Microbial Communities Associated with GeologicalHorizons in Coastal Subseafloor Sediments from the Sea ofOkhotsk

Inagaki, Fumio; Suzuki, Motoo; Takai, Ken; Oida, Hanako; Sakamoto, Tatsuhiko; Aoki, Kaori; Nealson, Kenneth H.; Horikoshi, Koki

doi:10.1128/aem.69.12.7224-7235.2003

Cited by 425 publications

(448 citation statements)

References 40 publications

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“…The porous sponge mimics the porous layers (ash and sand layers) of the subseafloor sediments. Inagaki et al, (2003) and Kobayashi et al, (2008) reported that cultivable microbial components were generally more numerous in the porous layers than in the pelagic clay layers. In addition, the distinguishing feature of the DHS reactor is that the sponges are not submerged and freely placed in the atmosphere (Uemura and Harada, 2010).…”

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Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

et al. 2011

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Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 1C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA-and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life.

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Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

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“…E-mail : hyunjh@hanyang.ac.kr 행되어왔다 (Gray and Herwig 1996;Ravenschlag et al 1999). 그러나 최근 분자생태기술의 발달을 통하여 제한된 환경에서만 서식한다고 알려져 있던 고세균이 일반 해양 환경 및 심해 퇴적물 (Vetriani et al 1999;Reed et al 2002;Inagaki et al 2003;Newberry et al 2004;Biddle et al 2006;Inagaki et al 2006), 남극 퇴적물 (Bowman and McCuaig 2003;Kendall et al 2007), 냉용수(cold seep)지역 (Knittel et al 2005;Arakawa et al 2006), 메탄 누출(methane seep)지역 (Lloyd et al 2006;Dang et al 2009), 해저 열수구(hydrothermal vent)지역 (Takai and Horikoshi 1999;Reysenbach et al 2000;Teske et al 2002), 빈영양(organic-poor)해역 (Sørensen et al 2004), 갯 벌(tidal flat) (Wilms et al 2006) 및 염습지(salt marsh) (Nelson et al 2009)와 같은 다양한 해양환경에서 광범위 하게 분포하고 있음이 밝혀졌으며, 이를 바탕으로, 고세균 도 진정세균과 마찬가지로 해양 퇴적물에서 생지화학적 물질순환에 중요한 역할을 담당하는 것으로 인식되고 있 다 (Knittel et al 2005;Biddle et al 2006;Hallam et al 2006;Nicol and Schleper 2006).…”

Section: 서 론unclassified

“…외국의 경우 다양한 해양 환경에서 미생물에 의한 물질 순환에 대한 연구와 함께 16S rRNA 유전자 분석을 통하 여 해양 저층 퇴적물에서 고세균 군집 다양성에 관한 연 구가 활발하게 진행되고 있다 (Vetriani et al 1999;Reed et al 2002;Inagaki et al 2003;Newberry et al 2004;Biddle et al 2006;Inagaki et al 2006). 이에 비해, 국내 에서는 주로 연안이나 갯벌에서 진정세균의 다양성에 대 한 연구가 다수 진행되었으나, 고세균에 대한 연구는 갯벌 과 동해 연안의 수심 500-650 m 정도의 퇴적물에서 암모 니아 산화와 관련한 연구에 불과한 실정이다 (이 등 2001;조 등 2004;Kim et al 2005;Park et al 2008).…”

Section: 서 론unclassified

“…이 그룹은 deep-sea archaeal group(DSAG)라고도 불리 며, 대부분 심해 저층 환경에서 광범위하게 나타난다 (Takai and Horikoshi 1999;Vetriani et al 1999;Reed et al 2002;Inagaki et al 2003). 본 연구에서 MBG B는 대 륙사면인 정점 M1의 표층(0-1 cm)에서는 단 하나의 클론 만 나타났지만 저층의 두 깊이(8-9, 18-19 cm)에서는 모두 약 40%의 비율을 차지하여 (Table 1) 전체 클론 중 가장 우점하는 그룹으로 나타났다.…”

Section: Marine Benthic Group B(mbg B)unclassified

“…Euryarchaeota에 속하는 MBG D는 정점 M1의 표층(0-1 cm)에서는 나타나지 않았고, 깊이 8-9 cm에서 31.8%, 깊이 18-19 cm에서 20.3%의 비율로 나타났다( Table 1) (Reed et al 2002;Inagaki et al 2003;Biddle et al 2006;Inagaki et al 2006;Sørensen and Teske 2006). 본 연구에서 나타난 MBG B/DSAG 그 룹에 속하는 클론들은 주로 오흐츠크 해의 냉용수 지역과 Eel River Basin의 메탄 누출지 등 저층의 혐기성 조건에 서 나타난 클론들과 연관되어 나타나는 것으로 조사되었 다 (Fig.…”

Section: Marine Benthic Group Dunclassified

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Community Structure, Diversity, and Vertical Distribution of Archaea Revealed by 16S rRNA Gene Analysis in the Deep Sea Sediment of the Ulleung Basin, East Sea

Kim¹,

Cho²,

Hyun³

2010

Ocean and Polar Research

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: To assess community structure and diversity of archaea, a clone sequencing analysis based on an archaeal 16S rRNA gene was conducted at three sediment depths of the continental slope and Ulleung Basin in the East Sea. A total of 311 and 342 clones were sequenced at the slope and basin sites, respectively. Marine Group I, which is known as the ammonia oxidizers, appeared to predominate in the surface sediment of both sites (97.3% at slope, 88.5% at basin). In the anoxic subsurface sediment of the slope and basin, the predominant archaeal group differed noticeably. Marine Benthic Group B dominated in the subsurface sediment of the slope. Marine Benthic Group D and Miscellaneous Crenarchaeotal Group were the second largest archaeal group at 8-9 cm and 18-19 cm depth, respectively. Marine Benthic Group C of Crenarchaeota occupied the highest proportion by accounting for more than 60% of total clones in the subsurface sediments of the basin site. While archaeal groups that use metal oxide as an electron acceptor were relatively more abundant at the basin sites with manganese (Mn) oxide-enriched surface sediment, archaeal groups related to the sulfur cycle were more abundant in the sulfidogenic sediments of the slope. Overall results indicate that archaeal communities in the Ulleung Basin show clear spatial variation with depth and sites according to geochemical properties the sediment. Archaeal communities also seem to play a significant role in the biogeochemical carbon (C), nitrogen (N), sulfur (S), and metal cycles at each site.

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Deep subsurface carbon cycling in the Nankai Trough (Japan)—Evidence of tectonically induced stimulation of a deep microbial biosphere

Riedinger

Strasser

Harris

et al. 2015

Geochem Geophys Geosyst

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The abundance of microbial life and the sources of energy necessary for deep subsurface microbial communities remain enigmatic. Here we investigate deep microbial processes and their potential relationships to tectonic events in sediments from the Nankai Trough offshore Japan, drilled and sampled during IODP (Integrated Ocean Drilling Program) Expedition 316. Observed methane isotope profiles indicate that microbially mediated methane production occurs at Sites C0006 and C0007 in sediments below 450 meters below seafloor (mbsf) and 425 mbsf, respectively. The active carbon cycling in these deep subsurface sediments is likely related to the highly dynamic tectonic regime at Nankai Trough. We propose that transient increases in temperature have restimulated organic matter degradation at these distinct depths and explore several candidate processes for transient heating. Our favored hypothesis is frictional heating associated with earthquakes. In concert with transient heating leading to the reactivation of recalcitrant organic matter, the heterogeneous sedimentary system provides niches for microbial life. The newly available/accessible organic carbon compounds fuel the microbial community-resulting in an onset of methanogenesis several hundred meters below the seafloor. This process is captured in the methane Cisotope signal, showing the efficacy of methane C-isotopes for delineating locations of active microbial processes in deeply buried sediments. Additionally, simple model approaches applied to observed chemical pore water profiles can potentially constrain timing relationships, which can then be linked to causative tectonic events. Our results suggest the occurrence of slip-to-the-trench earthquake(s) 200-400 year ago, which could relate to historical earthquakes (1707 Hoei and/or 1605 Keicho earthquakes).

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Microbial Communities Associated with GeologicalHorizons in Coastal Subseafloor Sediments from the Sea ofOkhotsk

Cited by 425 publications

References 40 publications

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

Community Structure, Diversity, and Vertical Distribution of Archaea Revealed by 16S rRNA Gene Analysis in the Deep Sea Sediment of the Ulleung Basin, East Sea

Deep subsurface carbon cycling in the Nankai Trough (Japan)—Evidence of tectonically induced stimulation of a deep microbial biosphere

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