Phylogenetic studies of newly isolated freshwater Magnetospirilla using cbb and mam genes

The phylogeny and general relatedness of prokaryotes is determined by comparisons of the sequences of rRNA genes, most commonly the 16S rRNA gene. Comparisons between other gene sequences have been used for this purpose and some have supported conclusions from 16S rRNA genes while others have not. In this study, 13 new magnetospirilla were phylogenetically characterized using the sequences of the 16S rRNA gene as well as the genes for forms I and II ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) (cbbL and cbbM, respectively) and for two magnetosome membrane proteins unique to magnetotactic bacteria, mamJ and mamK. Polymerase chain reaction (PCR) with degenerate primers designed for the specific genes under study was used to amplify a large portion of the genes. PCR products were cloned and sequenced and used for the construction of phylogenetic trees. Based on 16S rRNA gene sequences, the magnetospirilla phylogenetically span, more as a continuum rather than as clearly delineated groups, over two genera based on the current accepted sequence divergence between organisms for genera (\u3e5%). While almost all strains appear to fit into the genus Magnetospirillum, strain LM-1 appears to represent a new genus. Phylogeny of these strains based on cbbM sequences was reasonably consistent with that from 16S rRNA genes. The cbbL gene was not a good choice for this study as most strains did not possess this gene. Relatedness and phylogeny of the strains based on mamJ and mamK sequences was more complex. Although our data set is not complete, some specific strains shown to be closely related by 16S rRNA gene sequence, also appeared to be closely related based on one or both of the mam gene sequences (e.g., strains UT-1, LM-2 and M. gryphiswaldense strain MSR-1). Other strains did not show this type of relationship. Because of these somewhat inconsistent results, those from mam gene sequences might reflect evolution of the magnetosome gene island (MAI) in magnetospirilla rather than relatedness between strains

Novel magnetite-producing magnetotactic bacteria belonging to the \u3ci\u3eGammaproteobacteria\u3c/i\u3e

Two novel magnetotactic bacteria (MTB) were isolated from sediment and water collected from the Badwater Basin, Death Valley National Park and southeastern shore of the Salton Sea, respectively, and were designated as strains BW-2 and SS-5, respectively. Both organisms are rod-shaped, biomineralize magnetite, and are motile by means of flagella. The strains grow chemolithoautotrophically oxidizing thiosulfate and sulfide microaerobically as electron donors, with thiosulfate oxidized stoichiometrically to sulfate. They appear to utilize the Calvin–Benson–Bassham cycle for autotrophy based on ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) activity and the presence of partial sequences of RubisCO genes. Strains BW-2 and SS-5 biomineralize chains of octahedral magnetite crystals, although the crystals of SS-5 are elongated. Based on 16S rRNA gene sequences, both strains are phylogenetically affiliated with the Gammaproteobacteria class. Strain SS-5 belongs to the order Chromatiales; the cultured bacterium with the highest 16S rRNA gene sequence identity to SS-5 is Thiohalocapsa marina (93.0%). Strain BW-2 clearly belongs to the Thiotrichales; interestingly, the organism with the highest 16S rRNA gene sequence identity to this strain is Thiohalospira alkaliphila (90.2%), which belongs to the Chromatiales. Each strain represents a new genus. This is the first report of magnetite-producing MTB phylogenetically associated with the Gammaproteobacteria. This finding is important in that it significantly expands the phylogenetic diversity of the MTB. Physiology of these strains is similar to other MTB and continues to demonstrate their potential in nitrogen, iron, carbon and sulfur cycling in natural environments

Endothiovibrio diazotrophicus gen. nov., sp. nov., a novel nitrogen-fixing, sulfur-oxidizing gammaproteobacterium isolated from a salt marsh

International audienceA novel non-phototrophic, marine, sulfur-oxidizing bacterium, strain S-1T, was isolated from a coastal salt marsh in Massachusetts, USA. Cells are Gram-stain-negative vibrios motile by means of a single polar unsheathed flagellum. S-1T is an obligate microaerophile with limited metabolic capacity. It grows chemolithoautotrophically utilizing sulfide and thiosulfate as electron donors, converting these compounds to sulfate, and the Calvin–Benson–Bassham cycle for carbon fixation. Cells of S-1T did not grow on any of a large number of organic carbon sources and there was no evidence for chemoorganoheterotrophic growth. Cells produced internal sulfur globules during growth on sulfide and thiosulfate. S-1T is strongly diazotrophic, as demonstrated by 15N2 fixation and acetylene reduction activity by cells when a fixed nitrogen source is absent from the growth medium. The marine nature of this organism is evident from its ability to grow in 10 to 100 % artificial seawater but not at lower concentrations and NaCl alone cannot substitute for sea salts. The major cellular fatty acids are C16 : 1ω7c, C16 : 0, and C18 : 1ω7c. Phosphatidylethanolamine and phosphatidylglycerol are the major polar lipids. Q8 is the only respiratory quinone. S-1T genomic DNA has a G+C content of 67.6 mol%. Based on its 16S rRNA gene sequence, S-1T shows the closest phylogenetic relationship to non-phototrophic species within the family Thioalkalispiraceae of the class Gammaproteobacteria . The name Endothiovibrio diazotrophicus is proposed for this organism, with S-1T as the type strain (ATCC BAA-1439T=JCM 17961T)