Magnetospirillum sulfuroxidans sp. nov., capable of sulfur-dependent lithoautotrophy and a taxonomic reevaluation of the order Rhodospirillales.

A spiral-shaped, highly motile bacterium was isolated from freshwater sulfidic sediment. Strain J10T is a facultative autotroph utilizing sulfide, thiosulfate, and sulfur as the electron donors in microoxic conditions. Despite high 16S rRNA gene sequence sequence identity to Magnetospirillum gryphiswaldense MSR-1 T (99.6 %), digital DNA-DNA hybridisation homology and average nucleotide identity between the two strains was of the different species level (25 % and 83 %, respectively). Strain J10T is not magnetotactic. The DNA G + C content of strain J10T is 61.9 %. The predominant phospholipid ester-linked fatty acids are C18:1ω7, C16:1ω7, and C16:0. Strain J10T (=DSM 23205 T = VKM B-3486 T) is the first strain of the genus Magnetospirillum showing lithoautotrophic growth and is proposed here as a novel species, Magnetospirillum sulfuroxidans sp. nov. In addition, we propose to establish a framework for distinguishing genera and families within the order Rhodospirillales based on phylogenomic analysis using the threshold values for average amino acid identity at Ì´ 72 % for genera and Ì´ 60 % for families. According to this, we propose to divide the existing genus Magnetospirillum into three genera: Magnetospirillum, Paramagnetospirillum, and Phaeospirillum, constituting a separate family Magnetospirillaceae fam. nov. in the order Rhodospirillales. Furthermore, phylogenomic data suggest that this order should accomodate six more new family level groups including Magnetospiraceae fam. nov., Magnetovibrionaceae fam. nov., Dongiaceae fam. nov., Niveispirillaceae fam. nov., Fodinicurvataceae fam. nov., and Oceanibaculaceae fam. nov.

Vineibacter terrae gen. nov., sp. nov., an ammonium-assimilating and nitrate-reducing bacterium isolated from vineyard soil.

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT640T, isolated from vineyard soil sampled in Taiwan. Cells of strain CC-CFT640T were aerobic, non-motile, nitrate-reducing rods. Test results were positive for catalase, oxidase and proteinase activities. Optimal growth occurred at 30 °Ð¡ and pH 7. Strain CC-CFT640T showed highest 16S rRNA gene sequence similarity to members of the genus Enhydrobacter (90.0 %, n=1) followed by Hypericibacter (89.4-90.0 %, n=2), Reyranella (88.8-89.8 %, n=5) and Nitrospirillum (89.2-89.4 %, n=2), and formed a distinct phyletic lineage distantly associated with the clade that predominately accommodated Reynerella species. The DNA G+C composition of the genome (2.1 Mb) was 67.9 mol%. Genes involved in the reduction of nitrate to nitrite, nitric oxide and nitrous oxide were found. In addition, genes encoding dissimilatory nitrate reduction to ammonia, ammonium transport and ammonium assimilation were also detected. Average nucleotide identity values were 73.3 % (n=1), 74.0-74.6 % (n=2), 67.5-68.3 % (n=2) when compared within the type strains of the genera Enhydrobacter, Reyranella and Niveispirillum, respectively. The dominant cellular fatty acids (>5 %) included C16 : 0, iso-C17 : 1 ω10c, C19 : 0 cyclo ω8c, C18 : 1 2-OH and C18 : 1 ω7c/C18 : 1 ω6c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, three unidentified phospholipids and an unidentified aminophospholipid. The major respiratory quinone was ubiquinone 10 and the major polyamine was spermidine. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequencing, digital DNA-DNA hybridization, average nucleotide identity and phylogenomic placement, strain CC-CFT640T is considered to represent a novel genus and species of the family Rhodospirillaceae, for which the name Vineibacter terrae gen. nov., sp. nov. is proposed. The type strain is CC-CFT640T (=BCRC 81219T=JCM 33507T).

Pacificispira spongiicola gen. nov., sp. nov., a nitrate-reducing bacterium isolated from tropical western Pacific.

The Gram-stain-negative, strictly aerobic, curved-to-spiral rod-shaped bacterial strain, designated KN72T, was isolated from the Caroline Seamounts in the Pacific Ocean. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain KN72T was a member of the family Rhodospirillaceae and formed a distinct lineage. Strain KN72T contained ubiquinone-10 as the major respiratory quinone. The polar lipid profiles contained phosphatidylethanolamine, phosphatidylglycerol, one aminolipid and three phospholipids. The predominant cellular fatty acids were C16:0 and summed feature 8 (comprising C18:1ω7c/C18:1ω6c). The strain KN72T displayed highest 16S rRNA gene sequence similarities with Hwanghaeella grinnelliae Gri0909T (92.3%), Marivibrio halodurans ZB80T (91.0%) and Aestuariispira insulae AH-MY2T (90.1%). The DNA G+C content of strain KN72T was 61.1%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence presented, strain KN72T represents a novel species of a novel genus of the family Rhodospirillaceae, for which the name Pacificispira spongiicola gen. nov., sp. nov. is proposed. The type strain is KN72T (= CGMCC 1.17142T = KCTC 72429T).

Oleiliquidispirillum nitrogeniifigens gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from oil reservoir water.

A novel Gram-staining-negative, spiral-shaped bacterium, designated strain 64-1T, was isolated from oil reservoir water collected from Liaohe oilfield, north-eastern China. Growth occurred at 15-55 °C and pH 6.0-10.0. The sole respiratory quinone was Q-10. The predominant cellular fatty acids were summed feature 8 (C18 : 1 ω7c /C18 : 1 ω6c), C16 : 0 and C19 : 0 cyclo ω8c. The polar lipids consisted of phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), an unidentified aminophospholipid (UAPL), an unidentified aminolipid (UAL) and two unidentified polar lipids (UPL). The genomic DNA G+C content of strain 64-1T was 64.5 mol%. Strain 64-1T shared the highest 16S rRNA gene sequence similarities with Phaeospirillum chandramohanii JA145T (92.0 %) and Telmatospirillum siberiense 26-4b1T (91.8 %). In the phylogenetic trees, the strain constituted a sub-cluster within the family Rhodospirillaceae. Based on the results of morphological, physiological, biochemical and phylogenetic analysis, strain 64-1T represents a new species of a novel genus within the family Rhodospirillaceae, for which the name Oleiliquidispirillum nitrogeniifigens gen. nov., sp. nov. is proposed. The type strain is 64-1T (=CGMCC 1.16798T=LMG 31399T).

Hypericibacter terrae gen. nov., sp. nov. and Hypericibacter adhaerens sp. nov., two new members of the family Rhodospirillaceae isolated from the rhizosphere of Hypericum perforatum.

Two strains of the family Rhodospirillaceae were isolated from the rhizosphere of the medicinal plant Hypericum perforatum. Cells of both strains were Gram-stain-negative, motile by means of a single polar flagellum, non-spore-forming, non-capsulated, short rods that divided by binary fission. Colonies were small and white. Strains R5913T and R5959T were oxidase-positive, mesophilic, neutrophilic and grew optimally without NaCl. Both grew under aerobic and microaerophilic conditions and on a limited range of substrates with best results on yeast extract. Major fatty acids were C19 : 0 cyclo ω8c and C16 : 0; in addition, C18 : 1ω7c was also found as a predominant fatty acid in strain R5913T. The major respiratory quinone was ubiquinone 10 (Q-10). The DNA G+C contents of strains R5913T and R5959T were 66.0 and 67.4 mol%, respectively. 16S rRNA gene sequence comparison revealed that the closest relatives (<92 % similarity) of the strains are Oceanibaculum pacificum MCCC 1A02656T, Dongia mobilis CGMCC 1.7660T, Dongia soli D78T and Dongia rigui 04SU4-PT. The two novel strains shared 98.6 % sequence similarity and represent different species on the basis of low average nucleotide identity of their genomes (83.8 %). Based on the combined phenotypic, genomic and phylogenetic investigations, the two strains represent two novel species of a new genus in the family Rhodospirillaceae, for which the name Hypericibacter gen. nov. is proposed, comprising the type species Hypericibacter terrae sp. nov. (type strain R5913T=DSM 109816T=CECT 9472T) and Hypericibacter adhaerens sp. nov. (type strain R5959T=DSM 109817T=CECT 9620T).

Promising prospects of nanopore sequencing for algal hologenomics and structural variation discovery.

BACKGROUND: The MinION Access Program (MAP, 2014-2016) allowed selected users to test the prospects of long nanopore reads for diverse organisms and applications through the rapid development of improving chemistries. In 2014, faced with a fragmented Illumina assembly for the chloroplast genome of the green algal holobiont Caulerpa ashmeadii, we applied to the MAP to test the prospects of nanopore reads to investigate such intricacies, as well as further explore the hologenome of this species with native and hybrid approaches. RESULTS: The chloroplast genome could only be resolved as a circular molecule in nanopore assemblies, which also revealed structural variants (i.e. chloroplast polymorphism or heteroplasmy). Signal and Illumina polishing of nanopore-assembled organelle genomes (chloroplast and mitochondrion) reflected the importance of coverage on final quality and current limitations. In hybrid assembly, our modest nanopore data sets showed encouraging results to improve assembly length, contiguity, repeat content, and binning of the larger nuclear and bacterial genomes. Profiling of the holobiont with nanopore or Illumina data unveiled a dominant Rhodospirillaceae (Alphaproteobacteria) species among six putative endosymbionts. While very fragmented, the cumulative hybrid assembly length of C. ashmeadii's nuclear genome reached 24.4 Mbp, including 2.1 Mbp in repeat, ranging closely with GenomeScope's estimate (> 26.3 Mbp, including 4.8 Mbp in repeat). CONCLUSION: Our findings relying on a very modest number of nanopore R9 reads as compared to current output with newer chemistries demonstrate the promising prospects of the technology for the assembly and profiling of an algal hologenome and resolution of structural variation. The discovery of polymorphic 'chlorotypes' in C. ashmeadii, most likely mediated by homing endonucleases and/or retrohoming by reverse transcriptases, represents the first report of chloroplast heteroplasmy in the siphonous green algae. Improving contiguity of C. ashmeadii's nuclear and bacterial genomes will require deeper nanopore sequencing to greatly increase the coverage of these larger genomic compartments.

Hwanghaeella grinnelliae gen. nov., sp. nov., isolated from a marine red alga.

A Gram-stain-negative, strictly aerobic and moderately halophilic bacterium, designated strain Gri0909T, was isolated from a red marine alga, Grinnellia species, in the Yellow Sea of the Republic of Korea. Cells were motile by a single polar flagellum and short-rods showing oxidase and catalase activities. Growth was observed at 10-37 °C (optimum, 30 °C) and pH 6.0-9.0 (optimum, pH 8.0) and in the presence of 0-12.0 % (w/v) NaCl (optimum, 2.0-3.0 %). Strain Gri0909T contained C16 : 0, C18 : 1 2-OH, anteiso-C15 : 0 and summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c) as major fatty acids. Ubiquinone-10 was identified as the sole isoprenoid quinone. Major polar lipids consisted of phosphatidylethanolamine, an identified phospholipid, four unidentified aminolipids and five unidentified lipids. The G+C content of the genomic DNA calculated from the whole-genome sequence was 59.1 mol%. Strain Gri0909T was most closely related to Marivibriohalodurans ZC80T with 91.4 % 16S rRNA gene sequence similarity. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Gri0909T formed a phyletic lineage within the family Rhodospirillaceae. The very low 16S rRNA gene sequence similarities, together with distinct phenotypic and chemotaxonomic properties, served to differentiate strain Gri0909T from phylogenetically closely related genera. Here it is proposed that strain Gri0909T represents a new species of a novel genus of the family Rhodospirillaceae, for which the name Hwanghaeella grinnelliae gen. nov., sp. nov. is proposed. The type strain is Gri0909T (=KACC 19793T=JCM 32943T).

Current phylogeny of Rhodospirillaceae: A multi-approach study.

Rhodospirillaceae represents a major family of the class alphaproteobacteria that includes an increasing number of functionally diverse taxa. The aim of this work is to evaluate the present phylogenetic diversity of the Rhodospirillaceae, which includes several metagenome-assembled genomes of uncultivated bacteria, as well as cultivated bacteria that were previously classified in different families. Various methodological approaches have been followed to discern the phylogenetic diversity of the taxa associated with the Rhodospirillaceae, which are grouped in three major sub-divisions and several other taxonomic entities that are currently confined to the genus rank. These genera include Tistrella, Elstera, Dongia and Ferrovibrio among cultivated organisms and alphaproteobacteria bacterium 41-28 among uncultivated bacteria. Overall, this study adds at least 11 genera and over 40 species to the current set of taxa belonging to the Rhodospirillaceae, a taxonomic term that clearly requires amendment. We propose to re-classify all taxa associated with the Rhodospirillaceae family under the new order, Diaforabacterales ord. nov. (from the Greek word for diversity, διάφορα). This study also uncovers the likely root of Rhodospirillaceae among recently reported metagenome-assembled genomes of uncultivated marine and groundwater bacteria.

Ferruginivarius sediminum gen. nov., sp. nov., isolated from a marine solar saltern.

A novel Gram-stain-negative, facultatively anaerobic, oxidase-negative, catalase-positive bacillus, designated WD2A32T, was isolated from a marine solar saltern in the coast of Weihai, Shandong Province, PR China. Strain WD2A32T grew optimally at 37-40 °C (range, 20-45 °C) and pH 7.0-7.5 (range, 6.5-8.0) and was tolerant to 6-8 % (w/v) NaCl (range, 2-12 %). The 16S rDNA of strain WD2A32T was most similar (93.5 %) to that of Rhodovibrio salinarumDSM 9154T (the type species of the genus Rhodovibrio), followed by Limimonas halophilaDSM 25584T (92.4 %; the type species of the genus Limimonas). The similarities to the type strains of the genera Pelagibiusand Limibacilluswere less than 91.0 %. The draft genome sequence of strain WD2A32T contained 72 contigs (>507 bp) of 4 237 996 bp with a DNA G+C content of 65.5 mol%. The major polar lipids of strain WD2A32T were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and unidentified aminolipids; major cellular fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) and C19 : 0 cyclo ω8c; the major respiratory quinone was Q-10. On the basis of the results from chemotaxonomic, physiological and biochemical analyses, strain WD2A32T represents a novel species of a novel genus in the family Rhodospirillaceae, for which the name Ferruginivarius sediminum gen. nov., sp. nov. has been proposed. The type strain is WD2A32T (=KCTC 52888T=MCCC 1H00201T).

Azospirillum palustre sp. nov., a methylotrophic nitrogen-fixing species isolated from raised bog.

Nitrogen-fixing bacterial strain, designated B2T, was isolated from methane-oxidation enrichment originating from a Sphagnum-dominated raised peatland in Tver region, Russia, and its phenotypic, chemotaxonomic and genomic characteristics were investigated. Cells of isolate were Gram-negative, aerobic, rod or spiral-shaped, with motility provided by a single polar flagellum in liquid media and peritrichous flagella on solid media. Strain was able to grow at 15-40 °C, pH 5.5-8.5 and tolerated NaCl to 2.0 % (w/v). Strain B2T gave positive amplification for dinitrogen reductase (nifH gene) and acetylene reduction activity was recorded up to 1250 nmol ethylene h-1 (mg protein)-1. Analysis of 16S rRNA showed that B2T represents a member of the genus Azospirillum and had the highest sequence similarity with A. humicireducens SgZ-5T (97.92 %). The predominant quinone system was ubiquinone Q-10 and the major fatty acids were C18 : 1ω7, C16 : 1ω7 and C16 : 0. The strain was facultative methylotrophic and used methanol and formate for the growth. Genome sequencing revealed a genome size of 8.0 Mbp and a G+C content of 67.8 mol%. The mxaFI genes encoding methanol dehydrogenase were absent, but a homologous xoxF gene was detected. The genes encoding enzymes involved in the biosynthesis of tetrahydromethanopterin (H4MPT) (formaldehyde oxidation) and NAD-linked formate dehydrogenase (fdsABG) were identified. Pairwise determined whole genome average nucleotide identity (gANI) values confirmed that strain B2T represents a novel species, for which we propose the name Azospirillum palustre sp. nov. with the type strain B2T (VKM B-3233T, КСТС 62613Т).

Genomic evidence of the illumination response mechanism and evolutionary history of magnetotactic bacteria within the Rhodospirillaceae family.

BACKGROUND: Magnetotactic bacteria (MTB) are ubiquitous in natural aquatic environments. MTB can produce intracellular magnetic particles, navigate along geomagnetic field, and respond to light. However, the potential mechanism by which MTB respond to illumination and their evolutionary relationship with photosynthetic bacteria remain elusive. RESULTS: We utilized genomes of the well-sequenced genus Magnetospirillum, including the newly sequenced MTB strain Magnetospirillum sp. XM-1 to perform a comprehensive genomic comparison with phototrophic bacteria within the family Rhodospirillaceae regarding the illumination response mechanism. First, photoreceptor genes were identified in the genomes of both MTB and phototrophic bacteria in the Rhodospirillaceae family, but no photosynthesis genes were found in the MTB genomes. Most of the photoreceptor genes in the MTB genomes from this family encode phytochrome-domain photoreceptors that likely induce red/far-red light phototaxis. Second, illumination also causes damage within the cell, and in Rhodospirillaceae, both MTB and phototrophic bacteria possess complex but similar sets of response and repair genes, such as oxidative stress response, iron homeostasis and DNA repair system genes. Lastly, phylogenomic analysis showed that MTB cluster closely with phototrophic bacteria in this family. One photoheterotrophic genus, Phaeospirillum, clustered within and displays high genomic similarity with Magnetospirillum. Moreover, the phylogenetic tree topologies of magnetosome synthesis genes in MTB and photosynthesis genes in phototrophic bacteria from the Rhodospirillaceae family were reasonably congruent with the phylogenomic tree, suggesting that these two traits were most likely vertically transferred during the evolution of their lineages. CONCLUSION: Our new genomic data indicate that MTB and phototrophic bacteria within the family Rhodospirillaceae possess diversified photoreceptors that may be responsible for phototaxis. Their genomes also contain comprehensive stress response genes to mediate the negative effects caused by illumination. Based on phylogenetic studies, most of MTB and phototrophic bacteria in the Rhodospirillaceae family evolved vertically with magnetosome synthesis and photosynthesis genes. The ancestor of Rhodospirillaceae was likely a magnetotactic phototrophic bacteria, however, gain or loss of magnetotaxis and phototrophic abilities might have occurred during the evolution of ancestral Rhodospirillaceae lineages.

Oleisolibacter albus gen. nov., sp. nov., isolated from an oil-contaminated soil.

A Gram-stain-negative, aerobic, flagellated, rod-shaped bacterium, designated strain NAU-10T, was isolated from an oil-contaminated soil collected in PR China. Strain NAU-10T could grow at 10-42 °C (optimum, 30 °C), pH 5.0-9.0 (pH 7.0) and in the presence of 0-2.5 % (w/v) NaCl (0.5 % in Luria-Bertani broth). The major fatty acids were C18 : 1 ω7c (38.6 %), C17 : 1 ω6c (9.8 %), C18 : 1 2-OH (9.1 %), summed feature 3 (8.7 %), C16 : 0 3-OH (7.2 %) and C16 : 0 (6.7 %). The major respiratory quinones were Q9 and Q10. The total polar lipids were lipid, aminolipid, phospholipid, phosphatidylglycerol and phosphatidylethanolamine. Strain NAU-10T shared the highest 16S rRNA gene sequence similarities with Rhodocista pekingensis 3-pT (95.9 %), Niveispirillum cyanobacteriorum TH16T (95.3 %) and Niveispirillum fermenti CC-LY736T (95.3 %), and constituted a sub-cluster within the family Rhodospirillaceae. The DNA G+C content of strain NAU-10T was 68.2 mol% based on its draft genome sequence. Genome annotation of strain NAU-10T predicted the presence of 4309 genes, of which 4237 are coding proteins and 72 are RNA genes. Based on its phenotypic and chemotaxonomic characteristics, as well as the analysis of the 16S rRNA gene sequences, it was concluded that strain NAU-10T represents a novel genus, for which the name Oleisolibacter gen. nov., is proposed. The type species of this genus is Oleisolibacter albus with the type strain NAU-10T (=KCTC 62417T=CCTCC AB 2018015T).

Aerophototrophica crusticola gen. nov., sp. nov., isolated from desert biocrusts.

A pink-pigmented, Gram-stain-negative, rod-shaped, strictly aerobic bacterial strain MIMtkB3T, was isolated from moss crusts in Hunshandake desert of China. Cells grew at 15-45 °C (optimum of 28 °C), at pH of 6.0-8.5 (optimum of 7.0) and with 0-1.0 % (w/v) NaCl (optimum of 0 %). The strain could biosynthesize the green-coloured pigment bacteriochlorophyll a (BChl a). The respiratory quinone was ubiquinone Q-10, while C18 : 1 ω7c and C18 : 1 2OH were the major fatty acids. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid, one unidentified phospholipid, three unidentified glycolipid and one unidentified lipid were the major polar lipids. Strain MIMtkB3T was most closely related to Oleisolibacter albus NAU-10T, Niveispirillum fermenti CC-LY736T, and Rhodocista centenaria SW of the family Rhodospirillaceae with 16S rRNA gene similarities of 93.09, 92.02 and 91.73%, respectively. The genomic DNA G+C content calculated on complete genome sequencing was 69.3 mol%. The average nucleotide identity between strain MIMtkB3T and its closely related type strains in Rhodospirillaceae was below 77.96 % and digital DNA-DNA hybridization lower than 24.70 %. Full light utilization pathway of aerobic anoxygenic phototrophic bacteria was identified in the genome. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain MIMtkB3T represents a novel genus of the family Rhodospirillaceae, for which the name Aerophototrophica crusticola gen. nov., sp. nov. is proposed. The type strain is MIMtkB3T (=KCTC 42633T=MCCC 1K00570T).

Indioceanicola profundi gen. nov., sp. nov., isolated from Indian Ocean sediment.

A novel basophilic bacterial strain, designated as SCSIO 08040T, was recovered from a deep-sea sediment sample collected from the Indian Ocean. The strain was Gram-stain-negative, vibrioid or spiral, light pink, 0.6-1.0 µm wide and 1.0-2.5 µm long. Growth occurred at 20-45 °C, pH 7-11 and <5 % (w/v) NaCl, with optimum growth at 28-37 °C, pH 7 and 0-3 % (w/v) NaCl. Catalase-, oxidase and urease-positive, nitrate reduction-negative. Analysis of 16S rRNA gene sequencing revealed that strain SCSIO 08040T had the highest similarity of 95.3 % to Rhodocista pekingensis 3-pT. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences showed that the novel isolate formed a distinct phylogenetic lineage in the family Rhodospirillaceae. The whole-cell hydrolysate contained meso-diaminopimelic acid, galactose, mannose and xylose. The total cellular fatty acid profile was dominated by C18:1ω7c and C19:0cycloω8c. Q-10 was the predominant ubiquinone. The major phospholipids were diphosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. The DNA G+C content of strain SCSIO 08040T was 66.82 mol%. Based on these polyphasic data, a new genus, Indioceanicola gen. nov., is proposed in the family Rhodospirillaceae with the type species Indioceanicola profundi sp. nov. and the type strain SCSIO 08040T (=DSM 105146T=CGMCC 1.15812T).

Ferrovibrio soli sp. nov., a novel cellulolytic bacterium isolated from stream bank soil.

Two isolates of bacterial strains A15T and A17 were isolated from stream bank soil in Kyonggi University. Cells were aerobic, Gram-stain-negative, oxidase- and catalase-positive, motile, non-spore-forming, rod-shaped, opaque, and cream coloured. Both strains hydrolysed CM-cellulose. Strains were able to grow at 20-42 °C, pH 5.5-10.0 and at 1.5 % NaCl concentration (w/v). Indole test was positive. Analyses of phylogenetic trees based on its 16S rRNA gene sequences indicated that strain A15T formed a lineage within the family Rhodospirillaceae of the phylum Proteobacteria which was distinct from Ferrovibrio denitrificans S3T (98.4 % sequence similarity) and Ferrovibrio xuzhouensis LM-6T (97.4 %). The sole detected respiratory quinone was Q-10. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. The major cellular fatty acids were C19 : 0 cycloω8c, C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C18 : 0cyclo and C12 : 0. The DNA G+C contents of strains A15T and A17 were 63.4 and 62.9 mol%, respectively. DNA-DNA relatedness between strain A15T and other two members of the genus Ferrovibrioranged from 25 to 37 %. The polyphasic characterization revealed strains A15T and A17 represent a novel species in the genus Ferrovibrio, for which the name Ferrovibriosoli sp. nov. is proposed. The type strain is A15T (=KEMB 9005-522T=KACC 19102T=NBRC 112682T).

Haematospirillum and insect Wolbachia DNA in avian blood.

In this study, blood samples of 259 Acrocephalus sp. warblers were molecularly analysed for Anaplasmataceae and Rhodospirillaceae based on PCR amplification of 16S rRNA gene fragments. One bird blood sample (from Reed Warbler, Acrocephalus scirpaceus) yielded a sequence with 99.8% identity to Haematospirillum jordaniae. This is the first molecular evidence for the occurrence of this species in the blood of any vertebrate other than human. Another bird blood sample (from Marsh Warbler: Acrocephalus palustris) yielded a Wolbachia sequence, closely related to a moth endosymbiont with 99.8% identity. A nematode origin of Wolbachia DNA detected here in avian blood can be excluded, because results of phylogenetic analysis showed its closest alignment with insect wolbachiae. This is the first finding of insect Wolbachia DNA in the circulatory system of birds, which can be explained either by the inoculation of wolbachiae by blood-sucking vectors, or passing of Wolbachia DNA from the gut into the blood of this insectivorous bird species.

Marivibrio halodurans gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceae isolated from underground rock salt.

Gram-negative, spiral or curved rod-shaped cells of a bacterial strain, designated ZC80T, were isolated from a rock salt sample collected at Yunnan salt mine, China. Analysis of the strain's 16S rRNA gene sequence revealed a clear affiliation of this novel strain within the family Rhodospirillaceae. Strain ZC80T formed a robust cluster with Pelagibius litoralis CL-UU02T at a 16S rRNA gene sequence similarity level of 88.1 %. Strain ZC80T shared no more than 91.0 % 16S rRNA gene sequence similarity with the type strains of other species in the family Rhodospirillaceae. Strain ZC80T was able to grow in the presence of 2-15 % (w/v) NaCl, and grew at 10-50 °C and pH 6.0-10.0. The major fatty acids were C19 : 0 cyclo ω8c (41.3 %). The major isoprenoid quinone was ubiquinone 10 (Q-10). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and an unidentified aminolipid. The DNA G+C content of strain ZC80T was 60.8 mol%. On the basis of phylogenetic analyses and chemotaxonomic and physiological data, strain ZC80T is considered to represent a novel species of a new genus in the family Rhodospirillaceae, for which the name Marivibrio halodurans gen. nov., sp. nov. is proposed. The type strain of Marivibrio halodurans is ZC80T (=CGMCC 1.15697T=NBRC 112461T).

Skermanella mucosa sp. nov., isolated from crude oil contaminated soil.

A novel Gram-stain negative, small rod-shaped bacterium (strain 8-14-6T) was isolated from hydrocarbon contaminated desert soil collected from Kuwait. Strain 8-14-6T grew at 5-37 °C, pH 6.0-8.8 and 0-2% (w/v) of NaCl concentration. Casein, starch, Tween 20 and Tween 80 were hydrolyzed while urea, chitin, DNA and carboxymethyl-cellulose were not hydrolyzed by strain 8-14-6T. The major cellular fatty acids were identified as C18:1ω6c/C18:1ω7c, C16:0 and iso-C16:1I/C14:03-OH. Strain 8-14-6T produced diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipids, two unidentified lipids and five unidentified amino lipids as polar lipids. Genomic G+C content was 73.5 mol %. 16S rRNA gene sequence comparisons indicated that strain 8-14-6T represents a member of the genus Skermanella within family Rhodospirillaceae of the class Alphaproteobacteria. Strain 8-14-6T has a sequence similarity of 98.9% with Skermanella rosea M1T, 97.4% with Skermanella aerolata 5416T-32T, 96.9% with Skermanella stibiiresistens SB22T and <95.4% with the other two known species of the genus Skermanella. The DNA-DNA relatedness values between strain 8-14-6T and the type strains of the closely related species were clearly below the 70% threshold. From the combination of phenotypic and genotypic characteristics and distinct phylogenetic position, the strain is considered to represent a novel species of the genus Skermanella, for which the name Skermanella mucosa sp. nov. is proposed. The type strain is 8-14-6T (=KEMB 2255-438T =JCM 31590T).

Proteogenomic insights into salt tolerance by a halotolerant alpha-proteobacterium isolated from an Andean saline spring.

Tistlia consotensis is a halotolerant Rhodospirillaceae that was isolated from a saline spring located in the Colombian Andes with a salt concentration close to seawater (4.5%w/vol). We cultivated this microorganism in three NaCl concentrations, i.e. optimal (0.5%), without (0.0%) and high (4.0%) salt concentration, and analyzed its cellular proteome. For assigning tandem mass spectrometry data, we first sequenced its genome and constructed a six reading frame ORF database from the draft sequence. We annotated only the genes whose products (872) were detected. We compared the quantitative proteome data sets recorded for the three different growth conditions. At low salinity general stress proteins (chaperons, proteases and proteins associated with oxidative stress protection), were detected in higher amounts, probably linked to difficulties for proper protein folding and metabolism. Proteogenomics and comparative genomics pointed at the CrgA transcriptional regulator as a key-factor for the proteome remodeling upon low osmolarity. In hyper-osmotic condition, T. consotensis produced in larger amounts proteins involved in the sensing of changes in salt concentration, as well as a wide panel of transport systems for the transport of organic compatible solutes such as glutamate. We have described here a straightforward procedure in making a new environmental isolate quickly amenable to proteomics. BIOLOGICAL SIGNIFICANCE: The bacterium Tistlia consotensis was isolated from a saline spring in the Colombian Andes and represents an interesting environmental model to be compared with extremophiles or other moderate organisms. To explore the halotolerance molecular mechanisms of the bacterium T. consotensis, we developed an innovative proteogenomic strategy consisting of i) genome sequencing, ii) quick annotation of the genes whose products were detected by mass spectrometry, and iii) comparative proteomics of cells grown in three salt conditions. We highlighted in this manuscript how efficient such an approach can be compared to time-consuming genome annotation when pointing at the key proteins of a given biological question. We documented a large number of proteins found produced in greater amounts when cells are cultivated in either hypo-osmotic or hyper-osmotic conditions. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

Complete genome sequence of Rhodospirillum rubrum type strain (S1).

Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus Rhodospirillum, which is the type genus of the family Rhodospirillaceae in the class Alphaproteobacteria. The species is of special interest because it is an anoxygenic phototroph that produces extracellular elemental sulfur (instead of oxygen) while harvesting light. It contains one of the most simple photosynthetic systems currently known, lacking light harvesting complex 2. Strain S1(T) can grow on carbon monoxide as sole energy source. With currently over 1,750 PubMed entries, R. rubrum is one of the most intensively studied microbial species, in particular for physiological and genetic studies. Next to R. centenum strain SW, the genome sequence of strain S1(T) is only the second genome of a member of the genus Rhodospirillum to be published, but the first type strain genome from the genus. The 4,352,825 bp long chromosome and 53,732 bp plasmid with a total of 3,850 protein-coding and 83 RNA genes were sequenced as part of the DOE Joint Genome Institute Program DOEM 2002.