Phylogenetic and Functional Diversity of Soluble Di‐Iron Monooxygenases DOI Creative Commons

Sui Nin Nicholas Yang,

Michael A. Kertesz, Nicholas V. Coleman

et al.

Environmental Microbiology, Journal Year: 2025, Volume and Issue: 27(2)

Published: Feb. 1, 2025

ABSTRACT Monooxygenase (MO) enzymes are responsible for the oxidation of hydrocarbons and other compounds in carbon nitrogen cycles, important biodegradation pollutants can act as biocatalysts chemical manufacture. The soluble di‐iron monooxygenases (SDIMOs) interest due to their broad substrate range, high enantioselectivity ability oxidise inert substrates such methane. Here, we re‐examine phylogeny functions these enzymes, using recent advances field expansions sequence diversity databases highlight relationships between SDIMOs revisit classification. We discuss impact horizontal gene transfer on SDIMO phylogeny, potential importance heterologous expression a tool understanding enabling use biocatalysts. Our analysis highlights current knowledge gaps, most notably, unknown ranges physiological roles that have so far only been detected via genome or metagenome sequencing. Enhanced will enable better prediction management biogeochemical processes also new applications biocatalysis bioremediation.

Language: Английский

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity DOI Creative Commons
Zexin Li,

Donald Pan,

Guangshan Wei

et al.

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(8), P. 2366 - 2378

Published: March 1, 2021

Abstract In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse but little is about infecting these microorganisms. Here, we probed metagenomes from seven geographically across global oceans assess viral diversity, virus–host interaction, virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons inhabiting other ecosystems reveal that seep harbour considerable unexplored diversity. Most display high degrees endemism fluid flux being one main drivers community composition. silico predictions linked 14.2% populations many belonging poorly understood candidate bacterial archaeal phyla. Lysis was predicted be a predominant lifestyle based lineage-specific virus/host abundance ratios. Metabolic prokaryotic genomes AMGs suggest influence hydrocarbon biodegradation at seeps, as well carbon, sulfur nitrogen cycling via virus-induced mortality and/or augmentation. Overall, findings diversity biogeography indicate how may manipulate ecology biogeochemistry.

Language: Английский

Citations

170
Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments DOI Creative Commons
Xiyang Dong, Chuwen Zhang, Yongyi Peng

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Aug. 19, 2022

Microbially mediated nitrogen cycling in carbon-dominated cold seep environments remains poorly understood. So far anaerobic methanotrophic archaea (ANME-2) and their sulfate-reducing bacterial partners (SEEP-SRB1 clade) have been identified as diazotrophs deep sea sediments. However, it is unclear whether other microbial groups can perform fixation such ecosystems. To fill this gap, we analyzed 61 metagenomes, 1428 metagenome-assembled genomes, six metatranscriptomes derived from 11 globally distributed seeps. These sediments contain phylogenetically diverse nitrogenase genes corresponding to an expanded diversity of diazotrophic lineages. Diverse catabolic pathways were predicted provide ATP for fixation, suggesting diazotrophy seeps not necessarily associated with sulfate-dependent oxidation methane. Nitrogen among various inferred be genetically mobile subject purifying selection. Our findings extend the capacity five candidate phyla (Altarchaeia, Omnitrophota, FCPU426, Caldatribacteriota UBA6262), suggest that might contribute substantially global balance.

Language: Английский

Citations

76
Characteristics of microbial community composition and its relationship with carbon, nitrogen and sulfur in sediments DOI
Wenfei Liao, Di Tong, Zhongwu Li

et al.

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 795, P. 148848 - 148848

Published: July 3, 2021

Language: Английский

Citations

65
CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation DOI Creative Commons
Varada Khot, Jackie Zorz, Daniel A. Gittins

et al.

Frontiers in Microbiology, Journal Year: 2022, Volume and Issue: 12

Published: Jan. 5, 2022

Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the potential of microbial genomes metagenomes. Here we present Calgary approach ANnoTating HYDrocarbon genes (CANT-HYD), a database 37 HMMs marker involved in anaerobic aerobic aliphatic aromatic hydrocarbons. Using this database, understudied or overlooked many phyla. We also demonstrate its application analyzing high-throughput sequence data by predicting utilization large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.

Language: Английский

Citations

42
Anaerobic Degradation of Alkanes by Marine Archaea DOI Open Access
Gunter Wegener, Rafael Laso-Pérez, Victoria J. Orphan

et al.

Annual Review of Microbiology, Journal Year: 2022, Volume and Issue: 76(1), P. 553 - 577

Published: Aug. 2, 2022

Alkanes are saturated apolar hydrocarbons that range from their simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa can anaerobically degrade alkanes. Here we review recent discoveries in the oxidation of with a specific focus on archaea use methyl coenzyme M reductases activate substrates. Our understanding diversity uncultured alkane-oxidizing has expanded through environmental metagenomics and enrichment cultures syntrophic methane-, ethane-, propane-, butane-oxidizing marine sulfate-reducing bacteria. A recently cultured group directly couples long-chain alkane degradation methane formation, expanding substrates used for methanogenesis. This article summarizes rapidly growing knowledge diversity, physiology, habitat distribution alkane-degrading archaea.

Language: Английский

Citations

41
Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps DOI Creative Commons
Xiyang Dong, Yongyi Peng, Muhua Wang

et al.

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

Citations

30
The role of organic carbon in the Southern Uplands-Down-Longford Terrane accretionary prism, Scotland and Ireland DOI Creative Commons
John Parnell, Joseph Armstrong,

Nigel Blamey

et al.

Petroleum Geoscience, Journal Year: 2023, Volume and Issue: 29(3)

Published: June 15, 2023

Carbonaceous shales in the Southern Uplands-Down-Longford Terrane accretionary prism had extremely high potential for hydrocarbon generation Lower Paleozoic. Structural thickening enhanced rapid of oil. Shale horizons are separated by thick turbidites composed low-permeability greywackes, so oil under fluid pressure either pooled along shale bedding surfaces or migrated into fractured greywackes. Pooled became solidified to bitumen, which locally formed deposits on a scale tonnes, mined as coal. The carbon-rich also sequestered large amounts sulfur from seawater, precipitated pyrite firstly during early diagenesis, then further flow through beds. was sulfur-bearing. Deformation focused beds evolution would have been closely related bitumen and sulfides. palaeo-fluids were anomalously rich methane hydrogen, similar fluids venting modern prisms. Supplementary material: details localities searched coal Palaeozoic, (locations shown Fig. 6 ) available at https://doi.org/10.6084/m9.figshare.c.6691597

Language: Английский

Citations

27
The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules DOI Creative Commons
Chuwen Zhang, Yunxin Fang, Xiuran Yin

et al.

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

Citations

26
Anaerobic hexadecane degradation by a thermophilic Hadarchaeon from Guaymas Basin DOI Creative Commons
David Benito Merino, Julius S. Lipp, Guillaume Borrel

et al.

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

Published: Jan. 1, 2024

Abstract Hadarchaeota inhabit subsurface and hydrothermally heated environments, but previous to this study, they had not been cultured. Based on metagenome-assembled genomes, most are heterotrophs that grow sugars amino acids, or oxidize carbon monoxide reduce nitrite ammonium. A few other genomes encode alkyl-coenzyme M reductases (Acrs), β-oxidation, Wood-Ljungdahl pathways, pointing toward multicarbon alkane metabolism. To identify the organisms involved in thermophilic oil degradation, we established anaerobic sulfate-reducing hexadecane-degrading cultures from sediments of Guaymas Basin. Cultures at 70°C were enriched one Hadarchaeon propose as Candidatus Cerberiarchaeum oleivorans. Genomic chemical analyses indicate Ca. C. oleivorans uses an Acr activate hexadecane hexadecyl-coenzyme M. β-oxidation pathway a tetrahydromethanopterin methyl branch Wood–Ljungdahl (mWL) allow complete oxidation CO2. Our results suggest syntrophic lifestyle with sulfate reducers, lacks respiration pathway. Comparative genomics show Acr, mWL, restricted family Hadarchaeota, which Cerberiarchaeaceae. Phylogenetic further mWL is basal all Hadarchaeota. By contrast, dehydrogenase/acetyl-coenzyme synthase complex Cerberiarchaeaceae was horizontally acquired Bathyarchaeia. The genes highly similar those alkane-oxidizing archaea such Methanoliparia Helarchaeales. support use Acrs degradation petroleum alkanes role oil-rich environments.

Language: Английский

Citations

8
Microbial ecology of sulfur cycling near the sulfate–methane transition of deep‐sea cold seep sediments DOI
Wenli Li, Xiyang Dong, Rui Lu

et al.

Environmental Microbiology, Journal Year: 2021, Volume and Issue: 23(11), P. 6844 - 6858

Published: Oct. 9, 2021

Summary Microbial sulfate reduction is largely associated with anaerobic methane oxidation and alkane degradation in sulfate–methane transition zone (SMTZ) of deep‐sea cold seeps. How the sulfur cycling mediated by microbes near SMTZ has not been fully understood. In this study, we detected a shallow three eight sediment cores sampled from two seep areas South China Sea. One hundred ten genomes representing sulfur‐oxidizing bacteria (SOB) sulfur‐reducing (SRB) strains were identified SMTZ‐bearing cores. layers above SMTZ, SOB mostly constituted Campylobacterota, Gammaproteobacteria Alphaproteobacteria that probably depended on nitrogen oxides and/or oxygen for sulfide thiosulfate near‐surface layers. below deltaproteobacterial SRB metatranscriptomes revealed CO 2 fixation Wood–Ljungdahl pathway, syntrophic or fermentative lifestyle. A total 68% metagenome assembled adjacent to known species phylogenomic tree, indicating high diversity involved cycling. With large number SRB, our study uncovers microbial populations potentially mediate metabolism carbon cycles, which sheds light complex biogeochemical processes environments.

Language: Английский

Citations

55