Parvibaculum hydrocarboniclasticum sp. nov., a mesophilic, alkane-oxidizing alphaproteobacterium isolated from a deep-sea hydrothermal vent on the East Pacific Rise

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 96 509 N 1046 179 W). The cells of the novel strain were Gram-staining-negative rods that measured approximately 1.4 mm in length and 0.4 mm in width. Strain EPR92T grew at 20-40 6C(optimum 35 6C), with1.0-5.0 % (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 v7c, C 19 : 0 cyclo v8c, 11-methyl C 18 : 1 v7c 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 (5DSM 232095JCM 16666 T ).At deep-sea hydrothermal vents, natural hydrocarbons are largely formed by the thermal decomposition of organic matter (thermogenesis) or by microbial processes such as the reduction of fatty acyl-CoA. However, hydrocarbons can have an abiotic origin and, in hydrothermal systems, may form by water-rock interactions such as FisherTropsch reactions and the serpentinization of ultramafic rocks (Berndt et al., 1996;McCollom et al., 1999). Despite the observation that hydrocarbons, including n-alkanes, are enriched in deep-sea hydrothermal vents (Brault et al., 1988), our knowledge of the taxonomic and functional diversity of alkane-oxidizing bacteria from these environments remains very limited. In this study, we describe a novel, aerobic, alkane-oxidizing member of the class Alphaproteobacteria that was isolated from hydrothermal fluids collected at a deep-sea vent on the East Pacific Rise.In April 2004, during the 'AT 11-10' cruise of the research vessel 'Atlantis', hydrothermal fluids at a temperature of 15 u C were collected at a depth of 2513 m from the Tica vent (9 u 509 N 104 u 179 W) on the East Pacific Rise. The fluids were collected using titanium samplers operated by 3Th...

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

“…Among these, 42 genera were significantly affected by willows at both contamination levels, and the 24 bacterial and fungal genera among those are listed in Supplementary Table S2. Among the genera consistently activated by willows at both contamination levels, some were previously reported as having interesting characteristics for phytoremediation, for instance, Methylibium petroleiphilum is involved in aromatic hydrocarbon and methyl tertbutyl ether degradation (Nakatsu et al, 2006), Mesorhizobium is a well-known genus involved in nitrogen fixation, some species are resistant to metals (Vidal et al, 2009;Huang et al, 2010) and can degrade acetonitrile (Feng and Lee, 2009), some Variovorax species display plant growth promoting activities and are able to degrade various contaminants (Han et al, 2011) and Parvibaculum species are able to degrade linear carbon chains, including alkanes (Schleheck et al, 2004;Rosario-Passapera et al, 2012). Some other genera showed contrasting responses to willows when exposed to different concentrations of contaminants (Supplementary Table S2).…”

Pyruvatibacter mobilis gen. nov., sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122

“…These major cellular fatty acids of strain GYP-11 T are similar to those of members of the genera Parvibaculum (Lai et al, 2011;Rosario-Passapera et al, 2012), Tepidicaulis (Takeuchi et al, 2015) and Parvularcula (Arun et al, 2009;Yu et al, 2013;Li et al, 2014). However, members of the genera Parvibaculum, Tepidicaulis and Parvularcula are characterized by cyclo C 19 : 0 v8c (12.1-35.8 %), C 18 : 1 v7c/v6c (87.3 %) and C 16 : 0 (10.0-24.1 %), respectively.…”

“…Growth of Parvibaculum lavamentivorans DS-1 T on MAP was observed, but was much slower than strain GYP-11 T . Finally, strain GYP-11 T could be distinguished from all members of the genus Parvibaculum (Lai et al, 2011;Rosario-Passapera et al, 2012) by its inability to utilize alkane. Other cultural, physiological and biochemical properties of strainGYP-11 T are listed in Table 1 and in the genus and species descriptions.…”

“…Stalked cells were also observed in Tepidicaulis Table 1. Differential phenotypic properties between strain GYP-11 T and some other related genera Taxa: 1, strain GYP-11 T ; 2, Parvibaculum (Schleheck et al, 2004;Lai et al, 2011;Rosario-Passapera et al, 2012); 3, Parvularcula (Cho & Giovannoni, 2003;Arun et al, 2009;Yu et al, 2013;Li et al, 2014); 4, Tepidicaulis (Takeuchi et al, 2015). +, Positive; 2, negative; V, variable between species; W, weakly positive; ND, no data available.…”

Biogeochemical insights into microbe–mineral–fluid interactions in hydrothermal chimneys using enrichment culture

“…Leptothrix phylotypes were already detected in Table 1 Geochemical composition, organic acid concentrations and pH measured in the medium during the culture time nd not determined, bd below the detection limit (bd is 10 µM for H 2 S) a The day when pH falls down to 3. Alphaproteobacteria were detected at the end in D21 and in the solid fraction collected at the end of the culture, including sequences closely related to the Parvibaculum sp., sharing 99 % of similarity with Parvibaculum indicum (strain P31T) (8 % of the total clones), a mesophilic strain isolated from deep seawater collected in the SouthWest Indian Ridge (Lai et al 2011) and 99 % with Parvibaculum hydrocarboniclasticum, a mesophilic strain isolated from hydrothermal fluid (Rosario-Passapera et al 2012). In previous enrichment cultures, it was shown that Parvibaculum lavamentivorans, formerly described as an aerobic strain, is able to grow autotrophically in anaerobic condition, oxidizing Fe(II) using nitrates as electron Fig.…”