Temperature‐mediated microbial carbon utilization in China's lakes

Global Change Biology, Journal Year: 2023, Volume and Issue: 29(17), P. 5044 - 5061

Published: July 10, 2023

Microbes play an important role in aquatic carbon cycling but we have a limited understanding of their functional responses to changes temperature across large geographic areas. Here, explored how microbial communities utilized different substrates and the underlying ecological mechanisms along space-for-time substitution gradient future climate change. The included 47 lakes from five major lake regions China spanning difference nearly 15°C mean annual temperatures (MAT). Our results indicated that warmer generally had lower values variables related concentrations greater utilization than those colder regions. under higher could be attributed bacterial community composition, with abundance Cyanobacteria Actinobacteriota less Proteobacteria We also found core species networks changed increasing temperature, Hydrogenophaga Rhodobacteraceae, which inhibited amino acids carbohydrates, CL500-29-marine-group, promoted all almost substrates. Overall, our findings suggest can mediate by changing interactions between bacteria individual substrates, discovery affect provides insight into potential sequestration within inland water bodies warming.

Language: Английский

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Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps

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

Published: Feb. 28, 2023

Deep sea cold seep sediments host abundant and diverse microbial populations that significantly influence biogeochemical cycles. While numerous studies have revealed their community structure functional capabilities, little is known about genetic heterogeneity within species. Here, we examine intraspecies diversity patterns of 39 species identified in sediment layers down to 430 cm below the floor across six sites. These are grouped as aerobic methane-oxidizing bacteria, anaerobic methanotrophic archaea sulfate-reducing bacteria. Different evolutionary trajectories observed at genomic level among these physiologically phylogenetically populations, with generally low rates homologous recombination strong purifying selection. Functional genes related methane (pmoA mcrA) sulfate (dsrA) metabolisms under selection most investigated. differ phylogenetic clades but functionally conserved Intrapopulation diversification genomes mcrA dsrA depth-dependent subject different pressure throughout column redox zones results highlight interplay between ecological processes evolution key bacteria deep extreme environments, shedding light on adaptation subseafloor biosphere.

Language: Английский

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The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: March 2, 2023

Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon energy sources fueling light-independent biosphere. However, the type metabolism that dominates deep gas hydrate zone is poorly constrained. Here we studied microbial communities in hydrate-rich up to 49 m below seafloor recovered by drilling South China Sea. We focused on distinct geochemical conditions performed metagenomic metatranscriptomic analyses characterize their role mineralization.

Language: Английский

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A systematic analysis of marine lysogens and proviruses

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

Published: Sept. 27, 2023

Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting over 12,000 bacterial archaeal genomes) Temperate Viral (MTVGD). At least 40% MPGD genomes contain one or more proviral sequences, indicating that they lysogens. The MTVGD includes 12,900 viral contigs putative proviruses, clustered into 10,897 genera. We show lysogens proviruses abundant ecosystems, particularly deep sea, differ from non-lysogens multiple features growth properties. reveal several virus-host interaction networks potential ecological relevance, identify appear be able infect (or transferred between) different classes phyla. Auxiliary metabolic genes enriched functions related carbohydrate metabolism. Finally, experimentally demonstrate impact prophage on transcriptome representative Shewanella bacterium. Our work contributes better understanding ecology their viruses.

Language: Английский

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BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis

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

Published: March 11, 2024

Abstract Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency tools adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT ( B inning A cross a S eries ssemb l ies T oolkit) and refinement short- long-read sequencing data. employs multiple binners with thresholds to produce initial bins, then utilizes neural networks identify core sequences remove redundant bins refine non-redundant bins. Using same assemblies generated from Critical Assessment Metagenome Interpretation (CAMI) datasets, produces up twice as many MAGs VAMB, DASTool, or metaWRAP. Processing lake sediment dataset, ~30% more than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that can retrieve 47.6% opening-reading frames These results highlight robust handling metagenomic data BASALT.

Language: Английский

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Dynamics of carbon substrate competition among heterotrophic microorganisms

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

Published: Jan. 1, 2024

Abstract Growing evidence suggests that interactions among heterotrophic microorganisms influence the efficiency and rate of organic matter turnover. These are dynamic shaped by composition availability resources in their surrounding environment. Heterotrophic inhabiting marine environments often encounter fluctuations quality quantity carbon inputs, ranging from simple sugars to large, complex compounds. Here, we experimentally tested how chemical complexity substrates affects competition growth dynamics between two isolates. We tracked cell density using species-specific polymerase chain reaction (PCR) assays measured rates microbial CO2 production along with associated isotopic signatures (13C 14C) quantify impact these on remineralization. The observed densities revealed substrate-driven interactions: one species exhibited a competitive advantage quickly outgrew other when incubated labile compound whereas both seemed coexist harmoniously presence more matter. Rates respiration coincubation isolates enhanced turnover, sometimes nearly 2-fold, compared incubation as mono-cultures. Isotopic respired indicated resulted greater remineralization macromolecular results demonstrate promote high substrate reduces competitiveness promotes partitioning degradative activities into distinct niches, facilitating coordinated utilization pool. Taken together, this study yields new insight plays pivotal role determining within environments.

Language: Английский

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Global biogeography of microbes driving ocean ecological status under climate change

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

Published: May 31, 2024

Abstract Microbial communities play a crucial role in ocean ecology and global biogeochemical processes. However, understanding the intricate interactions among diversity, taxonomical composition, functional traits, how these factors respond to climate change remains significant challenge. Here, we propose seven distinct ecological statuses by systematically considering structure, potential of microbiome delineate their biogeography. Anthropogenic is expected alter status surface influencing environmental conditions, particularly nutrient oxygen contents. Our predictive model, which utilizes machine learning, indicates that approximately 32.44% may undergo changes from present end this century, assuming no policy interventions. These mainly include poleward shifts main taxa, increases photosynthetic carbon fixation decreases metabolism. proportion can decrease significantly with effective control greenhouse gas emissions. study underscores urgent necessity for implementing policies mitigate change, an perspective.

Language: Английский

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Microbial Community Structure and Causal Analysis. in Sediments of Shallow Eutrophic Freshwater Lakes. Under Heavy Metal Compound Pollution

Journal of Hazardous Materials, Journal Year: 2025, Volume and Issue: 487, P. 137135 - 137135

Published: Jan. 7, 2025

Language: Английский

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Niche Partitioning and Intraspecific Variation of Thaumarchaeota in Deep Ocean Sediments

Environmental Microbiology, Journal Year: 2025, Volume and Issue: 27(1)

Published: Jan. 1, 2025

ABSTRACT Deep‐sea sediments contain a large number of Thaumarchaeota that are phylogenetically distinct from their pelagic counterparts. However, ecology and evolutionary adaptations not well understood. Metagenomic analyses were conducted on samples various depths 750‐cm sediment core collected the Mariana Trench Challenger Deep. The abundance archaeal amoA generally decreased with depth, except for an unexpected peak midway through core. thaumarchaeotal metagenome‐assembled genomes classified into diverse phylogenetic clusters associated ‐NP‐γ, ‐NP‐θ, ‐NP‐δ ammonia‐oxidising non‐ammonia‐oxidising lineages. most abundant group was within which is usually found in coastal shallow habitats, indicating potential niche expansion marine to hadal environments. This benthic showed within‐species genomic variations compared previously identified Hadal water group, suggesting microdiversification along separation between Evolutionary benthic‐to‐pelagic transition included reduced genome size, loss motility/cell adhesion, altered energy metabolism, different mechanisms substrate acquisition regulation (e.g., ammonium). These findings offer new insights evolution demonstrate, first time, intraspecies‐level variation related benthic‐versus‐pelagic partitioning deep ocean.

Language: Английский

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Developing a microfluidic‐based epicPCR reveals diverse potential hosts of the mcrA gene in marine cold seep

mLife, Journal Year: 2025, Volume and Issue: 4(1), P. 70 - 82

Published: Feb. 1, 2025

Abstract Anaerobic methanotrophic (ANME) microbes play a crucial role in the bioprocess of anaerobic oxidation methane (AOM). However, due to their unculturable status, diversity is poorly understood. In this study, we established microfluidics‐based epicPCR (Emulsion, Paired Isolation, and Concatenation PCR) fuse 16S rRNA gene mcrA reveal ANME ( hosts) three sampling push‐cores from marine cold seep. A total 3725 amplicon sequence variants (ASVs) hosts were detected, classified into 78 genera across 23 phyla. Across all samples, dominant phyla with high relative abundance (>10%) well‐known Euryarchaeota , some bacterial such as Campylobacterota Proteobacteria Chloroflexi ; however, specificity these associations was not verified. addition, compositions significantly different layers, where archaeal increased depths sediments, indicating carriers AOM divergent depth. Furthermore, consensus phylogenetic trees showed congruence archaea bacteria, suggesting horizontal transfer may occur among host members. Finally, metagenomes found contain well other genes that encode enzymes pathway, which prospectively propose existence bacteria. This study describes improvements for potential method studying uncultured functional broadens our understanding ANMEs.

Language: Английский

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