Microbial Diversity in Deep-sea Methane Seep Sediments Presented by SSU rRNA Gene Tag Sequencing

Nunoura, Takuro; Takaki, Yoshihiro; Kazama, Hiromi; Hirai, Miho; Ashi, Juichiro; Imachi, Hiroyuki; Takai, Ken

doi:10.1264/jsme2.me12032

Cited by 105 publications

(80 citation statements)

References 39 publications

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“…Our RNA-based molecular ecological study demonstrated that the deeper sedimentary habitat, which is directly influenced by CO 2 leakage, is an extremely harsh environment for many microbes, and thus harbors only specialized sedimentary acidophilic microbes. Compared with the microbial diversity at the methane-seep sediment in the Nankai Trough, very low diversity scores for 16S rRNA-tagged sequences were obtained from the CO 2 -rich sediment (Nunoura et al, 2012). These results suggest that only life forms that can physiologically adapt to high-CO 2 and low-pH conditions can survive in this environment.…”

Section: Discussionmentioning

confidence: 83%

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: 83%

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

et al. 2012

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“…Prokaryotic SSU rRNA gene fragments were amplified with a primer set of 530F and 907R (50) from the original environmental DNA assemblages using LA Taq polymerase with GC buffer (Takara Bio) as previously described (50). For tag sequencing, primers with 10 bp of extended tag sequences in 5′-termini were used for the SSU rRNA gene amplification.…”

Section: Methodsmentioning

confidence: 99%

Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth

Nunoura

Takaki

Hirai

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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260

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Hadal oceans at water depths below 6,000 m are the least-explored aquatic biosphere. The Challenger Deep, located in the western equatorial Pacific, with a water depth of ∼11 km, is the deepest ocean on Earth. Microbial communities associated with waters from the sea surface to the trench bottom (0 ∼10,257 m) in the Challenger Deep were analyzed, and unprecedented trench microbial communities were identified in the hadal waters (6,000 ∼10,257 m) that were distinct from the abyssal microbial communities. The potentially chemolithotrophic populations were less abundant in the hadal water than those in the upper abyssal waters. The emerging members of chemolithotrophic nitrifiers in the hadal water that likely adapt to the higher flux of electron donors were also different from those in the abyssal waters that adapt to the lower flux of electron donors. Species-level niche separation in most of the dominant taxa was also found between the hadal and abyssal microbial communities. Considering the geomorphology and the isolated hydrotopographical nature of the Mariana Trench, we hypothesized that the distinct hadal microbial ecosystem was driven by the endogenous recycling of organic matter in the hadal waters associated with the trench geomorphology.hadal | trench | niche separation | nitrification | Challenger Deep

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“…PCR amplification was performed using the Premix Ex Taq Hot Start version (TaKaRa Bio, Otsu, Japan), and the PCR mixture was prepared according to the manufacturer's instructions. For PCR amplification, the whole prokaryotic 16S rRNA gene-targeted primer pair 530F and 907R (40) was used, adhering to the PCR conditions previously described (40). PCR products were checked for size by electrophoresis on a 1.5% agarose gel using RedSafe stain (FroggaBio Inc., Toronto, Canada), purified using the MinElute gel extraction kit (Qiagen, Venlo, Netherlands), and quantified using a Quant-iT PicoGreen double-stranded DNA (dsDNA) assay kit (Life Technologies, Carlsbad, CA).…”

Section: Methodsmentioning

confidence: 99%

Nitrogen and Oxygen Isotope Effects of Ammonia Oxidation by Thermophilic Thaumarchaeota from a Geothermal Water Stream

Nishizawa

Sakai

Konno

et al. 2016

Appl Environ Microbiol

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Ammonia oxidation regulates the balance of reduced and oxidized nitrogen pools in nature. Although ammonia-oxidizing archaea have been recently recognized to often outnumber ammonia-oxidizing bacteria in various environments, the contribution of ammonia-oxidizing archaea is still uncertain due to difficulties in the in situ quantification of ammonia oxidation activity. Nitrogen and oxygen isotope ratios of nitrite (␦ 15 N NO2؊ and ␦ 18 O NO2؊ , respectively) are geochemical tracers for evaluating the sources and the in situ rate of nitrite turnover determined from the activities of nitrification and denitrification; however, the isotope ratios of nitrite from archaeal ammonia oxidation have been characterized only for a few marine species. We first report the isotope effects of ammonia oxidation at 70°C by thermophilic Thaumarchaeota populations composed almost entirely of "Candidatus Nitrosocaldus." The nitrogen isotope effect of ammonia oxidation varied with ambient pH (25‰ to 32‰) and strongly suggests the oxidation of ammonia, not ammonium. The ␦ 18 O value of nitrite produced from ammonia oxidation varied with the ␦ 18 O value of water in the medium but was lower than the isotopic equilibrium value in water. Because experiments have shown that the half-life of abiotic oxygen isotope exchange between nitrite and water is longer than 33 h at 70°C and pH >6.6, the rate of ammonia oxidation by thermophilic Thaumarchaeota could be estimated using ␦ 18 O NO2؊ in geothermal environments, where the biological nitrite turnover is likely faster than 33 h. This study extended the range of application of nitrite isotopes as a geochemical clock of the ammonia oxidation activity to high-temperature environments. IMPORTANCEBecause ammonia oxidation is generally the rate-limiting step in nitrification that regulates the balance of reduced and oxidized nitrogen pools in nature, it is important to understand the biological and environmental factors underlying the regulation of the rate of ammonia oxidation. The discovery of ammonia-oxidizing archaea (AOA) in marine and terrestrial environments has transformed the concept that ammonia oxidation is operated only by bacterial species, suggesting that AOA play a significant role in the global nitrogen cycle. However, the archaeal contribution to ammonia oxidation in the global biosphere is not yet completely understood. This study successfully identified key factors controlling nitrogen and oxygen isotopic ratios of nitrite produced from thermophilic Thaumarchaeota and elucidated the applicability and its limit of nitrite isotopes as a geochemical clock of ammonia oxidation rate in nature. Oxygen isotope analysis in this study also provided new biochemical information on archaeal ammonia oxidation.

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Microbial Diversity in Deep-sea Methane Seep Sediments Presented by SSU rRNA Gene Tag Sequencing

Cited by 105 publications

References 39 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

Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth

Nitrogen and Oxygen Isotope Effects of Ammonia Oxidation by Thermophilic Thaumarchaeota from a Geothermal Water Stream

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