Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(6), P. 891 - 902

Published: April 3, 2023

Abstract The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms important biogeochemical industrial processes. These are common inhabitants of marine terrestrial subsurface environments contain members capable diverse physiologies in addition nitrite oxidation complete ammonia oxidation. Here, we use phylogenomics gene-based analysis with ancestral state reconstruction gene-tree–species-tree reconciliation methods investigate the life histories these two phyla. We find that basal clades both primarily inhabit environments. genomes appear smaller more densely coded than later-branching clades. extant share many traits inferred be present respective ancestors, including hydrogen, one-carbon, sulfur-based metabolisms. Later-branching groups, namely frequently studied classes Nitrospiria Nitrospinia, characterized by genome expansions driven either de novo origination or laterally transferred genes encode functions expanding metabolic repertoire. include gene clusters perform most well known for. Our analyses support replicated evolutionary bacterial phyla, modern representing a genomic repository for coding potential traits.

Language: Английский

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Tectonic settings influence the geochemical and microbial diversity of Peru hot springs

Communications Earth & Environment, Journal Year: 2023, Volume and Issue: 4(1)

Published: April 11, 2023

Abstract Tectonic processes control hot spring temperature and geochemistry, yet how this in turn shapes microbial community composition is poorly understood. Here, we present geochemical 16 S rRNA gene sequencing data from 14 springs contrasting styles of subduction along a convergent margin the Peruvian Andes. We find that tectonic influence on geochemistry composition. Hot flat-slab back-arc regions system had similar pH but differed microbiology, with significant relationships between composition, geologic setting. Flat-slab were chemically heterogeneous, modest surface temperatures (up to 45 °C), dominated by members metabolically diverse phylum Proteobacteria. Whereas, geochemically more homogenous, exhibited high concentrations dissolved metals gases, higher 81 host thermophilic archaeal bacterial lineages.

Language: Английский

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Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -independent approaches

FEMS Microbiology Ecology, Journal Year: 2023, Volume and Issue: 99(11)

Published: Oct. 3, 2023

The microbiome of Greenland Ice Sheet supraglacial habitats is still underinvestigated, and as a result there lack representative genomes from these environments. In this study, we investigated the through combination culturing-dependent -independent approaches. We explored ice, cryoconite, biofilm, snow biodiversity to answer: (1) how microbial diversity differs between habitats, (2) if obtained bacterial reflect dominant community members, (3) culturing versus high throughput sequencing changes our observations in habitats. Genomes acquired metagenomic (133 high-quality MAGs) whole genome (73 isolates) were compared metagenome assemblies investigate abundance within total environmental DNA. Isolates study not taxa habitat they sampled from, contrast MAGs. demonstrate here advantages using SSU rRNA genes whole-community diversity. Additionally, proof-of-concept application situ setting.

Language: Английский

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Profiling microbial communities in an extremely acidic environment influenced by a cold natural carbon dioxide spring: A study of the Mefite in Ansanto Valley, Southern Italy

Environmental Microbiology Reports, Journal Year: 2024, Volume and Issue: 16(1)

Published: Feb. 1, 2024

Abstract The Ansanto Valley's Mefite, one of the Earth's largest non‐volcanic CO 2 gas emissions, is distinguished by its cold natural carbon dioxide springs. These emissions originate from intricate tectonics and geodynamics southern Apennines in Italy. Known for over two millennia lethal concentration other harmful gases, Mefite has a reputation being toxic dangerous. Despite historical significance unique geological features, there lack information on microbial diversity associated with Mefite's emissions. This study presents an integrated exploration mud soil, using high‐throughput sequencing 16S rRNA (Prokaryotes) ITS2 (Fungi), alongside geochemical site characterisation. Our findings reveal that environment imposes significant bottleneck diversity, favouring select few groups such as Actinobacteria Firmicutes Prokaryotes, Basidiomycota Fungi.

Language: Английский

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Enhanced microbial degradation of hexabromocyclododecane in riparian sediments through regulating flooding regimes

Journal of Hazardous Materials, Journal Year: 2025, Volume and Issue: unknown, P. 137406 - 137406

Published: Jan. 1, 2025

Language: Английский

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Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(12)

Published: March 18, 2025

The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, the capabilities ecological roles these communities remain largely unknown. We observed widespread relatively abundant bacterial phylum (CSP1-3) in soils evaluated its phylogeny, ecology, metabolism, evolutionary history. Genome analysis indicated that members CSP1-3 were actively replicating situ widely involved carbon, nitrogen, sulfur cycles. identified potential adaptive traits for oligotrophic environments, including mixotrophic lifestyle, flexible energy metabolisms, conservation pathways. ancestor likely originated an aquatic environment, subsequently colonizing topsoil and, later, with major clades adapted to each distinct niches. transition into terrestrial environment was associated genome expansion, horizontal acquisition range genes carbohydrate metabolism one lineage, high-affinity terminal oxidases support microaerophilic lifestyle. Our results highlight ecology evolution microbes Critical Zone.

Language: Английский

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Exploring microbial diversity in relation to hydrological signatures and anthropic pressures in the Beauce Aquifer, France

The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 977, P. 179402 - 179402

Published: April 15, 2025

Groundwater is one of the largest reservoirs liquid fresh water on earth. Aquifers are complex environments where quality can be affected by geological origins, geochemistry and biological activity. These under pressure due to climate change pollution. Strongly involved in biogeochemistry groundwater ecosystems, microorganisms also contribute reducing pollution potentially used as indicators quality. However, diversity role remains largely unknown. The present work aimed characterize bacterial 60 wells over 8000 km2 Beauce Aquifer, France, determine baseline expected relation hydro geochemical signatures identify variations that could anthropogenic pressures. We analysed amplicon sequence variants (ASVs) 16S rRNA gene well abundance functional genes associated arsenic nitrate (aioA, arsB, narG), organic carbon contents composition. Bacterial co-occurrences were found according hydrogeochemical identified aquifer. A lower was measured confined aquifers, low oxygen conditions occurred with high levels dissolved iron manganese. This indicate a higher vulnerability face pressure. Finally, composition linked each signature several differed from this identified.

Language: Английский

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Chemoautotrophic sulphur oxidizers dominate microbial necromass carbon formation in coastal blue carbon ecosystems

Functional Ecology, Journal Year: 2023, Volume and Issue: 37(10), P. 2634 - 2651

Published: Aug. 24, 2023

Abstract Coastal blue carbon (C) ecosystems are recognized as efficient natural C sinks and play key roles in mitigating global climate change. Microbially driven C, nitrogen (N) sulphur (S) cycles crucial for ecosystem functioning, but how microorganisms drive sink formation sequestration coastal sediments remains unclear. In this study, we conducted a comprehensive analysis of amino sugars, N S cycling genes/pathways their associated taxa native ( Cyperus malaccensis Kandelia obovata ) alien Spartina alterniflora Sonneratia apetala vegetation. Compared to the alien‐vegetated sediment, native‐vegetated sediment had significantly p < 0.05) higher microbial necromass functional potentials chemoautotrophic fixation, degradation, methane cycling, 2 oxidation sulphate reduction. Also, our microbiomes showed that could be coupled with fixation and/or nitrate/nitrite oxidation, degradation were found pathways predicting C. Additionally, sulphur‐oxidizing Burkholderiales metagenome‐assembled genomes (MAGs) group dominated sediments. These results suggested oxidizers, particular novel lineage, might dominates through anabolism (C fixation);the coupling microbially processes; deposition derived This study provides insights into importance oxidizers shed new light on mechanism ecosystems, which also has important implications enhancing wetlands. Read free Plain Language Summary article Journal blog.

Language: Английский

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Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota

National Science Review, Journal Year: 2024, Volume and Issue: 11(11)

Published: Oct. 21, 2024

Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 metagenome-assembled genomes showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood-Ljungdahl (WLP) or Calvin-Benson-Bassham (CBB), hydrogen sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments fluorescence

Language: Английский

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Identifying and Understanding Microbial Methanogenesis in CO₂ Storage

Environmental Science & Technology, Journal Year: 2023, Volume and Issue: 57(26), P. 9459 - 9473

Published: June 16, 2023

Carbon capture and storage (CCS) is an important component in many national net-zero strategies. Ensuring that CO2 can be safely economically stored geological systems critical. To date, CCS research has focused on the physiochemical behavior of CO2, yet there been little consideration subsurface microbial impact storage. However, recent discoveries have shown processes (e.g., methanogenesis) significant. Importantly, methanogenesis may modify fluid composition dynamics within reservoir. Such changes subsequently reduce volume change mobility future trapping systematics evolved supercritical fluid. Here, we review current knowledge how could storage, including potential scale range geologic settings under which this process operates. We find possible all target types; however, kinetics energetics will likely limited by H2 generation. expect bioavailability (and thus greatest depleted hydrocarbon fields least saline aquifers. propose additional integrated monitoring requirements are needed for to trace any biogeochemical baseline, temporal, spatial studies. Finally, suggest areas where further should targeted order fully understand sites its impact.

Language: Английский

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