@article {ISI:000356841900006,
	title = {{Cetia pacifica gen. nov., sp nov., a chemolithoautotrophic, thermophilic, nitrate-ammonifying bacterium from a deep-sea hydrothermal vent}},
	journal = {INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY},
	volume = {65},
	number = {4},
	year = {2015},
	month = {apr},
	pages = {1144{\textendash}1150},
	type = {Article},
	abstract = {A thermophilic, anaerobic, chemolithoautotrophic bacterium, strain TB-6(T), was isolated from a deep-sea hydrothermal vent located on the East Pacific Rise at 9 degrees N. The cells were Gram-staining-negative and rod-shaped with one or more polar flagella. Cell size was approximately 1-1.5 mu m in length and 0.5 mu m in width. Strain TB-6(T) grew between 45 and 70 degrees C (optimum 55-60 degrees C), 0 and 35 g NaCl l(-1) (optimum 20-30 gl(-1)) and pH 4.5 and 7.5 (optimum pH 5.5-6.0). Generation time under optimal conditions was 2 h. Growth of strain TB-6(T) occurred with H-2 as the energy source, CO2 as the carbon source and nitrate or sulfur as electron acceptors, with formation of ammonium or hydrogen sulfide, respectively. Acetate, (+)-n-glucose, Casamino acids, sucrose and yeast extract were not used as carbon and energy sources. Inhibition of growth occurred in the presence of lactate, peptone and tryptone under a H-2/CO2 (80 :20; 200 kPa) gas phase. Thiosulfate, sulfite, arsenate, selenate and oxygen were not used as electron acceptors. The G +C content of the genomic DNA was 36.8 molo/o. Phylogenetic analysis of the 16S rRNA gene of strain TB-6(T) showed that this organism branched separately from the three most closely related genera, Caminibacter, Nautilia and Lebetimonas, within the family Nautiliaceae. Strain TB-6(T) contained several unique fatty acids in comparison with other members of the family Nautiliaceae. Based on experimental evidence, it is proposed that the organism represents a novel species and genus within the family Nautiliaceae, Cetia pacifica, gen. nov., sp. nov. The type strain is TB-6(T) (=DSM 27783T=JCM 19563(T)).},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {1466-5026},
	doi = {10.1099/ijs.0.000070},
	author = {Grosche, Ashley and Sekaran, Hema and Perez-Rodriguez, Ileana and Starovoytov, Valentin and Vetriani, Costantino}
}
@article {ISI:000353354100014,
	title = {{From deep-sea volcanoes to human pathogens: a conserved quorum-sensing signal in Epsilonproteobacteria}},
	journal = {ISME Journal},
	volume = {9},
	number = {5},
	year = {2015},
	month = {may},
	pages = {1222{\textendash}1234},
	type = {Article},
	abstract = {Chemosynthetic Epsilonproteobacteria from deep-sea hydrothermal vents colonize substrates exposed to steep thermal and redox gradients. In many bacteria, substrate attachment, biofilm formation, expression of virulence genes and host colonization are partly controlled via a cell density-dependent mechanism involving signal molecules, known as quorum sensing. Within the Epsilonproteobacteria, quorum sensing has been investigated only in human pathogens that use the luxS/autoinducer-2 (AI-2) mechanism to control the expression of some of these functions. In this study we showed that luxS is conserved in Epsilonproteobacteria and that pathogenic and mesophilic members of this class inherited this gene from a thermophilic ancestor. Furthermore, we provide evidence that the luxS gene is expressed-and a quorum-sensing signal is produced-during growth of Sulfurovum lithotrophicum and Caminibacter mediatlanticus, two Epsilonproteobacteria from deep-sea hydrothermal vents. Finally, we detected luxS transcripts in Epsilonproteobacteria-dominated biofilm communities collected from deep-sea hydrothermal vents. Taken together, our findings indicate that the epsiloproteobacterial lineage of the LuxS enzyme originated in high-temperature geothermal environments and that, in vent Epsilonproteobacteria, luxS expression is linked to the production of AI-2 signals, which are likely produced in situ at deep-sea vents. We conclude that the luxS gene is part of the ancestral epsilonproteobacterial genome and represents an evolutionary link that connects thermophiles to human pathogens.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {1751-7362},
	doi = {10.1038/ismej.2014.214},
	author = {Perez-Rodriguez, Ileana and Bolognini, Marie and Ricci, Jessica and Bini, Elisabetta and Vetriani, Costantino}
}
@article {ISI:000338213900015,
	title = {{Deep-sea hydrothermal vent Epsilonproteobacteria encode a conserved and widespread nitrate reduction pathway (Nap)}},
	journal = {ISME JOURNAL},
	volume = {8},
	number = {7},
	year = {2014},
	month = {jul},
	pages = {1510{\textendash}1521},
	type = {Article},
	abstract = {Despite the frequent isolation of nitrate-respiring Epsilonproteobacteria from deep-sea hydrothermal vents, the genes coding for the nitrate reduction pathway in these organisms have not been investigated in depth. In this study we have shown that the gene cluster coding for the periplasmic nitrate reductase complex (nap) is highly conserved in chemolithoautotrophic, nitrate-reducing Epsilonproteobacteria from deep-sea hydrothermal vents. Furthermore, we have shown that the napA gene is expressed in pure cultures of vent Epsilonproteobacteria and it is highly conserved in microbial communities collected from deep-sea vents characterized by different temperature and redox regimes. The diversity of nitrate-reducing Epsilonproteobacteria was found to be higher in moderate temperature, diffuse flow vents than in high temperature black smokers or in low temperatures, substrate-associated communities. As NapA has a high affinity for nitrate compared with the membrane-bound enzyme, its occurrence in vent Epsilonproteobacteria may represent an adaptation of these organisms to the low nitrate concentrations typically found in vent fluids. Taken together, our findings indicate that nitrate reduction is widespread in vent Epsilonproteobacteria and provide insight on alternative energy metabolism in vent microorganisms. The occurrence of the nap cluster in vent, commensal and pathogenic Epsilonproteobacteria suggests that the ability of these bacteria to respire nitrate is important in habitats as different as the deep-sea vents and the human body.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {1751-7362},
	doi = {10.1038/ismej.2013.246},
	author = {Vetriani, Costantino and Voordeckers, James W and Crespo-Medina, Melitza and O{\textquoteright}Brien, Charles E and Giovannelli, Donato and Lutz, Richard A}
}
@article {ISI:000325986500008,
	title = {{Detection and phylogenetic analysis of the membrane-bound nitrate reductase (Nar) in pure cultures and microbial communities from deep-sea hydrothermal vents}},
	journal = {FEMS MICROBIOLOGY ECOLOGY},
	volume = {86},
	number = {2},
	year = {2013},
	month = {nov},
	pages = {256{\textendash}267},
	type = {Article},
	abstract = {Over the past few years the relevance of nitrate respiration in microorganisms from deep-sea hydrothermal vents has become evident. In this study, we surveyed the membrane-bound nitrate reductase (Nar) encoding gene in three different deep-sea vent microbial communities from the East Pacific Rise and the Mid-Atlantic Ridge. Additionally, we tested pure cultures of vent strains for their ability to reduce nitrate and for the presence of the NarG-encoding gene in their genomes. By using the narG gene as a diagnostic marker for nitrate-reducing bacteria, we showed that nitrate reductases related to Gammaproteobacteria of the genus Marinobacter were numerically prevalent in the clone libraries derived from a black smoker and a diffuse flow vent. In contrast, NarG sequences retrieved from a community of filamentous bacteria located about 50cm above a diffuse flow vent revealed the presence of a yet to be identified group of enzymes. 16S rRNA gene-inferred community compositions, in accordance with previous studies, showed a shift from Alpha- and Gammaproteobacteria to Epsilonproteobacteria as the vent fluids become warmer and more reducing. Based on these findings, we argue that Nar-catalyzed nitrate reduction is likely relevant in temperate and less reducing environments where Alpha- and Gammaproteobacteria are more abundant and where nitrate concentrations reflect that of background deep seawater.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0168-6496},
	doi = {10.1111/1574-6941.12158},
	author = {Perez-Rodriguez, Ileana and Bohnert, Kenneth A and Cuebas, Mariola and Keddis, Ramaydalis and Vetriani, Costantino}
}
@article {ISI:000315070000017,
	title = {{Parvibaculum hydrocarboniclasticum sp. nov., a mesophilic, alkane-oxidizing alphaproteobacterium isolated from a deep-sea hydrothermal vent on the East Pacific Rise}},
	journal = {INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY},
	volume = {62},
	number = {12},
	year = {2012},
	month = {dec},
	pages = {2921{\textendash}2926},
	type = {Article},
	abstract = {An aerobic, alkane-oxidizing bacterium, designated strain EPR92(T), was isolated from hydrothermal fluids that had been collected from a deep-sea vent on the East Pacific Rise (at 9 degrees 50{\textquoteright} N 104 degrees 17{\textquoteright} W). The cells of the novel strain were Gram-staining-negative rods that measured approximately 1.4 mu m in length and 0.4 mu m in width. Strain EPR92T grew at 20-40 degrees C (optimum 35 degrees C), with 1.0-5.0{\%} (w/v) NaCl (optimum 2.5{\%}), and at pH 4.0-8.5 (optimum pH 7.5). The generation time under optimal conditions was 63 min. Strain EPR92(T) grew aerobically in artificial seawater minimal medium with n-alkanes as sole carbon and energy sources, and also in artificial seawater medium supplemented with peptone and yeast extract. The predominant fatty acids were C-18:1 omega 7c, C-19:0 cyclo omega 8c, 11-methyl C-18:1 omega 7c and a putative C-12:0 aldehyde. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and four unidentified aminolipids. The major respiratory quinone was Q-10 and the genomic DNA G+C content was 60.7 mol{\%}. Phylogenetic analyses of the 16S rRNA gene showed that strain EPR92(T) belongs in the class Alphaproteobacteria and the recognized species that were most closely related to the novel strain were identified as Parvibaculum indicum P-31(T) (98.7{\%} sequence similarity) and Parvibaculum lavamentivorans DS-1(T) (95.8{\%}). In DNA-DNA hybridizations, the level of DNA-DNA relatedness observed between strain EPR92(T) and P. indicum P-31(T) was 47.7{\%}, indicating that the two strains do not belong to the same species. Based on the phylogenetic, physiological, chemotaxonomic and genetic evidence, strain EPR92(T) represents a novel species within the genus Parvibaculum, for which the name Parvibaculum hydrocarboniclasticum sp. nov. is proposed. The type strain is EPR92(T) (=DSM 23209=JCM 16666(T)).},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {1466-5026},
	doi = {10.1099/ijs.0.039594-0},
	author = {Rosario-Passapera, Richard and Keddis, Ramaydalis and Wong, Ronald and Lutz, Richard A and Staroyoytov, Valentin and Vetriani, Costantino}
}
@article {ISI:000311587800012,
	title = {{Phorcysia thermohydrogeniphila gen. nov., sp nov., a thermophilic, chemolithoautotrophic, nitrate-ammonifying bacterium from a deep-sea hydrothermal vent}},
	journal = {INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY},
	volume = {62},
	number = {10},
	year = {2012},
	month = {oct},
	pages = {2388{\textendash}2394},
	type = {Article},
	abstract = {A novel hyperthermophilic, anaerobic, chemolithoautotrophic bacterium, designated strain HB-8(T), was isolated from the tube of Alvinella pompejana tubeworms collected from the wall of an actively venting sulfide structure on the East Pacific Rise at 13 degrees N. The cells were Gram-negative rods, approximately 1.0-1.5 mu m long and 0.5 mu m wide. Strain HB-8(T) grew between 65 and 80 degrees C (optimum 75 degrees C), 15 and 35 g NaCl l(-1) (optimum 30 gl(-1)) and pH 4.5 and 8.5 (optimum pH 6.0). Generation time under optimal conditions was 26 min. Growth occurred under chemolithoautotrophic conditions with H-2 as the energy source and CO2 as the carbon source. Nitrate and sulfur were used as electron acceptors, with concomitant formation of ammonium or hydrogen sulfide, respectively. The presence of lactate, formate, acetate or tryptone in the culture medium inhibited growth. The G+C content of the genomic DNA was 47.8 mol{\%}. Phylogenetic analysis of the 16S rRNA gene and of the alpha subunit of the ATP citrate lyase of strain HB-8(T) indicated that this organism formed a novel lineage within the class Aquificae, equally distant from the type strains of the type species of the three genera that represent the family Desulfurobacteriaceae: Thermovibrio ruber ED11/3LLK8(T), Balnearium lithotrophicum 17S(T) and Desulfurobacterium thermolithotrophum BSA(T). The polar lipids of strain HB-8(T) differed substantially from those of other members of the Desulfurobacteriaceae, and this bacterium produced novel quinones. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, it is proposed that the organism represents a novel genus and species within the family Desulfurobacteriaceae, Phorcysia thermohydrogeniphila gen. nov., sp. nov. The type strain of Phorcysia thermohydrogeniphila is HB-8(T) (=DSM 24425(T) =JCM 17384(T)).},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {1466-5026},
	doi = {10.1099/ijs.0.035642-0},
	author = {Perez-Rodriguez, Ileana and Grosche, Ashley and Massenburg, Lynnicia and Starovoytov, Valentin and Lutz, Richard A and Vetriani, Costantino}
}
@article {ISI:000278233400031,
	title = {{Nautilia nitratireducens sp nov., a thermophilic, anaerobic, chemosynthetic, nitrate-ammonifying bacterium isolated from a deep-sea hydrothermal vent}},
	journal = {INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY},
	volume = {60},
	number = {5},
	year = {2010},
	month = {may},
	pages = {1182{\textendash}1186},
	type = {Article},
	abstract = {A thermophilic, anaerobic, chemosynthetic bacterium, designated strain MB-1(T), was isolated from the walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at 9 degrees 50{\textquoteright} N 10 degrees 17{\textquoteright} W. The cells were Gram-negative-staining rods, approximately 1-1.5 mu m long and 0.3-0.5 mu m wide. Strain MB-1(T) grew at 25-65 degrees C (optimum 55 degrees C), with 10-35 g NaCl l(-1) (optimum 20 g l(-1)) and at pH 4.5-8.5 (optimum pH 7.0). Generation time under optimal conditions was 45.6 min. Growth occurred under chemolithoautotrophic conditions with H(2) as the energy source and CO(2) as the carbon source. Nitrate was used as the electron acceptor, with resulting production of ammonium. Thiosulfate, sulfur and selenate were also used as electron acceptors. No growth was observed in the presence of lactate, peptone or tryptone. Chemo-organotrophic growth occurred in the presence of acetate, formate, Casamino acids, sucrose, galactose and yeast extract under a N(2)/CO(2) gas phase. The G+C content of the genomic DNA was 36.0 mol{\%}. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Nautilia profundicola AmH(T), Nautilia abyssi PH1209(T) and Nautilia lithotrophica 525(T) (95, 94 and 93{\%} sequence identity, respectively). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the genus Nautilia, Nautilia nitratireducens sp. nov. The type strain is MB-1(T) (=DSM 22087(T) =JCM 15746(T)).},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {1466-5026},
	doi = {10.1099/ijs.0.013904-0},
	author = {Perez-Rodriguez, Ileana and Ricci, Jessica and Voordeckers, James W and Starovoytov, Valentin and Vetriani, Costantino}
}
