Comparison of the microbial diversity in cold-seep sediments from different depths in the Nankai Trough

Arakawa, Shizuka; Sato, Takako; Yoshida, Yasuhiko; Usami, Ron; Kato, Chiaki

doi:10.2323/jgam.52.47

Cited by 22 publications

(9 citation statements)

References 17 publications

(22 reference statements)

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“…Geographic distribution of AOM in association with gas hydrates or other methane-rich environments is widespread, which includes the Black Sea (Wakeham et al 2004;Leloup et al 2007), Cascadia margin (Cragg et al 1996;Bidle et al 1999;Marchesi et al 2001;Knittel et al 2005;Lanoil 2005;Inagaki et al 2006), Eel River Basin (Hallam et al 2003), Guaymas Basin (Teske et al 2002;Dhillon et al 2003), Gulf of Mexico (see below), Japan Trench (Li et al 1999;Inagaki et al 2002), Mediterranean Sea (Heijs et al 2005(Heijs et al , 2007Kormas et al 2005), and Nankai Trough (Newberry et al 2004;Arakawa et al 2006). In the Gulf of Mexico, microbiological studies of gas hydrates have been performed in the Green Canyon (GC), Atwater Canyon (AT), Keathley Canyon (KC), Garden Bank (GB) and Mississippi Canyon (MC).…”

Section: Introductionmentioning

confidence: 95%

Distribution and Diversity of Bacteria and Archaea in Marine Sediments Affected by Gas Hydrates at Mississippi Canyon in the Gulf of Mexico

Wang

Jiang

et al. 2009

Geomicrobiology Journal

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The microbial community structures of gas hydrate-bearing (Core 9) and non-hydrate-bearing (Core 1) marine sediments were investigated at Mississippi Canyon (MC) 118 in the Gulf of Mexico. Quantification by quantitative competitive (QC)-PCR showed that bacterial abundance was 2-3 orders of magnitude higher than archaeal abundance in these cores. Sulfate-reducing bacteria (SRB) were present at 10 3 -10 4 dsrAB gene copies/g in both cores; methanogens or anaerobic methanotrophs were only present in Core 9 (10 2 -10 5 mcrA gene copies/g). Denaturing gradient gel electrophoresis (DGGE) showed distinct patterns of bacterial community structure between Core 9 and Core 1 with ε-Proteobacteria predominating in the former and γ -Proteobacteria in the latter. Clone libraries were successfully constructed for both Archaea and Bacteria using functional genes (mcrA and dsrAB, respectively). The mcrA gene was present in Core 9, suggesting enhanced abundance or activity of methanogens or methane-oxidizing archaea in the hydrate-impacted sediment. The mcrA gene sequences were dominated by group c-d and group e. The majority (80%) of the dsrAB gene sequences fell into Syntrophobacteraceae-related group. the crew of R/V Pelican for helping with sampling.This study indicates that microbial community structures are considerably different between the hydrate-bearing and non-hydratebearing sediment at MC 118. Our study is among the initial steps toward a comprehensive and long-term monitoring of microbial dynamics associated with gas hydrates in the Gulf of Mexico.

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Section: Introductionmentioning

confidence: 95%

Distribution and Diversity of Bacteria and Archaea in Marine Sediments Affected by Gas Hydrates at Mississippi Canyon in the Gulf of Mexico

Wang

Jiang

et al. 2009

Geomicrobiology Journal

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“…Halobacteria and MBG-B were dominant archaeal communities in the abyssal cold seep at a water depth of 3,000 mbsf in Core DSH-1 (ZHANG et al 2012). However, MGI and ANME archaeal groups were dominant in cold seep surface sediments from the Nankai Trough along the western margin of the Pacific Ocean (ARAKAWA et al 2006). In the Gulf of Mexico hydrocarbon seep, Methanosarcinales, ANME-1, Thermoplasmales and Methanomicrobiales were found to be dominant (MILLS et al 2003), and ANME was the dominant group in the Sonora Margin cold seeps in Guaymas Basin (Gulf of California) (VIGNERON et al 2013).…”

Section: Archaeal Community Variation and Geobiochemical Reactionsmentioning

confidence: 91%

“…It was demonstrated that methanotrophic archaea carry out a process called anaerobic oxidation of methane (AOM), initiating the living processes of growth, reproduction and energy flow to make other organisms' existence possible. Considerable research of archaeal communities has been conducted in different typological cold seep areas around the world, such as Hydrate Ridge (KNITTEL et al 2005), Nankai Trough (ARAKAWA et al 2006), Tropical Timor Sea (WASMUND et al 2009), Northern South China Sea (Northern SCS) (ZHANG et al 2012), and Sonora Margin (VIGNERON et al 2013). These studies showed that different cold seep areas harbored different archaeal communities.…”

Section: Introductionmentioning

confidence: 99%

Vertical distribution of archaeal communities in cold seep sediments from the jiulong methane reef area in the south China sea

Cui¹,

Su²,

Fang³

et al. 2016

Biosci. J.

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Jiulong methane reef, a large cold seep area on the continental slope of the South China Sea (SCS), was characterized by chemosynthetic fauna, bacterial mats, methane-derived carbonate structures, and a shallow depth of sulfate-methane transition zone (SMTZ) in gravity cores. To characterize the microbial diversity and variation in correlation to methane venting in the cold seep area, the archaeal community in sediments of the gravity Core CL11 was analyzed, using the Illumina MiSeq sequencing system. A total of 96,917 valid sequences were obtained and classified into 275 OTUs. Taxonomic analysis showed that all the archaeal sequences belonged to the phyla of Crenarchaeota (69.41%) and Eurarchaeota (25.26%). Vertical distribution of the archaeal communities showed that the Marine Benthic Group B (MBG-B) was the predominant group (58.92%) in the topmost sediment of the core, while percentages of the South African Gold Mine Euryarchaeotal Group (SAGMEG) sequences increased with depth. Our findings indicate that the archaeal community in the cold seep of Jiulong Methane Reef is unique and provides us new insights into the archaeal community composition of the cold seep area.

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“…These sequences are affiliated with uncultivated Archaea from deep-sea sediments in the Weddell Sea (Brandt et al, 2007), the East Pacific Rise (Mason et al, 2007), the Nankai Trough (Arakawa et al, 2006), the Pacific nodule province (Xu et al, 2005), the Peru margin , the Eastern Mediterranean (Heijs et al, 2008) and the North Atlantic (Agogue et al, 2008). Phylotypes pTVGA19 and 37 shared 96% similarity with a clone obtained from sediment present in a tropical seawater tank at the Seattle Aquarium, which was closely related to Nitrosopumilus maritimus SCM1, the first cultured mesophilic representative of the Crenarchaeota belonging to the MGI group (Könneke et al, 2005).…”

Section: Archaeal Diversitymentioning

confidence: 98%

“…Numbers in the Venn diagrams indicate number of OTUs. Ridge (Schrenk et al, 2004), and clone pTVGA24 was distantly related to MGI clone ANT33-04 (Arakawa et al, 2006).…”

Section: Archaeal Diversitymentioning

confidence: 98%

Microbial community structure and nitrogenase gene diversity of sediment from a deep-sea hydrothermal vent field on the Southwest Indian Ridge

Cao

Wang

et al. 2014

Acta Oceanol. Sin.

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A sediment sample was collected from a deep-sea hydrothermal vent field located at a depth of 2 951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community using polymerase chain reaction (PCR) amplification of the 16S rRNA and nifH genes. Within the Archaea, the dominant clones were from marine benthic group E (MBGE) and marine group I (MGI) belonging to the phyla Euryarchaeota and Thaumarchaeota, respectively. More than half of the bacterial clones belonged to the Proteobacteria, and most fell within the Gammaproteobacteria. No epsilonproteobacterial sequence was observed. Additional phyla were detected including the Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Nitrospirae, Chloroflexi, Chlorobi, Chlamydiae, Verrucomicrobia, and candidate divisions OD1, OP11, WS3 and TM6, confirming their existence in hydrothermal vent environments. The detection of nifH gene suggests that biological nitrogen fixation may occur in the hydrothermal vent field of the Southwest Indian Ridge. Phylogenetic analysis indicated that only Clusters I and III NifH were present. This is consistent with the phylogenetic analysis of the microbial 16S rRNA genes, indicating that Bacteria play the main role in nitrogen fixation in this hydrothermal vent environment. . 2014. Microbial community structure and nitrogenase gene diversity of sediment from a deep-sea hydrothermal vent field on the Southwest Indian Ridge. Acta Oceanologica Sinica, 33(10):

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Comparison of the microbial diversity in cold-seep sediments from different depths in the Nankai Trough

Cited by 22 publications

References 17 publications

Distribution and Diversity of Bacteria and Archaea in Marine Sediments Affected by Gas Hydrates at Mississippi Canyon in the Gulf of Mexico

Distribution and Diversity of Bacteria and Archaea in Marine Sediments Affected by Gas Hydrates at Mississippi Canyon in the Gulf of Mexico

Vertical distribution of archaeal communities in cold seep sediments from the jiulong methane reef area in the south China sea

Microbial community structure and nitrogenase gene diversity of sediment from a deep-sea hydrothermal vent field on the Southwest Indian Ridge

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