Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 17, 2023

Abstract Bacterial gene repertoires reflect adaptive strategies, contribute to ecosystem functioning and are limited by genome size. However, functional diversity does not necessarily correlate with taxonomic because average size may vary community. Here, we analyse (by shotgun metagenomics) 16S rRNA amplicon sequencing) investigate soil bacterial communities along a natural pH gradient in 12 tropical, subtropical, temperate forests. We find that decrease, whereas increases, as rises from acid neutral; result, negatively correlated. The repertoire of acid-adapted oligotrophs is enriched functions signal transduction, cell motility, secretion system, degradation complex compounds, while neutral pH-adapted copiotrophs energy metabolism membrane transport. Our results indicate mismatch between can arise when environmental factors (such pH) select for strategies affect distributions.

Language: Английский

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

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(2), P. 421 - 433

Published: Feb. 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.

Language: Английский

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

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Sept. 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.

Language: Английский

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Increasing pesticide diversity impairs soil microbial functions

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(2)

Published: Jan. 9, 2025

Pesticide application is essential for stabilizing agricultural production. However, the effects of increasing pesticide diversity on soil microbial functions remain unclear, particularly under varying nitrogen (N) fertilizer management practices. In this study, we investigated stochasticity microbes and multitrophic networks through amplicon sequencing, assessed community related to carbon (C), N, phosphorus (P), sulfur (S) cycling, characterized dominant bacterial life history strategies via metagenomics along a gradient two N addition levels. Our findings show that higher enriches abundance specialists opportunists capable degrading or resisting pesticides, reducing proportion generalists in absence addition. These shifts can complicate networks. Under increased diversity, selective pressure may drive bacteria streamline their average genome size conserve energy while enhancing C, P, S metabolic capacities, thus accelerating nutrient loss. comparison, was found reduce niche differentiation at mitigating impacts network complexity functional traits associated with ultimately alleviating results reveal contrasting different input scenarios emphasize strategic mitigate ecological use systems.

Language: Английский

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

Microbiome, Journal Year: 2025, Volume and Issue: 13(1)

Published: Jan. 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.

Language: Английский

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A Global Relationship Between Genome Size and Encoded Carbon Metabolic Strategies of Soil Bacteria

Ecology Letters, Journal Year: 2025, Volume and Issue: 28(1)

Published: Jan. 1, 2025

Microbial traits are critical for carbon sequestration and degradation in terrestrial ecosystems. Yet, our understanding of the relationship between metabolic strategies genomic like genome size remains limited. To address this knowledge gap, we conducted a global-scale meta-analysis 2650 genomes, integrated whole-genome sequencing data, performed continental-scale metagenomic field study. We found that was tightly associated with an increase ratio genes encoding polysaccharide decomposition biomass synthesis defined as acquisition-to-biomass yield (A/Y). also show horizontal gene transfer played major evolutionary role expanded bacterial capacities acquisition. Our study further revealed significantly negative A/Y soil organic stocks. work demonstrates global encoded bacteria across microbiomes.

Language: Английский

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Ecological relevance of flagellar motility in soil bacterial communities

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Abstract Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all are capable of flagellar motility, and the distribution this trait, its ecological associations, life history strategies flagellated taxa remain poorly characterized. We developed validated genome-based approach infer potential for across 12 phyla (26 192 unique genomes). The capacity was associated with higher prevalence genes carbohydrate metabolism maximum growth rates, suggesting that more prevalent in environments carbon availability. To test hypothesis, we applied method whole communities from metagenomic data quantified four independent field studies each captured putative gradients soil availability (148 metagenomes). observed positive relationship between datasets. Since often correlated other factors could influence these observations using incubation experiment where directly manipulated glucose amendments. This confirmed consistently over confounding factors. work highlights value combining predictive genomic approaches expand our understanding microbial phenotypic traits reveal general environmental associations.

Language: Английский

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Soil viral–host interactions regulate microplastic-dependent carbon storage

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(45)

Published: Oct. 28, 2024

Microplastic is globally regarded as an important factor impacting biogeochemical cycles, yet our understanding of such influences limited by the uncertainties intricate microbial processes. By multiomics analysis, coupled with soil chemodiversity characterization and carbon use efficiency (CUE), we investigated how responses to microplastics impacted cycling in a long-term field experiment. We showed that biodegradable promoted organic accrual average 2.47%, while nondegradable inhibited it 17.4%, consequence virus–bacteria coadaptations disturbance. In relevant functional pathways, significantly ( P < 0.05) enhanced abundance transcriptional activity related complex carbohydrate metabolism, whereas functions involved amino acid metabolism glycolysis. Accordingly, viral lysis treatments introduce more compounds dissolved matters, thus benefiting oligotrophs high metabolic capabilities exploitation competition. contrast, enriched auxiliary genes through “piggyback-the-winner” strategy, conferring dominant copiotrophs, substrate utilization capabilities. These virus–host interactions were also demonstrated corresponding plastisphere, which would alter resource allocation via CUE, affecting storage consequently. Overall, results underscore importance viral–host microplastics-dependent ecosystem.

Language: Английский

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The size and diversity of microbes determine carbon use efficiency in soil

Environmental Microbiology, Journal Year: 2024, Volume and Issue: 26(5)

Published: May 1, 2024

Abstract Soil is home to a multitude of microorganisms from all three domains life. These organisms and their interactions are crucial in driving the cycling soil carbon. One key indicator this process Microbial Carbon Use Efficiency (CUE), which shows how microbes influence carbon storage through biomass production. Although CUE varies among different microorganisms, there have been few studies that directly examine biotic factors CUE. such factor could be body size, can impact microbial growth rates soil, thereby influencing Despite this, evidence demonstrating direct causal connection between biodiversity still scarce. To address these knowledge gaps, we conducted an experiment where manipulated size size‐selective filtering. Our findings show manipulating structure community reduce by approximately 65%. When restricted maximum community, observed reduction bacterial diversity functional potential, turn lowered community's Interestingly, when included large micro‐eukarya it shifted cycling, increasing 50% nitrogen ratio about 25%. metrics were able explain 36%–50% variation This highlights importance traits, trophic mediating cycling.

Language: Английский

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Distinct patterns of soil bacterial and fungal communities in the treeline ecotone

Soil Ecology Letters, Journal Year: 2025, Volume and Issue: 7(2)

Published: Jan. 25, 2025

Language: Английский

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