microbiome, Год журнала: 2025, Номер 13(1)

Опубликована: Янв. 13, 2025

The widespread selective pressure of antibiotics in the environment has led to propagation antibiotic resistance genes (ARGs). However, mechanisms by which microbes balance population growth with enrichment ARGs remain poorly understood. To address this, we employed microcosm cultivation at different (i.e., Oxytetracycline, OTC) stresses across concentrations from environmental clinical. Paired shot-gun metagenomics analysis and quantification bacterial growth, trait-based assessment soil microbiota was applied reveal association between key ARG subtypes, representative taxa, functional-gene features that drive ARGs. Our results illuminate resistome variation is closely associated growth. A non-monotonic change abundance richness observed over a concentration gradient none 10 mg/l. Soil exposed intermediate OTC 0.1 0.5 mg/l) showed greater increases total Community compositionally, i.e., Pseudomonadaceae considered boost increase It chromosomally carried kinds multidrug such as mexAB-oprM mexCD-oprJ could mediate intrinsic OTC. Streptomycetaceae shown better adaptive ability than other clinical concentrations. it contributed less represents stress-tolerant lifestyle grows slowly carries fewer In terms community genetic features, aggregated traits further indicates enhancement resource acquisition yield driving abundance. Moreover, optimizations energy production conversion, alongside streamlining bypass metabolic pathways, sub-inhibitory conditions. this study suggest competitive lifestyles are selected under stress nutrient scarcity. They possess substrate utilization capacity carry more ARGs, due they were faster growing leading This expanded application assessments understanding ecology propagation. And finding illustrated changes accompanied switching microbiome, theoretically supports control approach based on principle species exclusion.

Язык: Английский

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Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Nature Protocols, Год журнала: 2022, Номер 18(1), С. 208 - 238

Опубликована: Ноя. 14, 2022

Язык: Английский

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Implications of Soil Microbial Community Assembly for Ecosystem Restoration: Patterns, Process, and Potential

Microbial Ecology, Год журнала: 2023, Номер 85(3), С. 809 - 819

Опубликована: Фев. 3, 2023

Язык: Английский

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Microbial evolution—An under‐appreciated driver of soil carbon cycling

Global Change Biology, Год журнала: 2024, Номер 30(4)

Опубликована: Апрель 1, 2024

Abstract Although substantial advances in predicting the ecological impacts of global change have been made, predictions evolutionary lagged behind. In soil ecosystems, microbes act as primary energetic drivers carbon cycling; however, are also capable evolving on timescales comparable to rates change. Given importance ecosystems cycling, we assess potential impact microbial evolution carbon‐climate feedbacks this system. We begin by reviewing current state knowledge concerning response and its specific effect dynamics. Through integration, synthesize a roadmap detailing how integrate into ecosystem biogeochemical models. Specifically, highlight microscale mechanistic models, including choosing an appropriate model (e.g., adaptive dynamics, quantitative genetics), validating with ‘omics’ experimental data, scaling adaptations level processes, ecosystem‐scale measurements. The proposed steps will require significant investment scientific resources might 10–20 years be fully implemented. However, through application multi‐scale integrated approaches, advance integration predictive understanding providing clarity role within broader context environmental

Язык: Английский

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Ecological strategies of microbes: Thinking outside the triangle

Journal of Ecology, Год журнала: 2023, Номер 111(9), С. 1832 - 1843

Опубликована: Май 17, 2023

Abstract I asked whether Grime's triangle of competitive, stress tolerance and ruderal ecological strategies—which was originally developed for plants—applies to microbes. conducted a synthesis empirical studies that tested relationships among microbial traits presumed define the ruderal, other strategies. There broad support triangle. However, strategies were inconsistently linked shifts in communities under environmental changes like nitrogen phosphorus addition, warming, drought, etc. We may be missing important more closely influence community composition shifting conditions. need start by documenting response conditions at fine spatiotemporal scales relevant can then develop empirically based strategies, rather than modifying those on plant ecology. Synthesis . Microbes appear sort into similar as plants. these do not consistently predict how will shift change. By starting ‘from ground up’, we able delineate

Язык: Английский

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Groundwater flow regime shapes nitrogen functional traits by affecting microbial community assembly processes in the subsurface

The Science of The Total Environment, Год журнала: 2024, Номер 949, С. 175083 - 175083

Опубликована: Июль 26, 2024

Язык: Английский

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Genomic insights of Fictibacillus terranigra sp. nov., a versatile metabolic bacterium from Amazonian Dark Earths

Brazilian Journal of Microbiology, Год журнала: 2024, Номер 55(2), С. 1817 - 1828

Опубликована: Фев. 15, 2024

Язык: Английский

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