Pore-water dissolved inorganic carbon sources and cycling in the shallow sediments of the Haima cold seeps, South China Sea

Liu, Lu; Wu, Zucheng; Xu, Sinan; Wei, Jiangong; Peng, Xiaotong; Li, Jiangtao; Wang, Yiqing

doi:10.1016/j.jseaes.2020.104495

Cited by 23 publications

(24 citation statements)

References 61 publications

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“…In HM, push core sediment samples were collected from three active cold seep sites, including background (SY72-5), close to clam (SY70-4), and mussel (SY70-5) communities., These were dissected into sub-samples in 2 cm increments (Supplementary Data 1 ). The background samples in HM was described previously 51 . LQ biofilms were suctioned through a tube from the hydrothermal vent.…”

Section: Methodsmentioning

confidence: 99%

New globally distributed bacterial phyla within the FCB superphylum

Gong

Río

et al. 2022

Nat Commun

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Microbes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbacterota, Arandabacterota, and Joyebacterota) and a previously proposed phylum (AABM5-125-24), all of them within the FCB superphylum. Comparison of their rRNA genes with public databases reveals that these phyla are globally distributed in different habitats, including marine, freshwater, and terrestrial environments. Genomic analyses suggest these organisms are capable of mediating key steps in sedimentary biogeochemistry, including anaerobic degradation of polysaccharides and proteins, and respiration of sulfur and nitrogen. Interestingly, these genomes code for an unusually high proportion (~9% on average, up to 20% per genome) of protein families lacking representatives in public databases. Genes encoding hundreds of these protein families colocalize with genes predicted to be involved in sulfur reduction, nitrogen cycling, energy conservation, and degradation of organic compounds. Our findings advance our understanding of bacterial diversity, the ecological roles of these bacteria, and potential links between novel gene families and metabolic processes in the oceans.

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Section: Methodsmentioning

confidence: 99%

New globally distributed bacterial phyla within the FCB superphylum

Gong

Río

et al. 2022

Nat Commun

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“…The HM cold seep is an active cold seep site, where two seeps (Seep1 and Seep2) were discovered in 2015 and 2016, respectively (Liang et al, 2017). Methane fluids advect from the deep sediments of both seeps, sustaining large patches of bivalves in the surface sediment (Liu, Wu, et al, 2020; Wei et al, 2020). At these two seeps, two push cores were retrieved from the centre, one from the edge, and three from the adjacent bare sediment of the mussel ( Gigantidas sp.)…”

Section: Methodsmentioning

confidence: 99%

“…Subsequently, sediments for microbiological analysis were collected at the same depth resolution, frozen with liquid nitrogen, and stored at −80°C until DNA extraction. Methane (CH 4 ), sulphate (

{SO}_{4}^{2 -}

), dissolved inorganic carbon (DIC),

δ

13 C‐DIC,

δ

13 C‐CH 4 and cations (Ca 2+ , Mg 2+ , NH 4 + ) were measured as described previously (Liu, Wu, et al, 2020).…”

Section: Methodsmentioning

confidence: 99%

“…Organic matter mineralization by other electron acceptors, such as nitrate and oxides of iron and manganese, was ignored due to their relatively minor contributions at the studied sites (Liu, Wu, et al, 2020). Model parameters and boundary conditions for cores from HM had been determined previously (Liu, Wu, et al, 2020). The upper boundaries for solutes were set to measured values at the top of the core (Dirichlet-type boundary), and methane concentration was assumed to be zero.…”

Section: Methane Flux Estimation With Reactiontransport Modellingmentioning

confidence: 99%

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Methane supply drives prokaryotic community assembly and networks at cold seeps of the South China Sea

Niu

Deng

et al. 2022

Molecular Ecology

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Marine cold seeps are unique chemosynthetic habitats fuelled by deeply sourced hydrocarbon‐rich fluids discharged at the seafloor. Through oxidizing methane and other hydrocarbons, microorganisms inhabiting cold seeps supply subsurface‐derived energy to higher trophic levels, sustaining highly productive oases of life in the deep sea. Despite the central role of microbiota in mediating biogeochemical cycles, the factors that govern the assembly and network of prokaryotic communities in cold seeps remain poorly understood. Here we analysed the geochemical and microbiological profiles of 11 different sediment cores from two spatially distant cold seeps of the South China Sea. We show that prokaryotic communities belonging to the same methane‐supply regimes (high‐methane‐supply, low‐methane‐supply and non‐seep control sediments) had a highly similar community structure, regardless of geographical location, seep‐associated biota (mussel, clam, microbial mat) and sediment depth. Methane supply appeared to drive the niche partitioning of anaerobic methanotrophic archaea (ANME) at the regional scale, with ANME‐1 accounting for >60% sequence abundance of ANME in the high‐methane‐supply sediments, while ANME‐2 dominated (>90%) the low‐methane‐supply sediments. Increasing methane supply enhanced the contribution of environmental selection but lessened the contributions of dispersal limitation and drift to overall community assembly. High methane supply, moreover, promoted a more tightly connected, less stable prokaryotic network dominated by positive correlations. Together, these results provide a potentially new framework for understanding the niches and network interplay of prokaryotic communities across different methane seepage regimes in cold‐seep sediments.

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“…In HM, push core sediment samples were collected from three active cold seep sites, including background (SY72-5), close to clam (SY70-4), and mussel (SY70-5) communities., These were dissected into subsamples in 2 cm increments (Supplementary Data 1). The background samples in HM was described previously 51 . LQ biofilms were suctioned through a tube from the hydrothermal vent.…”

Section: Sampling and Metagenomic Sequencingmentioning

confidence: 99%

New globally distributed bacteria with high proportions of novel protein families involved in sulfur and nitrogen cycling

Gong¹,

Río

et al. 2022

Preprint

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Microbes are the most abundant form of life on Earth and play crucial roles in carbon and nutrient cycling. Despite their crucial role, our understanding of microbial diversity and physiology on the ocean floor is limited. To address this gap in knowledge, we obtained 55 novel bacterial metagenome-assembled genomes (MAGs) from coastal and deep sea sediments. Phylogenomic analyses revealed they belong to four new and one poorly described bacterial phyla. Comparison of their rRNA genes with public databases revealed they are all globally distributed. These novel bacteria are capable of the anaerobic degradation of polysaccharides and proteins, and the respiration of sulfur and nitrogen. These genomes code for an unusually high proportion (~ 9, and up to 20% per genome) of protein families lacking representatives in public databases. Hundreds of these protein families are predicted to be co-localized with genes for sulfur reduction, nitrogen cycling, energy conservation, and the degradation of organic compounds. These findings expand our understanding of microbial diversity and link previously overlooked gene families with key metabolic processes in the oceans.

show abstract

Pore-water dissolved inorganic carbon sources and cycling in the shallow sediments of the Haima cold seeps, South China Sea

Cited by 23 publications

References 61 publications

New globally distributed bacterial phyla within the FCB superphylum

New globally distributed bacterial phyla within the FCB superphylum

Methane supply drives prokaryotic community assembly and networks at cold seeps of the South China Sea

New globally distributed bacteria with high proportions of novel protein families involved in sulfur and nitrogen cycling

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