The taxonomic and genomic attributes of oligotrophic soil bacteria

ISME Communications, Год журнала: 2024, Номер 4(1)

Опубликована: Янв. 1, 2024

Abstract Not all bacteria are fast growers. In soil as in other environments, exist along a continuum—from copiotrophs that can grow rapidly under resource-rich conditions to oligotrophs adapted life the “slow lane.” However, field of microbiology is built almost exclusively on study due, part, ease studying them vitro. To begin understanding attributes oligotrophs, we analyzed three independent datasets represent contrasts organic carbon availability. These included 185 samples collected from profiles across USA, 950 paired bulk and rhizosphere Europe, soils microcosm experiment where availability was manipulated directly. Using combination marker gene sequencing targeted genomic analyses, identified specific oligotrophic taxa were consistently more abundant carbon-limited environments (subsurface, bulk, unamended soils) compared corresponding carbon-rich environment (surface, rhizosphere, glucose-amended soils), including members Dormibacterota Chloroflexi phyla. general, putative had smaller genomes, slower maximum potential growth rates, under-represented culture collections. The genomes likely be enriched pathways allow metabolize range energy sources store carbon, while genes associated with energy-intensive functions like chemotaxis motility under-represented. few shared, highlighting use different metabolic strategies regulatory thrive resource-limited soils.

Язык: Английский

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Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation

mSystems, Год журнала: 2025, Номер unknown

Опубликована: Фев. 24, 2025

ABSTRACT Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, soil connectivity. However, accurately representing the environment establishing a tractable community that limits confounding variables is difficult. Here, we use reduced-complexity consortium grown in glass bead porous media amended with chitin to test effects of structural matrix on phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, metabolomes, saw our significantly altered phenotypes compared liquid incubations, denoting importance incorporating pores surfaces for understanding soils. These phenotypic shifts were mainly driven differences expression Streptomyces Ensifer , which included significant decrease overall degradation between liquid. Our findings suggest success likely related its ability repurpose carbon via glyoxylate shunt amidst lack byproducts while potentially using polyhydroxyalkanoate granules C source. We also identified traits expressed others, including motility, stress resistance, conservation, influence metabolic profiles observed across treatments. Together, these results demonstrate incubations promote structure-induced are better proxy conditions than culture systems. Furthermore, they emphasize encompass not only multi-enzyme pathways involved but include complex interactions other members. IMPORTANCE critical shaping metabolism. laboratory experiments remains challenging frontier. Through reduced complexity experiment media, reveal predicting from gene-based alone often falls short capturing intricate cellular interactions. highlight affect decomposition, environmental (i.e., beads) shifting towards tolerance, resource acquisition, increased ultimately invoking unique strategies evident cultures. Moreover, find evidence changes relate regarding transporters, biofilm formation, degradation. Ultimately, showcase how communities can be informative present useful alternative cultures studying

Язык: Английский

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Snow algae exhibit diverse motile behaviors and thermal responses

mBio, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

ABSTRACT Snow algal blooms influence snow and glacier melt dynamics, yet the mechanisms involved in community assemblage, development, dispersal are not well understood. While microbial swimming behavior contributes significantly to productivity organization of aquatic terrestrial microbiomes, potential impact cell motility melting on formation visible, large-scale surface bloom patterns is largely unknown. Here, using video tracking phototaxis experiments unique isolates, we evaluated diverse taxa from green, red, golden colored response light thermal gradients. We show that many species efficient cryophilic microswimmers with speed optima below 10°C although cryotolerant traits were also identified. The significant algae at low temperatures, a result specialized adaptations, supports importance active movement life histories inhabiting meltwater. However, diversity performance reveal range evolutionary outcomes sensitivity motile stages dynamic environments. IMPORTANCE Swimming fundamental mechanism controls assembly, structure, microbiomes across environments highly sensitive temperature. Especially, role activity very temperatures snowmelt has been hypothesized, but studied. By examining modeling curves speed, data key may have further important impacts ecology rates ice polar alpine regions.

Язык: Английский

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Linking microbial metabolism and ecological strategies to soil carbon cycle function in agroecosystems

Soil and Tillage Research, Год журнала: 2025, Номер 251, С. 106562 - 106562

Опубликована: Апрель 2, 2025

Язык: Английский

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Unveiling the multifaceted potential of Pseudomonas khavaziana strain SR9: a promising biocontrol agent for wheat crown rot

Microbiology Spectrum, Год журнала: 2024, Номер 12(10)

Опубликована: Авг. 20, 2024

ABSTRACT Fusarium pseudograminearum , a soil-borne fungus, is the cause of devastating wheat disease known as crown rot (WCR). The persistence this pathogen in soil and crop residues contributes to increased occurrence severity WCR. Therefore, developing effective strategies prevent manage WCR great importance. In study, we isolated bacterial strain, designated SR9, from stem wheat, that exhibited potent antagonistic effects against F. well biocontrol efficacy SR9 on was quantified at 83.99% ± 0.11%. We identified Pseudomonas khavaziana demonstrated its potential plant probiotic. displayed broad-spectrum antagonism other fungal pathogens, including Neurospora dictyophora Botrytis californica Botryosphaeria dothidea . Whole-genome sequencing analysis revealed harbored genes encoding various cell wall-degrading enzymes, cellulases, lipases, along with antifungal metabolites, which are responsible for activity. Gene knockout quantitative PCR analyses reveal phenazine essential factor antagonism. possessed related auxin synthesis, flagellar biosynthesis, biofilm adhesion, chemotaxis system, play pivotal roles colonization growth promotion; also evaluated Arabidopsis Our findings strongly suggest holds promise agent sustainable agriculture. IMPORTANCE escalating prevalence rot, primarily attributed necessitates development cost-effective eco-friendly strategies. While endophytes recognized their potential, reports strains targeting sparse. This study introduces strain an efficacious antagonist Demonstrating significant reduction incidence notable promotion, emerges key contributor health agricultural sustainability. outlines biological approach tackle establishing groundwork innovative practices.

Язык: Английский

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Cultivar-specific wheat-associated bacterial communities and metabolites in response to nitrogen deficiency

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Авг. 9, 2024

Background and Aims Nitrogen (N) deficiency in soil constrains plant growth, which may potentially be alleviated by beneficial bacterial communities. However, there is limited knowledge of the plant-bacteria interactions wheat cultivars with different N-use efficiency (NUE) under N deficiency. Methods We investigated responses root endosphere communities as well metabolites two (cv. Mace Gladius) reported high low NUE, respectively, using a glasshouse experiment hydroponic three levels. Results The rhizosphere community shifted deficiency, but not its endosphere. Conversely, Gladius remained unchanged metagenomic analysis illustrated increased detection genes related to growth motility Mace, Gladius, A 4-fold increase octadecanoic acid suggesting potential role shaping rhizobacterial higher NUE. Conclusion Our study highlights divergent wheat-associated microorganisms cultivars. found that NUE secretion, shaped communities, thereby enhancing their N-limited conditions.

Язык: Английский

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Active segregation in binary mixtures under flow

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 24, 2024

Abstract Many bacterial habitats, from the gut to soil, feature narrow channels where confined flow is a key constraint that might influence spatial organization, and thus functioning, of complex, phenotypically heterogeneous communities these microbes form. Here, we investigate how model community motile non-motile Escherichia coli organizes under Poiseuille flow. We discovered new mode active self-organization, bacteria induce rapid sideways segregation cells one side channel, eventually resulting in asymmetric biofilm formation. Our experiments modeling elucidated purely physical mechanism: rheotactic drift cells, which stems shear acting on their chiral flagella, induces conveyer-belt-like backflow advecting cells. The latter then accumulate thanks sedimentation countering incompressibility. This unexpected consequence motility can affect organization complex colonizing environments

Язык: Английский

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Emergence and disruption of cooperativity in a denitrifying microbial community

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 24, 2024

ABSTRACT Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in emission nitrous oxide (N 2 O), a potent greenhouse gas and ozone depleting substance, causing urgency identifying sources sinks N O. Microbial denitrification primary contributor biotic production O anoxic regions soil, marine systems, wastewater treatment facilities. Here, comprehensive genome analysis, we show that pathway partitioning ubiquitous mechanism complete within microbial communities. We have investigated mechanisms consequences process detailed physiological characterization kinetic modeling community Rhodanobacter R12 Acidovorax 3H11 . discovered these two bacterial isolates, from heavily nitrate (NO 3 − ) contaminated superfund site, exchange nitrite nitric (NO). The other processes, including amino acid metabolism, contribute increased cooperativity this denitrifying community. demonstrate certain contexts, such as high NO , cause unbalanced growth members, due differences their substrate utilization kinetics. altered characteristics members drives accumulation toxic which disrupts off gassing.

Язык: Английский

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Long-term warming inverts the relationship between ecosystem function and microbial resource acquisition

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 26, 2024

Abstract Soil microbial traits drive ecosystem functions, which can explain the positive correlation between functional diversity and function. However, adaptation to climate change related warming stress shift with direct implications for soil carbon cycling. Here, we investigated how long-term affects relationship trait Soils were sampled after 24 years of +5°C alongside unheated control soils from Harvard Forest Long-Term Ecological Research site. Ecosystem function was estimated six different enzyme activities biomass. Functional calculated metatranscriptomics sequencing, where reads assigned yield, acquisition, or categories. We found that in organic horizon soils, decreased richness acquisition-related traits. In mineral observed heated exhibited a negative These results suggest communities exposed are shifting away resource acquisition life history strategy.

Язык: Английский

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Cultivar-specific wheat-associated bacterial communities and metabolites in response to nitrogen deficiency

Plant and Soil, Год журнала: 2024, Номер unknown

Опубликована: Окт. 31, 2024

Язык: Английский

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