Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils

Soil Biology and Biochemistry, Journal Year: 2025, Volume and Issue: unknown, P. 109741 - 109741

Published: Feb. 1, 2025

Language: Английский

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The performance of different methods in characterizing soil live prokaryotic diversity and abundance is highly variable

iMetaOmics., Journal Year: 2025, Volume and Issue: unknown

Published: March 28, 2025

Abstract The long‐term persistence of extracellular DNA in soils is well‐documented, yet its impacts on analyzing soil microbial abundance and diversity remain controversial. This primarily arises from our limited comprehension regarding the reliability various methods for studying live microbiotas. In this study, we systematically compared assessed commonly used diversity, including alkaline buffer washing, propidium monoazide (PMA) treatment, DNase pre‐digestion, rRNA‐based analysis, using collected a wide range locations across China. We found that elimination substantially influenced analysis prokaryotic abundance, community profiles, co‐occurrence patterns, but not assembly mechanisms. However, effects varied considerably different methods. pre‐digestion PMA treatment led to significant decreases while washing had negligible effects. As richness, significantly decreased increased it, respectively. Although 67.8% amplicon sequence variants were shared, differences their relative observed While removal simplified network, it also enhanced robustness. According assessment experiments, showed highest efficiency characterizing accuracy. Concerns other include low efficiency, instability, uncertainties result explanation. study suggests characterized by exhibit high variability, recommended communities. These findings provide crucial information optimizing microbiome research methodologies.

Language: Английский

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Seven years of microbial community metagenomes from temperate soils affected by an ongoing coal seam fire

Microbiology Resource Announcements, Journal Year: 2024, Volume and Issue: 13(6)

Published: May 16, 2024

We examined the dynamics of soil microbiomes under heat press disturbance from an underground coal mine fire in Centralia, PA. Here, we present metagenomic sequencing and assembly data across seven consecutive years at repeatedly sampled fire-affected sites along with unaffected reference sites.

Language: Английский

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Bacterial community response to novel and repeated disturbances

Environmental Microbiology Reports, Journal Year: 2024, Volume and Issue: 16(5)

Published: Oct. 1, 2024

Disturbance response and recovery are increasingly important in microbial ecology, as microbes may recover from disturbances differently than macro communities. Past can alter community structure their to subsequent disturbance events, but it remains unclear if the same patterns persist after long-term exposure stress. Here, we compare bacterial composition a that experienced 2 years of monthly salinity addition with has not additions. We then track an additional based on past exposure. tested following hypotheses: first, communities repeated history will have different without history; second, exposed undergo trajectory experiencing novel disturbance. find affect years, primarily through increased resistance. This work enhances our understanding temporal dynamics suggests pose threat function.

Language: Английский

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Resting for Viability: Gordonia Polyisoprenivorans Zm27, a Robust Generalist for Petroleum Bioremediation Under Hypersaline Stress

Published: Jan. 1, 2024

The intrinsic issue associated with applying microbes for practical pollution remediation is maintaining the expected activity of engaged strains or consortiums as effectively under laboratory conditions. Faced various stress factors, degraders dormancy ability are more likely to survive and exhibit degradation activity. In this study, a hydrocarbonoclastic halotolerant strain, Gordoniapolyisoprenivorans ZM27, was isolated via stimulation resuscitation-promoting factor (Rpf). Long-term dual 10% NaCl incubation starvation could induce ZM27 into viable but nonculturable (VBNC)-like state, cells be resuscitated by Rpf stimulation. Notable changes in both morphological physiological characteristics between VBNC-like confirmed response its robust resistance against harsh environments. Whole-genome sequencing analysis indicated generalist degrader ability. Subsequently, applied soil microcosm experiment investigate application potential combined exhibited most effective biodegradation performance, initial n-hexadecane content (1,000 mg kg-1) decreased 63.29% after 14-day incubation. Based on 16S rRNA analysis, Gordonia positive stimulation, significant competitiveness niches. absolute abundance genus negatively correlated that Alcanivorax, obligate hydrocarbon top during profile community may efficient than specialist Alcanivorax including sustainable culturability long-term stress, performance microcosm, valuable remediating petroleum stressful Our work validated importance remediation.

Language: Английский

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Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 27, 2024

Abstract Viruses are important components of the soil microbiome, influencing microbial population dynamics and functions their hosts. However, relationships feedbacks between virus dynamics, host environmental disturbance is not understood. Centralia, PA, USA, site an underground coal seam fire that has been burning for over 60 years. As moves along seam, previously heated soils cool to ambient temperature, creating a gradient heat intensity recovery. We examined annual viral seven consecutive years in Centralia using untargeted metagenome sequencing. Viral communities changed time were distinct fire-affected reference sites. Dissimilarity was greater across sites (space) than within (time), cumulative diversity more rapidly stabilized year There also changes CRISPR investment as cooled, corresponding shifts diversity. Finally, there differences viral-encoded auxiliary metabolic genes These results indicate despite high site-to-site diversity, surprising community consistency shifting host-viral interactions recovering from disturbance. Together, these provide insights into how collectively respond unpredicted Highlights In seven-year study temperate affected by fire, displayed variability (spatial) (temporal). unheated throughout sampling. Soil bacterial composition correlated composition, though this relationship weakened when accounting edaphic properties temperature pH. may be less resilient press communities. Viral-host shift during recovery long-term heating.

Language: Английский

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Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment

Trends in Microbiology, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 1, 2024

Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse abundant array of microbes present in samples. These eNA signals, largely representing whole organisms, serve as powerful complement to signals derived fragments or remnants larger organisms. Integrating microbial data into the toolbox ecosystem assessments biotic indices therefore has potential transform how we use understand biodiversity dynamics functions, inform next generation monitoring. Incorporating holobiont Tree Life approaches analyses offers further holistic insight range ecological interactions between other paving way for advancing our understanding of, ultimately manipulating properties pertinent management, conservation, wildlife health, food production.

Language: Английский

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