Adaptation of Archaeal Communities to Summer Hypoxia in the Sediment of Bohai Sea

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 1, 2025

ABSTRACT Understanding the adaptation of archaea to hypoxia is essential for deciphering functions and mechanisms microbes when suffering environmental changes. However, dynamics responses sedimentary in Bohai Sea are still unclear. In this study, diversity, composition, distribution archaeal community sediment along an inshore–offshore transect across oxygen‐depleted area were investigated June, July, August 2021 by employing high‐throughput sequencing 16S rRNA gene. Results indicated that communities dominated Thermoproteota (80.61%), Asgardarchaeota (8.70%), Thermoplasmatota (5.27%). Dissolved oxygen (DO) NO 3 − two key factors shaping communities, accounting 49.5% 38.3% total variabilities ( p < 0.05), respectively. With intensity depletion, diversity increased significantly. Microbial networks revealed Bathyarchaeia played a role interacting with both bacteria other groups. Furthermore, adaptions also displayed variation relative abundance predicted ecological metabolic pathways. The enrichment specific nitrogen transformation enzymes showed potential fixation removal, which might contribute balance N budget thus facilitate restoration under eutrophication Sea. Our results provided new picture on archaea, will be beneficial further investigations extreme environments theoretically practically.

Language: Английский

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Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter

The Journal of Microbiology, Journal Year: 2025, Volume and Issue: 63(4), P. e2502002 - e2502002

Published: April 29, 2025

Language: Английский

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Microbial aerotrophy enables continuous primary production in diverse cave ecosystems

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

Published: June 1, 2024

Most aerated cave ecosystems are assumed to be oligotrophic given they receive minimal inputs of light energy. Diverse microorganisms have nevertheless been detected within caves, though it remains unclear what strategies enable them meet their energy and carbon needs. Here we determined the processes mediators primary production in limestone basalt caves through paired metagenomic biogeochemical profiling. Based on 1458 metagenome-assembled genomes, over half microbial cells encode enzymes use atmospheric trace gases as sources. The most abundant microbes these systems chemosynthetic producers, notably novel gammaproteobacterial methanotrophic order Ca. Methylocavales two uncultivated actinobacterial genera predicted grow hydrogen, dioxide, monoxide. In situ ex isotopic measurements consistently confirmed that rapidly consumed at rates sufficient community-wide needs drive continual production. Conventional chemolithoautotrophs, which lithic compounds such ammonium sulfide, also enriched active alongside gas scavengers. These results indicate unique both composition sustain them. findings, propose first known where primarily growth rather than survival define this process "aerotrophy". Cave aerotrophy may a hidden supporting global biogeochemistry.

Language: Английский

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Microbial mechanisms of biochar addition on carbon and nitrogen synergistic retention during distilled grain waste composting: Insights from metagenomic analysis

Bioresource Technology, Journal Year: 2024, Volume and Issue: 411, P. 131346 - 131346

Published: Aug. 24, 2024

Language: Английский

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Microdiversity in marine pelagic ammonia‐oxidizing archaeal populations in a Mediterranean long‐read metagenome

Environmental Microbiology, Journal Year: 2024, Volume and Issue: 26(8)

Published: July 1, 2024

Abstract The knowledge of the different population‐level processes operating within a species, and genetic variability individual prokaryotic genomes, is key to understanding adaptability microbial populations. Here, we characterized flexible genome ammonia‐oxidizing archaeal (AOA) populations using metagenomic recruitment approach long‐read (PacBio HiFi) sequencing. In lower photic zone western Mediterranean Sea (75 m deep), genomes Nitrosopelagicus brevis CN25 Nitrosopumilus catalinensis SPOT1 had highest values among available complete AOA genomes. They were used analyse diversity genes (variable from strain strain) by examining long‐reads located genomic islands (fGIs) identified their under‐recruitment. Both large fGI involved in glycosylation exposed structures, highly variable, rich glycosyltransferases. N. two fGIs related transport phosphorus ammonium respectively. transportation metal uptake. A fGI5 previously reported as ‘unassigned function’ could be associated with defense. These findings demonstrate that microdiversity marine microbe populations, including AOA, can effectively an incorporates third‐generation sequencing metagenomics.

Language: Английский

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Discovery of Candidatus Nitrosomaritimum as a New Genus of Ammonia-Oxidizing Archaea Widespread in Anoxic Saltmarsh Intertidal Aquifers

Environmental Science & Technology, Journal Year: 2024, Volume and Issue: 58(36), P. 16040 - 16054

Published: Aug. 8, 2024

Ammonia-oxidizing archaea (AOA) are widely distributed in marine and terrestrial habitats, contributing significantly to global nitrogen carbon cycles. However, their genomic diversity, ecological niches, metabolic potentials the anoxic intertidal aquifers remain poorly understood. Here, we discovered named a novel AOA genus, Candidatus Nitrosomaritimum, from of Yancheng Wetland, showing close metagenomic abundance previously acknowledged dominant Nitrosopumilus AOA. Further construction ammonia monooxygenase-based phylogeny demonstrated widespread distribution Nitrosomaritimum estuarine-coastal niches sediment. Niche differentiation among sublineages this new genus is driven by salinity dissolved oxygen gradients. Comparative genomics revealed that has genetic capacity utilize urea possesses high-affinity phosphate transporter systems (phnCDE) for surviving phosphorus-limited conditions. Additionally, it contains putative nosZ genes encoding nitrous-oxide (N2O) reductase reducing N2O gas. Furthermore, gained first insights into archaeal phylum Hydrothermarchaeota populations residing potential hydroxylamine-detoxification mutualism with through utilizing AOA-released extracellular hydroxylamine using oxidoreductase. Together, study unravels overlooked role priorly unknown but abundant lineages newly biological transformation pollution mitigation coastal environments.

Language: Английский

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Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea

mBio, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 3, 2024

ABSTRACT Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including archaea (AOA) as key player. Although much known about AOA abundance and diversity across environments, genetic drivers of ecophysiological adaptations are often less clearly defined. This especially true for within genus Nitrosocosmicus , which have several unique physiological traits (e.g., high substrate tolerance, low affinity, large cell size). To better understand what separates physiology AOA, we performed comparative genomics with genomes from 39 cultured five AOA. The absence canonical high-affinity type ammonium transporter typical S-layer structural genes was found to be conserved all In agreement, cryo-electron tomography confirmed visible outermost structure, has been observed other contrast highlighted possibility that may possess glycoprotein or glycolipid-based glycocalyx covering outer layer. Together, genomic, physiological, metabolic properties revealed this study provide insight into niche adaptation mechanisms overall ecophysiology members clade various terrestrial ecosystems. IMPORTANCE vital biogeochemical but plays significant role eutrophication aquatic ecosystems production greenhouse gas nitrous oxide (N 2 O) industrial agriculture While types microorganisms play critical N cycle, most abundant nitrifiers natural environments. Members one prevalent groups detected undisturbed previously reported range characteristics set their apart species. provides progress understanding these drivers. Our results highlight how studies based on genomics-driven hypotheses can contribute

Language: Английский

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Formation and Fate of Reactive Nitrogen during Biological Nitrogen Removal from Water: Important Yet Often Ignored Chemical Aspects of the Nitrogen Cycle

Environmental Science & Technology, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 13, 2024

Hydroxylamine, nitrous acid, and nitric oxide are obligate intermediates or side metabolites in different nitrogen-converting microorganisms. These compounds unstable susceptible to the formation of highly reactive nitrogen species, including dioxide, dinitrogen trioxide, nitroxyl, peroxynitrite. Due high reactivity cytotoxicity, buildup can affect interplay microorganisms/microbial processes, stimulate reactions with organic like micropollutants (OMP) act as precursors (N2O). However, there is little understanding occurrence significance during biological conversions engineered water systems. In this review, we evaluate fate produced by microorganisms involved removal (BNR) i.e., nitritation/nitrification, denitratation/denitrification, anammox, combined processes. While entirely controlled microbial activities, consumption be either purely chemical. Changes environmental conditions, such redox transition, pH, substrate availability, imbalance production these intermediates, thus leading transient accumulation species. Based on previous experimental evidence, relevance BNR systems, particularly related abiotic N2O OMP transformation, demonstrated.

Language: Английский

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Metabolism diversification of ammonia-oxidizing archaea and bacteria under different precipitation gradients and land legacies

Applied Soil Ecology, Journal Year: 2024, Volume and Issue: 206, P. 105831 - 105831

Published: Dec. 16, 2024

Language: Английский

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Probing the microbiome in stormwater pipeline sediments: Co-occurrence patterns and novel functionalities

Current Research in Biotechnology, Journal Year: 2024, Volume and Issue: 7, P. 100199 - 100199

Published: Jan. 1, 2024

Stormwater pipeline is an essential pathway to transfer stormwater runoff into nearby receiving water bodies. Understanding the composition, co-occurrence patterns, and function of microbial communities in sediments can help provide management control strategies for pollution safeguard safety ecological health urban environment. This study employs 16S rRNA gene amplicon sequencing probe a highly urbanized area Guangzhou, China. Results show that sediment bacterial community rich Listeria, Prevotella, Stenotrophomonas, Pseudomonas, which all pertain pathogens. Methanogens (Methanobacterium, Methanosaeta, Methanosarcina, Methanobrevibacter) ammonia-oxidizing archaea (Ca. Nitrosopelagicus, Ca. Nitrososphaera, Nitrosotenuis) dominated archaeal sediments. These functions are further validated by prediction overall community. The network microbe-environment correlation analyses suggest particulate C-N-P components play more crucial role, comparison dissolved ones regulating microbiome, although not samples follow this mechanism. findings expected contribute systems valuable guidance improving environmental well-being ecosystems.

Language: Английский

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