Molecular phylogenetic analyses of reverse‐transcribed bacterial rRNA obtained from deep‐sea cold seep sediments

Inagaki, Fumio; Sakihama, Yuri; Inoue, Akihisa; Kato, Chiaki; Horikoshi, Koki

doi:10.1046/j.1462-2920.2002.00294.x

Cited by 88 publications

(63 citation statements)

References 56 publications

(79 reference statements)

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“…In addition to sulfate reducers, chemolithoautotrophic sulfur oxidizers, such as members of the Epsilonproteobacteria, were detected in the RNA-based sequence library constructed from sample collected at the top of the sediment. The reduced sulfur compounds may support some sulfur oxidizers (Inagaki et al, 2002(Inagaki et al, , 2003 that were not detected in the deeper sediment, possibly owing to the lack of available electron acceptors (for example, O 2 and nitrate) in the CO 2 -rich low-pH sediment. The seafloor sediment in the Yonaguni Knoll IV hydrothermal field harbors a remarkable number and diversity of microbes (Inagaki et al, 2006;Nunoura and Takai, 2009;Nunoura et al, 2010).…”

Section: Discussionmentioning

confidence: 96%

Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes

et al. 2012

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Sediment-hosting hydrothermal systems in the Okinawa Trough maintain a large amount of liquid, supercritical and hydrate phases of CO 2 in the seabed. The emission of CO 2 may critically impact the geochemical, geophysical and ecological characteristics of the deep-sea sedimentary environment. So far it remains unclear whether microbial communities that have been detected in such high-CO 2 and low-pH habitats are metabolically active, and if so, what the biogeochemical and ecological consequences for the environment are. In this study, RNA-based molecular approaches and radioactive tracer-based respiration rate assays were combined to study the density, diversity and metabolic activity of microbial communities in CO 2 -seep sediment at the Yonaguni Knoll IV hydrothermal field of the southern Okinawa Trough. In general, the number of microbes decreased sharply with increasing sediment depth and CO 2 concentration. Phylogenetic analyses of community structure using reverse-transcribed 16S ribosomal RNA showed that the active microbial community became less diverse with increasing sediment depth and CO 2 concentration, indicating that microbial activity and community structure are sensitive to CO 2 venting. Analyses of RNA-based pyrosequences and catalyzed reporter deposition-fluorescence in situ hybridization data revealed that members of the SEEP-SRB2 group within the Deltaproteobacteria and anaerobic methanotrophic archaea (ANME-2a and -2c) were confined to the top seafloor, and active archaea were not detected in deeper sediments (13-30 cm in depth) characterized by high CO 2 . Measurement of the potential sulfate reduction rate at pH conditions of 3-9 with and without methane in the headspace indicated that acidophilic sulfate reduction possibly occurs in the presence of methane, even at very low pH of 3. These results suggest that some members of the anaerobic methanotrophs and sulfate reducers can adapt to the CO 2 -seep sedimentary environment; however, CO 2 and pH in the deep-sea sediment were found to severely impact the activity and structure of the microbial community.

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Section: Discussionmentioning

confidence: 96%

Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes

et al. 2012

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“…The growth temperature ranges and the ability to utilize hydrogen or oxygen of these genera might fit with the geochemical settings of indigenous habitats. We have previously reported that members of e-proteobacterial group F coexist with sulfate reducers within the d-Proteobacteria in deep-sea cold seep environments (Inagaki et al, 2002). Mesophilic sulfur-oxidizing bacteria phylogenetically related to isolate 42BKT T might contribute to sulfur (re)cycling in global deep-sea environments.…”

Section: Phylogenetic Position and Ecological Significancementioning

confidence: 98%

“…3). Group F contains large numbers of environmental sequences obtained from deep-sea hydrothermal systems (Reysenbach et al, 2000;Teske et al, 2002) and cold seep environments (Li et al, 1999;Inagaki et al, 2002) (Fig. 3).…”

Section: Phylogenetic Position and Ecological Significancementioning

confidence: 99%

Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the ε-Proteobacteria isolated from Okinawa Trough hydrothermal sediments

Inagaki

Takai

Nealson

et al. 2004

International Journal of Systematic and Evolutionary Microbiology

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A novel mesophilic sulfur- and thiosulfate-oxidizing bacterium, strain 42BKTT, was isolated from the gas-bubbling sediment at the Iheya North hydrothermal system in the mid-Okinawa Trough, Japan. The isolate was a Gram-negative, non-motile and coccoid to oval-shaped bacterium. Growth was observed at 10–40 °C (optimum 28–30 °C) and in the pH range 5·0–9·0 (optimum 6·5–7·0). Strain 42BKTT grew chemolithoautotrophically with elemental sulfur or thiosulfate as a sole electron donor and oxygen (optimum 5 % in gas phase) or nitrate as an electron acceptor. The G+C content of the genomic DNA was 48·0 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate belonged to the previously uncultivated Group F within the ε-Proteobacteria, which includes phylotypes of vent epibiont and environmental sequences from global deep-sea cold seep and hydrothermal vent fields. On the basis of the physiological and molecular characteristics of this isolate, the type species of a novel genus, Sulfurovum lithotrophicum gen. nov., sp. nov., is proposed. The type strain is 42BKTT (=ATCC BAA-797T=JCM 12117T).

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“…Sediment depth-related patterns in bacterial community structure were, for instance, detected for a variety of benthic habitats, such as cold seep sediments (Inagaki et al, 2002), the warm deep Mediterranean sea (Luna et al, 2004), the western Pacific coast (Urakawa et al 2000), the Antarctic continental shelves (Bowman and McCuaig, 2003), coral reef sediments , as well as for continental shelf sediments of the southern North Sea (Franco et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands

et al. 2009

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Bacterial community structure and microbial activity were determined together with a large number of contextual environmental parameters over 2 years in subtidal sands of the German Wadden Sea in order to identify the main factors shaping microbial community structure and activity in this habitat. Seasonal changes in temperature were directly reflected in bacterial activities and total community respiration, but could not explain variations in the community structure. Strong sediment depthrelated patterns were observed for bacterial abundances, carbon production rates and extracellular enzymatic activities. Bacterial community structure also showed a clear vertical variation with higher operational taxonomic unit (OTU) numbers at 10-15 cm depth than in the top 10 cm, probably because of the decreasing disturbance by hydrodynamic forces with sediment depth. The depthrelated variations in bacterial community structure could be attributed to vertical changes in bacterial abundances, chlorophyll a and NO 3 À , indicating that spatial patterns of microbes are partially environmentally controlled. Time was the most important single factor affecting microbial community structure with an OTU replacement of up to 47% over 2 years and a contribution of 34% to the total variation. A large part of this variation was not related to any environmental parameters, suggesting that temporal variations in bacterial community structure are caused by yet unknown environmental drivers and/or by stochastic events in coastal sand habitats. Principal ecosystem functions such as benthic oxygen consumption and extracellular hydrolysis of organic matter were, however, at a high level at all times, indicating functional redundancy in the microbial communities.

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Molecular phylogenetic analyses of reverse‐transcribed bacterial rRNA obtained from deep‐sea cold seep sediments

Cited by 88 publications

References 56 publications

Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes

Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes

Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the ε-Proteobacteria isolated from Okinawa Trough hydrothermal sediments

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands

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