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Shigeaki Harayama - One of the best experts on this subject based on the ideXlab platform.

  • molecular characterization of bacterial populations in petroleum contaminated groundwater discharged from underground crude oil storage cavities
    Applied and Environmental Microbiology, 2000
    Co-Authors: Kazuya Watanabe, Kazuaki Syutsubo, Yumiko Kodama, Kanako Watanabe, Shigeaki Harayama
    Abstract:

    Petroleum-contaminated groundwater discharged from underground crude oil storage cavities (cavity groundwater) harbored more than 106 microorganisms ml−1, a density 100 times higher than the densities in groundwater around the cavities (control groundwater). To characterize bacterial populations growing in the cavity groundwater, 46 PCR-amplified almost full-length 16S ribosomal DNA (rDNA) fragments were cloned and sequenced, and 28 different sequences were obtained. All of the sequences were affiliated with the Proteobacteria; 25 sequences (43 clones) were affiliated with the epsilon subclass, 2 were affiliated with the beta subclass, and 1 was affiliated with the delta subclass. Two major clusters (designated clusters 1 and 2) were found for the epsilon subclass proteobacterial clones; cluster 1 (25 clones) was most closely related to Thiomicrospira denitrificans (88% identical in nucleotide sequence), while cluster 2 (11 clones) was closely related to Arcobacterspp. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rDNA fragments showed that one band was detected most strongly in cavity groundwater profiles independent of storage oil type and season. The sequence of this major band was identical to the sequences of most of the cluster 1 clones. Fluorescence in situ hybridization (FISH) indicated that the cluster 1 population accounted for 12 to 24% of the total bacterial population. This phylotype was not detected in the control groundwater by DGGE and FISH analyses. These results indicate that the novel members of the epsilon subclass of the Proteobacteria grow as major populations in the petroleum-contaminated cavity groundwater.

  • molecular characterization of bacterial populations in petroleum contaminated groundwater discharged from underground crude oil storage cavities
    Applied and Environmental Microbiology, 2000
    Co-Authors: Kazuya Watanabe, Kazuaki Syutsubo, Yumiko Kodama, Kanako Watanabe, Shigeaki Harayama
    Abstract:

    water) harbored more than 10 6 microorganisms ml 21 , a density 100 times higher than the densities in groundwater around the cavities (control groundwater). To characterize bacterial populations growing in the cavity groundwater, 46 PCR-amplified almost full-length 16S ribosomal DNA (rDNA) fragments were cloned and sequenced, and 28 different sequences were obtained. All of the sequences were affiliated with the Proteobacteria; 25 sequences (43 clones) were affiliated with the epsilon subclass, 2 were affiliated with the beta subclass, and 1 was affiliated with the delta subclass. Two major clusters (designated clusters 1 and 2) were found for the epsilon subclass proteobacterial clones; cluster 1 (25 clones) was most closely related to Thiomicrospira denitrificans (88% identical in nucleotide sequence), while cluster 2 (11 clones) was closely related to Arcobacter spp. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rDNA fragments showed that one band was detected most strongly in cavity groundwater profiles independent of storage oil type and season. The sequence of this major band was identical to the sequences of most of the cluster 1 clones. Fluorescence in situ hybridization (FISH) indicated that the cluster 1 population accounted for 12 to 24% of the total bacterial population. This phylotype was not detected in the control groundwater by DGGE and FISH analyses. These results indicate that the novel members of the epsilon subclass of the Proteobacteria grow as major populations in the petroleum-contaminated cavity groundwater. Underground cavities have been used for long-term storage of crude oil in several countries, such as Japan, Korea, and Norway, and are constructed in groundwater-rich rocky strata where high groundwater pressure confines the stored oil in the cavities (Fig. 1). Consequently, groundwater migrates into and accumulates at the bottom of a cavity (cavity groundwater), and this cavity groundwater is discharged to maintain the oil storage capacity of the cavity. The discharged groundwater, which is contaminated with petroleum hydrocarbons, is then purified by using water clarifiers before release into the sea. Some of the purified water is also injected back into the rock surrounding the cavity to maintain the groundwater pressure. This flow of groundwater may establish a continuous culture in which microorganisms grow on petroleum hydrocarbons. The habitat in the cavity groundwater can be characterized by (i) immediate contact with a large quantity of crude oil and (ii) an excess of electron donors (i.e., hydrocarbons) but a shortage of

Kazuya Watanabe - One of the best experts on this subject based on the ideXlab platform.

  • molecular characterization of bacterial populations in petroleum contaminated groundwater discharged from underground crude oil storage cavities
    Applied and Environmental Microbiology, 2000
    Co-Authors: Kazuya Watanabe, Kazuaki Syutsubo, Yumiko Kodama, Kanako Watanabe, Shigeaki Harayama
    Abstract:

    Petroleum-contaminated groundwater discharged from underground crude oil storage cavities (cavity groundwater) harbored more than 106 microorganisms ml−1, a density 100 times higher than the densities in groundwater around the cavities (control groundwater). To characterize bacterial populations growing in the cavity groundwater, 46 PCR-amplified almost full-length 16S ribosomal DNA (rDNA) fragments were cloned and sequenced, and 28 different sequences were obtained. All of the sequences were affiliated with the Proteobacteria; 25 sequences (43 clones) were affiliated with the epsilon subclass, 2 were affiliated with the beta subclass, and 1 was affiliated with the delta subclass. Two major clusters (designated clusters 1 and 2) were found for the epsilon subclass proteobacterial clones; cluster 1 (25 clones) was most closely related to Thiomicrospira denitrificans (88% identical in nucleotide sequence), while cluster 2 (11 clones) was closely related to Arcobacterspp. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rDNA fragments showed that one band was detected most strongly in cavity groundwater profiles independent of storage oil type and season. The sequence of this major band was identical to the sequences of most of the cluster 1 clones. Fluorescence in situ hybridization (FISH) indicated that the cluster 1 population accounted for 12 to 24% of the total bacterial population. This phylotype was not detected in the control groundwater by DGGE and FISH analyses. These results indicate that the novel members of the epsilon subclass of the Proteobacteria grow as major populations in the petroleum-contaminated cavity groundwater.

  • molecular characterization of bacterial populations in petroleum contaminated groundwater discharged from underground crude oil storage cavities
    Applied and Environmental Microbiology, 2000
    Co-Authors: Kazuya Watanabe, Kazuaki Syutsubo, Yumiko Kodama, Kanako Watanabe, Shigeaki Harayama
    Abstract:

    water) harbored more than 10 6 microorganisms ml 21 , a density 100 times higher than the densities in groundwater around the cavities (control groundwater). To characterize bacterial populations growing in the cavity groundwater, 46 PCR-amplified almost full-length 16S ribosomal DNA (rDNA) fragments were cloned and sequenced, and 28 different sequences were obtained. All of the sequences were affiliated with the Proteobacteria; 25 sequences (43 clones) were affiliated with the epsilon subclass, 2 were affiliated with the beta subclass, and 1 was affiliated with the delta subclass. Two major clusters (designated clusters 1 and 2) were found for the epsilon subclass proteobacterial clones; cluster 1 (25 clones) was most closely related to Thiomicrospira denitrificans (88% identical in nucleotide sequence), while cluster 2 (11 clones) was closely related to Arcobacter spp. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rDNA fragments showed that one band was detected most strongly in cavity groundwater profiles independent of storage oil type and season. The sequence of this major band was identical to the sequences of most of the cluster 1 clones. Fluorescence in situ hybridization (FISH) indicated that the cluster 1 population accounted for 12 to 24% of the total bacterial population. This phylotype was not detected in the control groundwater by DGGE and FISH analyses. These results indicate that the novel members of the epsilon subclass of the Proteobacteria grow as major populations in the petroleum-contaminated cavity groundwater. Underground cavities have been used for long-term storage of crude oil in several countries, such as Japan, Korea, and Norway, and are constructed in groundwater-rich rocky strata where high groundwater pressure confines the stored oil in the cavities (Fig. 1). Consequently, groundwater migrates into and accumulates at the bottom of a cavity (cavity groundwater), and this cavity groundwater is discharged to maintain the oil storage capacity of the cavity. The discharged groundwater, which is contaminated with petroleum hydrocarbons, is then purified by using water clarifiers before release into the sea. Some of the purified water is also injected back into the rock surrounding the cavity to maintain the groundwater pressure. This flow of groundwater may establish a continuous culture in which microorganisms grow on petroleum hydrocarbons. The habitat in the cavity groundwater can be characterized by (i) immediate contact with a large quantity of crude oil and (ii) an excess of electron donors (i.e., hydrocarbons) but a shortage of

Koki Horikoshi - One of the best experts on this subject based on the ideXlab platform.

  • distribution phylogenetic diversity and physiological characteristics of epsilon proteobacteria in a deep sea hydrothermal field
    Environmental Microbiology, 2005
    Co-Authors: Satoshi Nakagawa, Takuro Nunoura, Fumio Inagaki, Hisako Hirayama, Koki Horikoshi, Yoshihiko Sako
    Abstract:

    Summary 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.

  • novel chemoautotrophic endosymbiosis between a member of the epsilonproteobacteria and the hydrothermal vent gastropod alviniconcha aff hessleri gastropoda provannidae from the indian ocean
    Applied and Environmental Microbiology, 2005
    Co-Authors: Yohey Suzuki, Takenori Sasaki, Masae Suzuki, Yuichi Nogi, Tetsuya Miwa, Ken Takai, Kenneth H Nealson, Koki Horikoshi
    Abstract:

    ABSTRACT 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 13C enriched relative to the gastropod biomass and that the monounsaturated C16 fatty acid that originates from the endosymbiont is as 13C 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 13C-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.

  • hydrogenimonas thermophila gen nov sp nov a novel thermophilic hydrogen oxidizing chemolithoautotroph within the e proteobacteria isolated from a black smoker in a central indian ridge hydrothermal field
    International Journal of Systematic and Evolutionary Microbiology, 2004
    Co-Authors: Ken Takai, Kenneth H Nealson, Koki Horikoshi
    Abstract:

    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.

  • Molecular phylogenetic analyses of reverse-transcribed bacterial rRNA obtained from deep-sea cold seep sediments.
    Environmental microbiology, 2002
    Co-Authors: Fumio Inagaki, Chiaki Kato, Yuri Sakihama, Akira Inoue, Koki Horikoshi
    Abstract:

    A depth profile of naturally occurring bacterial community structures associated with the deep-sea cold seep push-core sediment in the Japan Trench at a depth of 5343 m were evaluated using molecular phylogenetic analyses of RNA reverse transcription-PCR (RT-PCR) amplified 16S crDNA fragments. A total of 137 clones of bacterial crDNA (complimentary rDNA) phylotypes (phylogenetic types) obtained at three different depths (2-4, 8-10 and 14-16 cm) were identified in partial crDNA sequencings. crDNA phylotypes from the cold seep sediment were dominantly composed of delta- and Epsilon-Proteobacteria (36% and 42% respectively). Phylotype analysis of crDNA clone libraries and terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that the majority of bacterial components shifted from delta- Proteobacteria to Epsilon-Proteobacteria with increasing depth. Among the delta-proteobacterial crDNA clones, the sequences related to the genus Desulfosarcina were dominant. Almost all sequences of crDNA belonging to Epsilon-Proteobacteria were affiliated with the same cluster (epsilon-CSG: Epsilon-Proteobacterial cold seep group), and were closely related with rDNA sequences from deep-sea hydrothermal vent environments.

Guilin Wang - One of the best experts on this subject based on the ideXlab platform.

  • the complete genome sequence and analysis of the epsilonproteobacterium arcobacter butzleri
    PLOS ONE, 2007
    Co-Authors: Craig T Parker, Marc Rubenfield, George L Mendz, Marc M S M Wosten, David W Ussery, John F Stolz, Tim T Binnewies, Peter Fischer Hallin, Guilin Wang
    Abstract:

    Background Arcobacter butzleri is a member of the epsilon subdivision of the Proteobacteria and a close taxonomic relative of established pathogens, such as Campylobacter jejuni and Helicobacter pylori. Here we present the complete genome sequence of the human clinical isolate, A. butzleri strain RM4018. Methodology/Principal Findings Arcobacter butzleri is a member of the Campylobacteraceae, but the majority of its proteome is most similar to those of Sulfuromonas denitrificans and Wolinella succinogenes, both members of the Helicobacteraceae, and those of the deep-sea vent Epsilonproteobacteria Sulfurovum and Nitratiruptor. In addition, many of the genes and pathways described here, e.g. those involved in signal transduction and sulfur metabolism, have been identified previously within the epsilon subdivision only in S. denitrificans, W. succinogenes, Sulfurovum, and/or Nitratiruptor, or are unique to the subdivision. In addition, the analyses indicated also that a substantial proportion of the A. butzleri genome is devoted to growth and survival under diverse environmental conditions, with a large number of respiration-associated proteins, signal transduction and chemotaxis proteins and proteins involved in DNA repair and adaptation. To investigate the genomic diversity of A. butzleri strains, we constructed an A. butzleri DNA microarray comprising 2238 genes from strain RM4018. Comparative genomic indexing analysis of 12 additional A. butzleri strains identified both the core genes of A. butzleri and intraspecies hypervariable regions, where <70% of the genes were present in at least two strains. Conclusion/Significance The presence of pathways and loci associated often with non-host-associated organisms, as well as genes associated with virulence, suggests that A. butzleri is a free-living, water-borne organism that might be classified rightfully as an emerging pathogen. The genome sequence and analyses presented in this study are an important first step in understanding the physiology and genetics of this organism, which constitutes a bridge between the environment and mammalian hosts.

  • the complete genome sequence and analysis of the epsilonproteobacterium arcobacter butzleri
    PLOS ONE, 2007
    Co-Authors: Craig T Parker, Marc Rubenfield, George L Mendz, Marc M S M Wosten, David W Ussery, John F Stolz, Tim T Binnewies, Peter Fischer Hallin, Guilin Wang
    Abstract:

    Background Arcobacter butzleri is a member of the epsilon subdivision of the Proteobacteria and a close taxonomic relative of established pathogens, such as Campylobacter jejuni and Helicobacter pylori. Here we present the complete genome sequence of the human clinical isolate, A. butzleri strain RM4018.

Kazuaki Syutsubo - One of the best experts on this subject based on the ideXlab platform.

  • molecular characterization of bacterial populations in petroleum contaminated groundwater discharged from underground crude oil storage cavities
    Applied and Environmental Microbiology, 2000
    Co-Authors: Kazuya Watanabe, Kazuaki Syutsubo, Yumiko Kodama, Kanako Watanabe, Shigeaki Harayama
    Abstract:

    Petroleum-contaminated groundwater discharged from underground crude oil storage cavities (cavity groundwater) harbored more than 106 microorganisms ml−1, a density 100 times higher than the densities in groundwater around the cavities (control groundwater). To characterize bacterial populations growing in the cavity groundwater, 46 PCR-amplified almost full-length 16S ribosomal DNA (rDNA) fragments were cloned and sequenced, and 28 different sequences were obtained. All of the sequences were affiliated with the Proteobacteria; 25 sequences (43 clones) were affiliated with the epsilon subclass, 2 were affiliated with the beta subclass, and 1 was affiliated with the delta subclass. Two major clusters (designated clusters 1 and 2) were found for the epsilon subclass proteobacterial clones; cluster 1 (25 clones) was most closely related to Thiomicrospira denitrificans (88% identical in nucleotide sequence), while cluster 2 (11 clones) was closely related to Arcobacterspp. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rDNA fragments showed that one band was detected most strongly in cavity groundwater profiles independent of storage oil type and season. The sequence of this major band was identical to the sequences of most of the cluster 1 clones. Fluorescence in situ hybridization (FISH) indicated that the cluster 1 population accounted for 12 to 24% of the total bacterial population. This phylotype was not detected in the control groundwater by DGGE and FISH analyses. These results indicate that the novel members of the epsilon subclass of the Proteobacteria grow as major populations in the petroleum-contaminated cavity groundwater.

  • molecular characterization of bacterial populations in petroleum contaminated groundwater discharged from underground crude oil storage cavities
    Applied and Environmental Microbiology, 2000
    Co-Authors: Kazuya Watanabe, Kazuaki Syutsubo, Yumiko Kodama, Kanako Watanabe, Shigeaki Harayama
    Abstract:

    water) harbored more than 10 6 microorganisms ml 21 , a density 100 times higher than the densities in groundwater around the cavities (control groundwater). To characterize bacterial populations growing in the cavity groundwater, 46 PCR-amplified almost full-length 16S ribosomal DNA (rDNA) fragments were cloned and sequenced, and 28 different sequences were obtained. All of the sequences were affiliated with the Proteobacteria; 25 sequences (43 clones) were affiliated with the epsilon subclass, 2 were affiliated with the beta subclass, and 1 was affiliated with the delta subclass. Two major clusters (designated clusters 1 and 2) were found for the epsilon subclass proteobacterial clones; cluster 1 (25 clones) was most closely related to Thiomicrospira denitrificans (88% identical in nucleotide sequence), while cluster 2 (11 clones) was closely related to Arcobacter spp. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rDNA fragments showed that one band was detected most strongly in cavity groundwater profiles independent of storage oil type and season. The sequence of this major band was identical to the sequences of most of the cluster 1 clones. Fluorescence in situ hybridization (FISH) indicated that the cluster 1 population accounted for 12 to 24% of the total bacterial population. This phylotype was not detected in the control groundwater by DGGE and FISH analyses. These results indicate that the novel members of the epsilon subclass of the Proteobacteria grow as major populations in the petroleum-contaminated cavity groundwater. Underground cavities have been used for long-term storage of crude oil in several countries, such as Japan, Korea, and Norway, and are constructed in groundwater-rich rocky strata where high groundwater pressure confines the stored oil in the cavities (Fig. 1). Consequently, groundwater migrates into and accumulates at the bottom of a cavity (cavity groundwater), and this cavity groundwater is discharged to maintain the oil storage capacity of the cavity. The discharged groundwater, which is contaminated with petroleum hydrocarbons, is then purified by using water clarifiers before release into the sea. Some of the purified water is also injected back into the rock surrounding the cavity to maintain the groundwater pressure. This flow of groundwater may establish a continuous culture in which microorganisms grow on petroleum hydrocarbons. The habitat in the cavity groundwater can be characterized by (i) immediate contact with a large quantity of crude oil and (ii) an excess of electron donors (i.e., hydrocarbons) but a shortage of