Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments

Dong, Xiyang; Zhang, Chuwen; Peng, Yongyi; Zhang, Hongxi; Shi, Ling-Dong; Wei, Guangshan; Hubert, Claude; Wang, Yong; Greening, Chris

doi:10.1038/s41467-022-32503-w

Cited by 54 publications

(51 citation statements)

References 123 publications

(190 reference statements)

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“…Sea oor cold seeps occur in a variety of geological settings along plate margins 17,18 . In cold seep environments, microbial sulfate reduction, anaerobic methane oxidation and methanogenesis are highly active, supporting a diverse community of chemosynthetic organisms and microbial populations [19][20][21] . Sulfate-reducing bacteria, methanogens, and anaerobic methane oxidation archaea (ANME) in sea oor cold seeps may play an important role to induce Hg(II) methylation or MeHg demethylation 22,23 .…”

Section: Introductionmentioning

confidence: 99%

Deep sea cold seep is an atmospheric Hg sink and MeHg source

Li¹,

Dong²,

Tang³

et al. 2022

Preprint

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Mercury (Hg) is an important element in seafloor cold seeps that might govern methane emission. However, so far, the knowledge of biogeochemical Hg cycle in it remains poorly understood. In this study, Hg geochemical characteristics and microorganisms involved in Hg biogeochemical cycling were examined in three (active, inactive seep vs reference) different types of sediments sampled from the Haima cold seep in the South China Sea. Sediments in the active seep area were significantly enriched in mercury and methylmercury (MeHg) compared to the reference. Accordingly, abundant genes related to Hg methylation (hgcAB), demethylation (merB) and reduction (merA) were detected in the active seep sediments, phylogenetically associated with various bacterial and archaeal linages (e.g. Desulfobacterota, Gammaproteobacteria and Halobacteriota). Hg odd-mass number isotopes (Δ199Hg and Δ201Hg) pointed to their source from the upper ocean and the occurrence of abiotic dark oxidation. The δ202Hg values indicate Hg mass fractionation, migration and transformation in the active seep sediments. These geochemical and microbial data highlight active Hg biogeochemical cycles in seafloor cold seeps, functioning as important Hg-sinks and MeHg sources in the deep ocean.

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Section: Introductionmentioning

confidence: 99%

Deep sea cold seep is an atmospheric Hg sink and MeHg source

Li¹,

Dong²,

Tang³

et al. 2022

Preprint

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“…For a better understanding of microbial processes in methane seeps, two metagenomes from two sediment layers were studied. Although numerous publications deal with metagenomic studies of cold methane seeps [ 59 , 60 , 61 , 62 , 63 , 64 , 65 ], a full complex of such studies, including direct radiotracer measurements of the rates of microbial methane oxidation and sulfate reduction, has not been carried out in the Arctic seas. The studied metagenomes contained both ANME archaea and sulfate-reducing Desulfobacterota , as well as all the genes responsible for AOM and dissimilatory sulfate reduction.…”

Section: Discussionmentioning

confidence: 99%

Biogeochemical Activity of Methane-Related Microbial Communities in Bottom Sediments of Cold Seeps of the Laptev Sea

et al. 2023

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Bottom sediments at methane discharge sites of the Laptev Sea shelf were investigated. The rates of microbial methanogenesis and methane oxidation were measured, and the communities responsible for these processes were analyzed. Methane content in the sediments varied from 0.9 to 37 µmol CH4 dm−3. Methane carbon isotopic composition (δ13C-CH4) varied from −98.9 to −77.6‰, indicating its biogenic origin. The rates of hydrogenotrophic methanogenesis were low (0.4–5.0 nmol dm−3 day−1). Methane oxidation rates varied from 0.4 to 1.2 µmol dm−3 day−1 at the seep stations. Four ANME methanotrophic lineages (1, 2a–2b, 2c, and 3) (Methanosarciniales, phylum Halobacterota) were predominant (up to 46.3% of the whole community). Aerobic ammonium-oxidizing Crenarchaeota (family Nitrosopumilaceae) predominated in the upper sediments. Most archaea (up to 8%) were represented by new lineages, for which the metabolic pathways are presently unknown. Predominant bacteria in the upper sediments were heterotrophic Actinobacteriota and Bacteroidota. Members of the genera Sulfurovum and Sulfurimonas occurred in the sediments of the seep stations. Mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae) occurred in the sediments of all stations. The microbial community composition was similar to that of methane seep sediments from geographically remote areas of the global ocean.

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“…1 ). Among them, 65 metagenomes and 10 metatranscriptomes were compiled from our previous publications 8 , 59 , and other 22 metagenomes were downloaded from NCBI Sequencing Read Archive (SRA). A detailed description of sampling locations and sequencing information for metagenomic and metatranscriptomic data is given in Supplementary Data 1 .…”

Section: Methodsmentioning

confidence: 99%

“…AOM removes approximately 80% of upward venting methane, acting as an efficient methane filter 7 . Additionally, deep-sea cold seep sediments also contain diverse and abundant diazotrophs that might contribute substantially to the global nitrogen balance 8 . Cold seeps are therefore biologically and geochemically significant on a global scale.…”

Section: Introductionmentioning

confidence: 99%

Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

Zhang

Shi

et al. 2023

npj Biofilms Microbiomes

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Cold seeps, where cold hydrocarbon-rich fluid escapes from the seafloor, show strong enrichment of toxic metalloid arsenic (As). The toxicity and mobility of As can be greatly altered by microbial processes that play an important role in global As biogeochemical cycling. However, a global overview of genes and microbes involved in As transformation at seeps remains to be fully unveiled. Using 87 sediment metagenomes and 33 metatranscriptomes derived from 13 globally distributed cold seeps, we show that As detoxification genes (arsM, arsP, arsC1/arsC2, acr3) were prevalent at seeps and more phylogenetically diverse than previously expected. Asgardarchaeota and a variety of unidentified bacterial phyla (e.g. 4484-113, AABM5-125-24 and RBG-13-66-14) may also function as the key players in As transformation. The abundances of As cycling genes and the compositions of As-associated microbiome shifted across different sediment depths or types of cold seep. The energy-conserving arsenate reduction or arsenite oxidation could impact biogeochemical cycling of carbon and nitrogen, via supporting carbon fixation, hydrocarbon degradation and nitrogen fixation. Overall, this study provides a comprehensive overview of As cycling genes and microbes at As-enriched cold seeps, laying a solid foundation for further studies of As cycling in deep sea microbiome at the enzymatic and processual levels.

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Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments

Cited by 54 publications

References 123 publications

Deep sea cold seep is an atmospheric Hg sink and MeHg source

Deep sea cold seep is an atmospheric Hg sink and MeHg source

Biogeochemical Activity of Methane-Related Microbial Communities in Bottom Sediments of Cold Seeps of the Laptev Sea

Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

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