Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

Wang, Yong; Gao, Zhaoming; Li, Jiangtao; Bougouffa, Salim; Tian, Ren Mao; Bajic, Vladimir B.; Qian, Pei‐Yuan

doi:10.1007/s11434-016-1135-6

Cited by 18 publications

(18 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…5 and Fig. S12), as has been reported in Aerophobetes obtained from the Red Sea (26). We found that most of the deep-sea genotypes in B3 encode the W-L pathway (Fig.…”

supporting

confidence: 81%

“…The Lokiarchaeota and Heimdallarchaeota detected here, belonging to Asgard superphylum, are close relatives of eukaryotes and are frequently reported in anoxic marine sediments worldwide (23)(24)(25). The acetogenic, strictly anaerobic bacteria Aerophobetes, which may fix CO 2 and conserve energy by the Wood-Ljungdahl (W-L) pathway (26,27), are the most abundant group based on their coverage in metagenomic data. Candidate phyla LCP-89 and B38 (undescribed phyla) were also identified.…”

mentioning

confidence: 73%

See 1 more Smart Citation

New Microbial Lineages Capable of Carbon Fixation and Nutrient Cycling in Deep-Sea Sediments of the Northern South China Sea

Huang

Baker²,

et al. 2019

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

Metagenomics of marine sediments has uncovered a broad diversity of new uncultured taxa and provided insights into their metabolic capabilities. Here, we detected microbial lineages from a sediment core near the Jiulong methane reef of the northern South China Sea (at 1,100-m depth). Assembly and binning of the metagenomes resulted in 11 genomes (Ͼ85% complete) that represented nine distinct phyla, including candidate phyla TA06 and LCP-89, Lokiarchaeota, Heimdallarchaeota, and a newly described globally distributed phylum (B38). The genome of LCP-89 has pathways for nitrate, selenate, and sulfate reduction, suggesting that they may be involved in mediating these important processes. B38 are able to participate in the cycling of hydrogen and selenocompounds. Many of these uncultured microbes may also be capable of autotrophic CO 2 fixation, as exemplified by identification of the Wood-Ljungdahl (W-L) pathway. Genes encoding carbohydrate degradation, W-L pathway, Rnf-dependent energy conservation, and Ni/Fe hydrogenases were detected in the transcriptomes of these novel members. Characterization of these new lineages provides insight to the undescribed branches in the tree of life. IMPORTANCE Sedimentary microorganisms in the South China Sea (SCS) remain largely unknown due to the complexity of sediment communities impacted by continent rifting and extension. Distinct geochemical environments may breed special microbial communities including microbes that are still enigmatic. Functional inference of their metabolisms and transcriptional activity provides insight in the ecological roles and substrate-based interactivity of these uncultured Archaea and Bacteria. These microorganisms play different roles in utilizing inorganic carbon and scavenging diverse organic compounds involved in the deep-sea carbon cycle. The genomes recovered here contributed undescribed species to the tree of life and laid the foundation for future study on these novel phyla persisting in marginal sediments of the SCS.

show abstract

“…5 and Fig. S12), as has been reported in Aerophobetes obtained from the Red Sea (26). We found that most of the deep-sea genotypes in B3 encode the W-L pathway (Fig.…”

supporting

confidence: 81%

mentioning

confidence: 73%

New Microbial Lineages Capable of Carbon Fixation and Nutrient Cycling in Deep-Sea Sediments of the Northern South China Sea

Huang

Baker²,

et al. 2019

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

show abstract

“…Acetothermia are a dominant taxon in subsurface environments and were suggested as the earliest bacterial lineage to possess the WL pathway (12). Aerophobetes have been mainly found in brackish lakes and cold seep environments (22), where they have been hypothesized to function as carbon recyclers, either taking advantage of saline sediment organic matter or fixing carbon under nutrient-poor conditions (29). Division CSP1-3 has been indicated as an important member of the carbon fixing community in subsurface aquifer ecosystems (23).…”

Section: Resultsmentioning

confidence: 99%

Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

Adam

Borrel

Gribaldo

2018

Proc. Natl. Acad. Sci. U.S.A.

170

154

View full text Add to dashboard Cite

Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is a five-subunit enzyme complex responsible for the carbonyl branch of the Wood-Ljungdahl (WL) pathway, considered one of the most ancient metabolisms for anaerobic carbon fixation, but its origin and evolutionary history have been unclear. While traditionally associated with methanogens and acetogens, the presence of CODH/ACS homologs has been reported in a large number of uncultured anaerobic lineages. Here, we have carried out an exhaustive phylogenomic study of CODH/ACS in over 6,400 archaeal and bacterial genomes. The identification of complete and likely functional CODH/ACS complexes in these genomes significantly expands its distribution in microbial lineages. The CODH/ACS complex displays astounding conservation and vertical inheritance over geological times. Rare intradomain and interdomain transfer events might tie into important functional transitions, including the acquisition of CODH/ACS in some archaeal methanogens not known to fix carbon, the tinkering of the complex in a clade of model bacterial acetogens, or emergence of archaeal-bacterial hybrid complexes. Once these transfers were clearly identified, our results allowed us to infer the presence of a CODH/ACS complex with at least four subunits in the last universal common ancestor (LUCA). Different scenarios on the possible role of ancestral CODH/ACS are discussed. Despite common assumptions, all are equally compatible with an autotrophic, mixotrophic, or heterotrophic LUCA. Functional characterization of CODH/ACS from a larger spectrum of bacterial and archaeal lineages and detailed evolutionary analysis of the WL methyl branch will help resolve this issue.

show abstract

“…6), including those affiliated with phyla previously inferred to mediate acetogenesis in deep-sea sediments through either the tetrahydrofolate-dependent bacterial pathway (e.g. Chloroflexi and Aerophobetes) 5,28 or the tetrahydromethanopterin-dependent archaeal variant (e.g. Bathyarchaeota and Asgard group) 29,30 .…”

Section: Resultsmentioning

confidence: 99%

Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments

et al. 2019

View full text Add to dashboard Cite

The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.

show abstract

Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

Cited by 18 publications

References 53 publications

New Microbial Lineages Capable of Carbon Fixation and Nutrient Cycling in Deep-Sea Sediments of the Northern South China Sea

New Microbial Lineages Capable of Carbon Fixation and Nutrient Cycling in Deep-Sea Sediments of the Northern South China Sea

Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments

Contact Info

Product

Resources

About