Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient

Nature Microbiology, Journal Year: 2018, Volume and Issue: 4(1), P. 55 - 61

Published: Oct. 25, 2018

Language: Английский

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Impacts of wildfire on soil microbiome in Boreal environments

Current Opinion in Environmental Science & Health, Journal Year: 2021, Volume and Issue: 22, P. 100258 - 100258

Published: April 21, 2021

The temperature changes for the future climate are predicted to be most pronounced in boreal and arctic regions, affecting stability of permafrost fire dynamics these areas. Fires can affect soil microbiome (archaea, bacteria, fungi, protists) directly via generated heat, whereas fire-altered properties have an indirect effect on microbiome. usually decrease microbial biomass alter community composition. These take decades recover prefire states. As occurrence times expected change future, return intervals, intensity, severity increase environments, fire-related microbiome, including its recovery resilience, inevitable.

Language: Английский

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Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance

Ecology Letters, Journal Year: 2024, Volume and Issue: 27(3)

Published: March 1, 2024

Long-term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems their functions. Many critical ecosystem functions, such as biogeochemical cycling, facilitated by microbial communities. Understanding functional consequences of microbiome responses to press requires ongoing observations active populations that contribute This study leverages a 7-year time series 60-year-old coal seam fire (Centralia, Pennsylvania, USA) examine resilience soil bacterial microbiomes disturbance. Using 16S rRNA gene amplicon sequencing, we assessed interannual dynamics subset 'whole' community. Contrary our hypothesis, whole communities demonstrated greater than subsets, suggesting inactive members contributed overall structural resilience. Thus, in addition selection mechanisms populations, perceived is also supported dispersal, persistence, revival from local dormant pool.

Language: Английский

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Host Immunity Alters Community Ecology and Stability of the Microbiome in a Caenorhabditis elegans Model

mSystems, Journal Year: 2021, Volume and Issue: 6(2)

Published: April 24, 2021

Here, we used a Caenorhabditis elegans microbiome model to demonstrate how genetic differences in innate immunity alter composition, diversity, and stability by changing the ecological processes that shape these communities. These results provide insight into role of host genetics controlling ecology host-associated microbiota, resulting community successional trajectories, response perturbation.

Language: Английский

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Spatial distribution characteristics of bacterial community structure and gene abundance in sediments of the Bohai Sea

Acta Oceanologica Sinica, Journal Year: 2020, Volume and Issue: 39(2), P. 69 - 78

Published: Feb. 1, 2020

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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Learning from the unknown: exploring the range of bacterial functionality

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(19), P. 10162 - 10175

Published: Sept. 22, 2023

Determining the repertoire of a microbe's molecular functions is central question in microbial biology. Modern techniques achieve this goal by comparing genetic material against reference databases functionally annotated genes/proteins or known taxonomic markers such as 16S rRNA. Here, we describe novel approach to exploring bacterial functional repertoires without databases. Our Fusion scheme establishes relationships between bacteria and assigns organisms Fusion-taxa that differ from otherwise defined clades. Three key findings our work stand out. First, comparisons outperform marker genes assigning profiles are also better for task than other annotation schemes. Second, robust addition are, arguably, able capture environment-driven diversity. Finally, alignment-free nucleic acid-based Siamese Neural Network model, created using functions, enables finding shared functionality very distant, possibly structurally different, homologs. can thus help annotate further guide understanding communities.

Language: Английский

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Unraveling the bacterial community composition across aquatic sediments in the Southwestern coast of India by employing high-throughput 16S rRNA gene sequencing

Regional Studies in Marine Science, Journal Year: 2021, Volume and Issue: 46, P. 101890 - 101890

Published: June 12, 2021

Language: Английский

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Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2018, Volume and Issue: unknown

Published: March 5, 2018

Summary Small bacterial and archaeal genomes provide insights into the minimal requirements for life 1 seem to be widespread on microbial phylogenetic tree 2 . We know that evolutionary processes, mainly selection drift, can result in genome reduction 3,4 However, we do not precise environmental pressures constrain size free-living microorganisms. A study including isolates 5 has shown bacteria with high optimum growth temperatures, thermophiles, often have small 6 It is unclear how well this relationship may extend generally microorganisms nature 7,8 , particular those microbes inhabiting complex highly variable environments like soil 3,6,9 To understand genomic traits of thermally-adapted microorganisms, here investigated metagenomes from a 45°C gradient temperate-to-thermal soils overlying ongoing Centralia, Pennsylvania (USA) coal seam fire. There was strong between average temperature: hot had relative ambient (Pearson’s r = −0.910, p < 0.001). also an inverse temperature cell −0.65, 0.021), providing evidence wild are together constrained by temperature. Notably, different community structures than soils, implicating ecological thermo-tolerant cells genomes, rather contemporary streamlining within local populations. Hot notably lacked genes described two-component regulatory systems antimicrobial production resistance. Our work provides field diverse, over wide range temperatures support life. findings demonstrate thermophiles smaller sizes situ possibly because they reminiscent more ancestral state.

Language: Английский

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Microbiota recovery in a chronosquences of impoverished Cerrado soils with biosolids applications

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 931, P. 172958 - 172958

Published: May 5, 2024

Language: Английский

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