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Ken Takai

Publications and source records attributed to Ken Takai.

At least 37 records · Page 2Linked to original sources
PubMed2005

Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field.

Epsilon-Proteobacteria is increasingly recognized as an ecologically significant group of bacteria, particularly in deep-sea hydrothermal environments. In this study, we studied the spatial distribution, diversity and physiological characteristics of the epsilon-Proteobacteria in various microbial habitats in the vicinity of a deep-sea hydrothermal vent occurring in the Iheya North field in the Mid-Okinawa Trough, by using culture-dependent and -independent approaches. The habitats studied were inside and outside hydrothermal plume, and annelid polychaete tubes. In addition, we deployed colonization devices near the vent emission. The polychaete tubes harboured physiologically and phylogenetically diverse microbial community. The in situ samplers were predominantly colonized by epsilon-Proteobacteria. Energy metabolism of epsilon-Proteobacteria isolates was highly versatile. Tree topology generated from the metabolic traits was significantly different (P = 0.000) from that of 16S rRNA tree, indicating current 16S rRNA gene-based analyses do not provide sufficient information to infer the physiological characteristics of epsilon-Proteobacteria. Nevertheless, culturability of epsilon-Proteobacteria in various microbial habitats differed among the phylogenetic subgroups. Members of Sulfurimonas were characterized by the robust culturability, and the other phylogenetic subgroups appeared to lose culturability in seawater, probably because of the sensitivity to oxygen. These results provide new insight into the ecophysiological characteristics of the deep-sea hydrothermal vent epsilon-Proteobacteria, which has never been assessed by comparative analysis of the 16S rRNA genes.

Culture Media↗
PubMed2005

Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments.

Within a phylum Crenarchaeota, only some members of the hyperthermophilic class Thermoprotei, have been cultivated and characterized. In this study, we have constructed a metagenomic library from a microbial mat formation in a subsurface hot water stream of the Hishikari gold mine, Japan, and sequenced genome fragments of two different phylogroups of uncultivated thermophilic Crenarchaeota: (i) hot water crenarchaeotic group (HWCG) I (41.2 kb), and (ii) HWCG III (49.3 kb). The genome fragment of HWCG I contained a 16S rRNA gene, two tRNA genes and 35 genes encoding proteins but no 23S rRNA gene. Among the genes encoding proteins, several genes for putative aerobic-type carbon monoxide dehydrogenase represented a potential clue with regard to the yet unknown metabolism of HWCG I Archaea. The genome fragment of HWCG III contained a 16S/23S rRNA operon and 44 genes encoding proteins. In the 23S rRNA gene, we detected a homing-endonuclease encoding a group I intron similar to those detected in hyperthermophilic Crenarchaeota and Bacteria, as well as eukaryotic organelles. The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota.

Aerobiosis↗
PubMed2005

Enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of Epsilonproteobacteria.

The carbon and energy metabolisms of a variety of cultured chemolithoautotrophic Epsilonproteobacteria from deep-sea hydrothermal environments were characterized by both enzymatic and genetic analyses. All the Epsilonproteobacteria tested had all three key reductive tricarboxylic acid (rTCA) cycle enzymatic activities--ATP-dependent citrate lyase, pyruvate:ferredoxin oxidoreductase, and 2-oxoglutarate:ferredoxin oxidoreductase--while they had no ribulose 1,5-bisphosphate carboxylase (RubisCO) activity, the key enzyme in the Calvin-Benson cycle. These results paralleled the successful amplification of the key rTCA cycle genes aclB, porAB, and oorAB and the lack of success at amplifying the form I and II RubisCO genes, cbbL and cbbM. The combination of enzymatic and genetic analyses demonstrates that the Epsilonproteobacteria tested use the rTCA cycle for carbon assimilation. The energy metabolisms of deep-sea Epsilonproteobacteria were also well specified by the enzymatic and genetic characterization: hydrogen-oxidizing strains had evident soluble acceptor:methyl viologen hydrogenase activity and hydrogen uptake hydrogenase genes (hyn operon), while sulfur-oxidizing strains lacked both the enzyme activity and the genes. Although the energy metabolism of reduced sulfur compounds was not genetically analyzed and was not fully clarified, sulfur-oxidizing Epsilonproteobacteria showed enzyme activity of a potential sulfite:acceptor oxidoreductase for a direct oxidation pathway to sulfate but no activity of AMP-dependent adenosine 5'-phosphate sulfate reductase for a indirect oxidation pathway. No activity of thiosulfate-oxidizing enzymes was detected. The enzymatic and genetic characteristics described here were consistent with cellular carbon and energy metabolisms and suggest that molecular tools may have great potential for in situ elucidation of the ecophysiological roles of deep-sea Epsilonproteobacteria.

Bacterial Proteins↗
PubMed2005

Novel chemoautotrophic endosymbiosis between a member of the Epsilonproteobacteria and the hydrothermal-vent gastropod Alviniconcha aff. hessleri (Gastropoda: Provannidae) from the Indian Ocean.

The hydrothermal-vent gastropod Alviniconcha aff. hessleri from the Kairei hydrothermal field on the Central Indian Ridge houses bacterium-like cells internally in its greatly enlarged gill. A single 16S rRNA gene sequence was obtained from the DNA extract of the gill, and phylogenetic analysis placed the source organism within a lineage of the epsilon subdivision of the Proteobacteria. Fluorescence in situ hybridization analysis with an oligonucleotide probe targeting the specific epsilonproteobacterial subgroup showed the bacterium densely colonizing the gill filaments. Carbon isotopic homogeneity among the gastropod tissue parts, regardless of the abundance of the endosymbiont cells, suggests that the carbon isotopic composition of the endosymbiont biomass is approximately the same as that of the gastropod. Compound-specific carbon isotopic analysis revealed that fatty acids from the gastropod tissues are all (13)C enriched relative to the gastropod biomass and that the monounsaturated C(16) fatty acid that originates from the endosymbiont is as (13)C enriched relative to the gastropod biomass as that of the epsilonproteobacterial cultures grown under chemoautotrophic conditions. This fractionation pattern is most likely due to chemoautotrophy based on the reductive tricarboxylic-acid (rTCA) cycle and subsequent fatty acid biosynthesis from (13)C-enriched acetyl coenzyme A. Enzymatic characterization revealed evident activity of several key enzymes of the rTCA cycle, as well as the absence of ribulose-1,5-bisphosphate carboxylase/oxygenase activity in the gill tissue. The results from anatomic, molecular phylogenetic, bulk and compound-specific carbon isotopic, and enzymatic analyses all support the inference that a novel nutritional strategy relying on chemoautotrophy in the epsilonproteobacterial endosymbiont is utilized by the hydrothermal-vent gastropod from the Indian Ocean. The discrepancies between the data of the present study and those of previous ones for Alviniconcha gastropods from the Pacific Ocean imply that at least two lineages of chemoautotrophic bacteria, phylogenetically distinct at the subdivision level, occur as the primary endosymbiont in one host animal type.

Animals↗
PubMed2004

Marinobacter alkaliphilus sp. nov., a novel alkaliphilic bacterium isolated from subseafloor alkaline serpentine mud from Ocean Drilling Program Site 1200 at South Chamorro Seamount, Mariana Forearc.

Novel alkaliphilic, mesophilic bacteria were isolated from subseafloor alkaline serpentine mud from the Ocean Drilling Program (ODP) Hole 1200D at a serpentine mud volcano, South Chamorro Seamount in the Mariana Forearc. The cells of type strain ODP1200D-1.5T were motile rods with a single polar flagellum. Growth was observed between 10 and 45-50 degrees C (optimum temperature: 30-35 degrees C, 45-min doubling time), between pH 6.5 and 10.8-11.4 (optimum: pH 8.5-9.0), and between NaCl concentrations of 0 and 21% (w/v) (optimum NaCl concentration: 2.5-3.5%). The isolate was a facultatively anaerobic heterotroph utilizing various complex substrates, hydrocarbons, carbohydrates, organic acids, and amino acids. Nitrate or fumarate could serve as an electron acceptor to support growth under anaerobic conditions. The G+C content of the genomic DNA was 57.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Marinobacter and was the most closely related to M. aquaeolei strain VT8T and M. hydrocarbonoclasticus strain SP.17T, while DNA-DNA hybridization demonstrated that the new isolate could be genetically differentiated from the previously described species of Marinobacter. Based on the physiological and molecular properties of the new isolate, we propose the name Marinobacter alkaliphilus sp. nov., type strain: ODP1200D-1.5T (JCM12291T and ATCC BAA-889T).

Alteromonadaceae↗
PubMed2004

Geochemical and microbiological evidence for a hydrogen-based, hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field.

Subsurface microbial communities supported by geologically and abiologically derived hydrogen and carbon dioxide from the Earth's interior are of great interest, not only with regard to the nature of primitive life on Earth, but as potential analogs for extraterrestrial life. Here, for the first time, we present geochemical and microbiological evidence pointing to the existence of hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) dominated by hyperthermophilic methanogens beneath an active deep-sea hydrothermal field in the Central Indian Ridge. Geochemical and isotopic analyses of gaseous components in the hydrothermal fluids revealed heterogeneity of both concentration and carbon isotopic compositions of methane between the main hydrothermal vent (0.08 mM and -13.8 per thousand PDB, respectively) and the adjacent divergent vent site (0.2 mM and -18.5 per thousand PDB, respectively), representing potential subsurface microbial methanogenesis, at least in the divergent vent emitting more 13C-depleted methane. Extremely high abundance of magmatic energy sources such as hydrogen (2.5 mM) in the fluids also encourages a hydrogen-based, lithoautotrophic microbial activity. Both cultivation and cultivation-independent molecular analyses suggested the predominance of Methanococcales members in the superheated hydrothermal emissions and chimney interiors along with the other major microbial components of Thermococcales members. These results imply that a HyperSLiME, consisting of methanogens and fermenters, occurs in this tectonically active subsurface zone, strongly supporting the existence of hydrogen-driven subsurface microbial communities.

Archaea↗
PubMed2004

Phylogenetic diversity of sulfate-reducing prokaryotes in active deep-sea hydrothermal vent chimney structures.

The phylogenetic diversity of sulfate-reducing prokaryotes occurring in active deep-sea hydrothermal vent chimney structures was characterized based on the deduced amino acid sequence analysis of the polymerase chain reaction-amplified dissimilatory sulfite reductase (DSR) gene. The DSR genes were successfully amplified from microbial assemblages of the chimney structures, derived from three geographically and geologically distinct deep-sea hydrothermal systems in the Central Indian Ridge (CIR), in the Izu-Bonin Arc (IBA), and the Okinawa Trough (OT), respectively. Phylogenetic analysis revealed seven major phylogenetic groups. More than half of the clones from the CIR chimney structure were related to DSR amino acid sequences of the hyperthermophilic archaeal members of the genus Archaeoglobus, and those of environmental DSR clones within the class Thermodesulfobacteria. From the OT chimney structure, a different group was obtained, which comprised a novel, deep lineage associated with the DSRs of the thermophilic sulfate-reducing bacterium Thermodesulfovibrio. Most of the DSR clones from the IBA chimney structure were phylogenetically associated with the delta-proteobacterial sulfate-reducing bacteria represented by the genus Desulfobulbus. Sequence analysis of DSR clones demonstrated a diverse sulfate-reducing prokaryotic community in the active deep-sea hydrothermal chimney structures.

Genetic Variation↗
PubMed2004

Hydrogenimonas thermophila gen. nov., sp. nov., a novel thermophilic, hydrogen-oxidizing chemolithoautotroph within the epsilon-Proteobacteria, isolated from a black smoker in a Central Indian Ridge hydrothermal field.

A novel thermophilic bacterium, strain EP1-55-1%T, was isolated from an in-situ colonization system deployed in a superheated, deep-sea, hydrothermal vent emission at the Kairei Field on the Central Indian Ridge in the Indian Ocean. The cells were highly motile rods, each possessing a single polar flagellum. Growth was observed between 35 and 65 degrees C (optimum temperature, 55 degrees C; 70 min doubling time) and between pH 4.9 and 7.2 (optimum, pH 5.9). The isolate was a microaerobic-to-anaerobic chemolithoautotroph capable of using molecular hydrogen as the sole energy source and carbon dioxide as the sole carbon source. Molecular oxygen, nitrate or elemental sulfur (S0) could serve as electron acceptors to support growth. The G+C content of the genomic DNA was 34.6 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that strain EP1-55-1%T represents the first strain for which taxonomic properties have been characterized within the previously uncultivated phylogroup classified as belonging to the uncultivated epsilon-Proteobacteria group A; the name Hydrogenimonas thermophila gen. nov., sp. nov. is proposed, with strain EP1-55-1%T (=JCM 11971T=ATCC BAA-737T) as the type strain.

Cell Division↗
PubMed2004

Aeropyrum camini sp. nov., a strictly aerobic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney.

A novel hyperthermophilic archaeon, designated strain SY1(T), was isolated from a deep-sea hydrothermal vent chimney sample collected from the Suiyo Seamount in the Izu-Bonin Arc, Japan, at a depth of 1385 m. The cells were irregular cocci (1.2 to 2.1 micro m in diameter), occurring singly or in pairs, and stained Gram-negative. Growth was observed between 70 and 97 degrees C (optimum, 85 degrees C; 220 min doubling time), pH 6.5 and 8.8 (optimum, pH 8.0), and salinity of 2.2 and 5.3 % (optimum, 3.5 %). It was a strictly aerobic heterotroph capable of growing on complex proteinaceous substrates such as yeast extract and tryptone. The G+C content of the genomic DNA was 54.4 mol%. Phylogenetic analysis based on the 16S rDNA sequence of the isolate indicated that the isolate was closely related to Aeropyrum pernix strain K1(T). However, no significant genetic relatedness was observed between them by DNA-DNA hybridization. On the basis of the molecular and physiological traits of the new isolate, the name Aeropyrum camini sp. nov. is proposed, with the type strain SY1(T) (=JCM 12091(T)=ATCC BAA-758(T)).

Aerobiosis↗
PubMed2004

Methanotorris formicicus sp. nov., a novel extremely thermophilic, methane-producing archaeon isolated from a black smoker chimney in the Central Indian Ridge.

A novel extremely thermophilic, methane-producing archaeon was isolated from a black smoker chimney at the Kairei field in the Central Indian Ridge. Cells of this isolate were irregular cocci with several flagella; motility was not observed. Growth was observed between 55 and 83 degrees C (optimum of 75 degrees C; 30 min doubling time) and between pH 6.0 and 8.5 (optimum of pH 6.7). The isolate was a strictly anaerobic, methanogenic autotroph capable of using hydrogen and carbon dioxide as sole energy and carbon sources. Formate was utilized as an alternative energy source. The G+C content of the genomic DNA was 33.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate was most closely related to Methanotorris igneus strain Kol 5T. The isolate, however, could be genetically differentiated from this species by DNA-DNA hybridization analysis and on the basis of its physiological properties. The name Methanotorris formicicus sp. nov. is proposed for this isolate; the type strain is Mc-S-70T (=JCM 11930T=ATCC BAA-687T).

Anaerobiosis↗
PubMed2004

Hydrogenivirga caldilitoris gen. nov., sp. nov., a novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium from a coastal hydrothermal field.

A novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium, designated strain IBSK3(T), was isolated from a coastal hot spring in Ibusuki, Kagoshima Prefecture, Japan. The cells were motile, straight to slightly curved rods (1.2-3.0 microm long and 0.3-0.4 microm wide). Strain IBSK3(T) was an obligate chemolithoautotroph growing by respiratory nitrate reduction with H(2), forming N(2)O as an end product. Low concentrations of O(2) (0.4-7.7 %, v/v; optimum 2.0 %, v/v) could serve as an alternative electron acceptor to growth. In addition, strain IBSK3(T) was able to utilize elemental sulfur as a sole electron donor with either nitrate or low concentrations of O(2) as an electron acceptor. Growth was observed between 55 and 77.5 degrees C (optimum 75 degrees C; 2 h doubling time), pH 5.5 and 8.3 (optimum pH 6.5-7.0), and in the presence of 0.5 and 4.0 % NaCl (optimum 2.0 %). The G+C content of the genomic DNA was 49.2 mol%. On the basis of 16S rRNA gene sequence analysis, strain IBSK3(T) belonged to the family Aquificaceae, but it only demonstrated a distant phylogenetic relationship with any recognized species within the family (sequence similarity was less than 92 %). On the basis of the physiological and molecular characteristics of the novel isolate, a new genus and novel species are proposed: the type strain of Hydrogenivirga caldilitoris gen. nov., sp. nov. is IBSK3(T) (=JCM 12173(T)=ATCC BAA-821(T)).

Base Composition↗
PubMed2004

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

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 degrees C (optimum 28-30 degrees 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 epsilon-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).

Base Composition↗
PubMed2004

Thiomicrospira thermophila sp. nov., a novel microaerobic, thermotolerant, sulfur-oxidizing chemolithomixotroph isolated from a deep-sea hydrothermal fumarole in the TOTO caldera, Mariana Arc, Western Pacific.

A novel thermotolerant bacterium, designated strain I78(T), was isolated from a self-temperature-recording in situ colonization system deployed in a hydrothermal diffusing flow (maximal temperature 78 degrees C) at the TOTO caldera in the Mariana Arc, Western Pacific. Cells were highly motile curved rods with a single polar flagellum. Growth was observed at 15-55 degrees C (optimum 35-40 degrees C; 60 min doubling time) and pH 5.0-8.0 (optimum pH 6.0). The isolate was a microaerobic chemolithomixotroph capable of using thiosulfate, elemental sulfur or sulfide as the sole energy source, and molecular oxygen as the sole electron acceptor. The isolate was able to grow chemolithoautotrophically with carbon dioxide. Various organic substrates such as complex proteinaceous compounds, carbohydrates, organic acids, amino acids and sugars could also support growth as the carbon source instead of carbon dioxide with sulfur oxidation. The G+C content of the genomic DNA was 43.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Thiomicrospira and was most closely related to Thiomicrospira crunogena strain TH-55(T) and Thiomicrospira sp. strain L-12, while DNA-DNA hybridization demonstrated that the novel isolate could be genetically differentiated from previously described strains of Thiomicrospira. On the basis of its physiological and molecular properties the isolate is representative of a novel Thiomicrospira species, for which the name Thiomicrospira thermophila sp. nov. is proposed (type strain, I78(T)=JCM 12397(T)=DSM 16397(T)).

Bacterial Typing Techniques↗
PubMed2004

Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes.

Samples from three submerged sites (MC, a core obtained in the methane seep area; MR, a reference core obtained at a distance from the methane seep; and HC, a gas-bubbling carbonate sample) at the Kuroshima Knoll in the southern Ryuku arc were analyzed to gain insight into the organisms present and the processes involved in this oxic-anoxic methane seep environment. 16S rRNA gene analyses by quantitative real-time PCR and clone library sequencing revealed that the MC core sediments contained abundant archaea (approximately 34% of the total prokaryotes), including both mesophilic methanogens related to the genus Methanolobus and ANME-2 members of the Methanosarcinales, as well as members of the delta-Proteobacteria, suggesting that both anaerobic methane oxidation and methanogenesis occurred at this site. In addition, several functional genes connected with methane metabolism were analyzed by quantitative competitive-PCR, including the genes encoding particulate methane monooxygenase (pmoA), soluble methane monooxygenase (mmoX), methanol dehydrogenese (mxaF), and methyl coenzyme M reductase (mcrA). In the MC core sediments, the most abundant gene was mcrA (2.5 x 10(6) copies/g [wet weight]), while the pmoA gene of the type I methanotrophs (5.9 x 10(6) copies/g [wet weight]) was most abundant at the surface of the MC core. These results indicate that there is a very complex environment in which methane production, anaerobic methane oxidation, and aerobic methane oxidation all occur in close proximity. The HC carbonate site was rich in gamma-Proteobacteria and had a high copy number of mxaF (7.1 x 10(6) copies/g [wet weight]) and a much lower copy number of the pmoA gene (3.2 x 10(2) copies/g [wet weight]). The mmoX gene was never detected. In contrast, the reference core contained familiar sequences of marine sedimentary archaeal and bacterial groups but not groups specific to C1 metabolism. Geochemical characterization of the amounts and isotopic composition of pore water methane and sulfate strongly supported the notion that in this zone both aerobic methane oxidation and anaerobic methane oxidation, as well as methanogenesis, occur.

Alcohol Oxidoreductases↗
PubMed2004

Spatial distribution of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems.

Distribution profiles of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems were mapped with culture-independent molecular techniques. Planktonic samples were obtained from the waters surrounding two geographically and geologically distinct hydrothermal systems, and the abundance of marine crenarchaeota group I was examined by 16S ribosomal DNA clone analysis, quantitative PCR, and whole-cell fluorescence in situ hybridization. A much higher proportion of marine crenarchaeota group I within the microbial community was detected in deep-sea hydrothermal environments than in normal deep and surface seawaters. The highest proportion was always obtained from the ambient seawater adjacent to hydrothermal emissions and chimneys but not from the hydrothermal plumes. These profiles were markedly different from the profiles of epsilon-Proteobacteria, which are abundant in the low temperatures of deep-sea hydrothermal environments.

Base Sequence↗
PubMed2003

Distribution and phylogenetic diversity of the subsurface microbial community in a Japanese epithermal gold mine.

Distribution and phylogenetic diversity of microbial communities in hot, deep underground environments in the Hishikari epithermal gold mine, southern part of Kyushu, Japan, were evaluated using molecular phylogenetic analyses. Samples included drilled cores such as andesitic volcanic rock (0.95-1.78 Ma) and the oceanic sedimentary basement rock of Shimanto-Supergroup (100 Ma), as well as geothermal hot aquifer waters directly collected from two different sites: AW-site (71.5 degrees C, pH 6.19) and XW-site (85.0 degrees C, pH 6.80) at a depth of 350 mbls (meters below land surface). Based on PCR-amplified 16S rRNA gene clone analysis, the microbial communities in the drilled cores and the hot aquifer water from the XW-site consisted largely of the 16S rRNA gene sequences, closely related to the sequences often found in marine environments, while the aquifer water from the AW-site contained 16S rRNA gene sequences representing members of Aquificales, thermophilic methanotrophs within the gamma-subdivision of the Proteobacteria and uncultivated strains within the beta-subdivision of Proteobacteria. The cultivable microbial community detected by enrichment cultivation analysis largely matched that detected by the culture-independent molecular analysis.

Bacteria↗
PubMed2003

Isolation and phylogenetic diversity of members of previously uncultivated epsilon-Proteobacteria in deep-sea hydrothermal fields.

We report the successful cultivation and partial characterization of novel members of epsilon-Proteobacteria, which have long been recognized solely as genetic signatures of small subunit ribosomal RNA genes (rDNA) from a variety of habitats occurring in deep-sea hydrothermal fields. A newly designed microhabitat designated 'in situ colonization system' was used for enrichment. Based on phylogenetic analysis of the rDNA of the isolates, most of these represent the first cultivated members harboring previously uncultivated phylotypes classified into the Uncultivated epsilon-Proteobacteria Groups A, B, F and G, as well as some novel members of Group D. Preliminary characterization of the isolates indicates that all are mesophilic or thermophilic chemolithoautotrophs using H(2) or reduced sulfur compounds (elemental sulfur or thiosulfate) as an electron donor and O(2), nitrate or elemental sulfur as an electron acceptor. The successful cultivation will enable the subsequent characterization of physiological properties and ecological impacts of a diversity of epsilon-Proteobacteria in the deep-sea hydrothermal environments.

DNA, Bacterial↗