Halomonas alkalisoli sp. nov., a novel haloalkalophilic species from saline-alkaline soil,and reclassification of Halomonas daqingensis Wu et al. 2008 as a later heterotypic synonym of Halomonas desiderata Berendes et al. 1996

Two Gram-stain-negative, strictly aerobic, moderately halophilic, non-spore-forming and rod-shaped bacteria, designated M5N1S17^T and M5N1S15, were isolated from saline soil in Baotou, China. A phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains clustered closely with Halomonas montanilacus PYC7W^T and shared 99.1 and 99.3% sequence similarities, respectively. The average nucleotide identity based on BLAST (ANIb) and MUMmer (ANIm) values of the two strains with each other were 95.5% and 96.7%, respectively, while the ANIb and ANIm values between the two strains and 15 closer Halomonas species were 74.8–91.3% and 84.1–92.6%, respectively. The major polar lipids of M5N1S17^T are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, and an unidentified phospholipid. The major polar lipids of M5N1S15 are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids, and an unidentified lipid. The predominant ubiquinone in the two strains is Q-9. The major fatty acids of the two strains are C_18:1 ω6c and/or C_18:1 ω7c, C_16:0, and C_16:1 ω7c and/or C_16:1 ω6c. Based on phylogenetic, phenotypic, and physiological results, strains M5N1S17^T and M5N1S15 should be identified as a novel species of the genus Halomonas, for which Halomonas alkalisoli sp. nov. is proposed. The type strain is M5N1S17^T (= CGMCC 1.19023^T = KCTC 92130^T). The phylogenetic trees showed that Halomonas daqingensis CGMCC 1.6443^T clustered tightly with Halomonas desiderata FB2^T, and the two strains shared >98.0% of ANI values with each other. Therefore, we propose the reclassification of H. daqingensis Wu et al. 2008 as a later heterotypic synonym of H. desiderata Berendes et al. 1996.     

Lipids in the classification of Nocardioides: Reclassification of Arthrobacter simplex (Jensen) lochhead in the genus Nocardioides (Prauser) emend. O'Donnell et al. as Nocardioides simplex comb. nov.

The tubulin proteins of Blastocladiella emersonii have been characterized, and the pool sizes of soluble tubulins measured to evaluate turnover during early development. The axonemal tubulins and soluble tubulin dimers were typical of tubulin proteins from other eukaryotes.[³H]cholchicine binding assays were used to estimate the soluble tubulin pools of zoospores and during early development. The free colchicine-binding pool of tubulin in zoospores represents 1% of the soluble protein. It increases by 49% after encystment (at 30 min), decreases to 21% below the spore level by 50 min, and then increases slowly with growth. Neither deflagellation of zoospores prior to encystment, nor inhibition of axonemal disassembly, alter the postencystment pool increases. Disassembly of cytoskeletal microtubules occurs in either circumstance, but can account for only 54% of the pool increase. It was concluded that (1) the retracted axonemal tubulins are not returned to the soluble pool detected by cholchicine binding and are probably degraded; (2) new microtubules are supplied by the preexisting cytoplasmic pool that expands from disassembly of cytoplasmic microtubules; and (3) that the tubulins of the axonemes and soluble pools may be distinct.     

Reclassification of Aeromonas hydrophila subsp. dhakensis Huys et al. 2002 and Aeromonas aquariorum Martínez-Murcia et al. 2008 as Aeromonas dhakensis sp. nov. comb nov. and emendation of the species Aeromonas hydrophila

Previous studies indicate that Aeromonas aquariorum and Aeromonas hydrophila subsp. dhakensis are the same taxon and suggest that they should be synonymized. Using a polyphasic approach, the phenotypic and phylogenetic relationship of A. aquariorum with the 3 defined A. hydrophila subspecies (i.e. dhakensis, hydrophila, ranae) was investigated. Phylogenetic trees derived from the 16S rRNA, rpoD or gyrB genes and a multilocus phylogenetic analysis (with the concatenated sequences of gyrB, rpoD, recA, dnaJ and gyrA) confirmed that both A. aquariorum and A. hydrophila subsp. dhakensis are a unique taxon, different from the other A. hydrophila subspecies, corroborating the phenotypic and DNA–DNA hybridization (DDH) results. A formal synonymization of A. aquariorum and A. hydrophila subsp. dhakensis and a reclassification of both as Aeromonas dhakensis sp. nov. comb nov. is therefore proposed.     

Reclassification of Methylobacterium chloromethanicum and Methylobacterium dichloromethanicum as later subjective synonyms of Methylobacterium extorquens and of Methylobacterium lusitanum as a later subjective synonym of Methylobacterium rhodesianum

Phylogenetic analysis based on 16S rDNA sequences was performed on all type strains of the 14 validly described Methylobacterium species to ascertain the genealogic relationships among these species. The results showed that type strains of Methylobacterium were divided into two monophyletic groups whose members were distinct species with sequence similarity values greater than 97.0% between any two of the members in the same group. Only M. organophilum JCM 2833(T) and ATCC 27886(T) were not divided into those two groups. In particular, strains of M. dichloromethanicum and M. chloromethanicum exhibited extremely high similarity values (99.9 and 100%, respectively) with the type strain of M. extorquens. To clarify the relationships among Methylobacterium species in more detail, phylogenetic analysis based on the 5' end hyper-variable region of 16S rDNA (HV region), ribotyping analysis, fatty acid analysis, G+C content analysis and DNA-DNA hybridization experiments was performed on 58 strains of Methylobacterium species. Results of the ribotyping analysis and the phylogenetic analysis based on HV region sequences indicated that many Methylobacterium strains, including M. 'organophilum' DSM 760(T), have been erroneously identified. The DNA G+C content of Methylobacterium strains were between 68.1 and 71.3%. Results of whole-cell fatty-acid profiles showed that all strains contained 18 : 1omega7c as the primary fatty acid component (82.8-90.1%), with 16 : 0 and 18 : 0 as minor components. M. dichloromethanicum DSM 6343(T), M. chloromethanicum NCIMB 13688(T), and M. extorquens IAM 12631(T) exhibited high DNA-DNA relatedness values between each other (69-80%). M. lusitanum NCIMB 13779(T) also showed a close relationship with M. rhodesianum DSM 5687(T) at DNA-DNA relatedness levels of 89-92%. According to these results, many Methylobacterium strains should be reclassified, with M. dichloromethanicum and M. chloromethanicum regarded as a synonym of M. extorquens, and M. lusitanum a synonym for M. rhodesianum.     

The coral bleaching Vibrio shiloi Kushmaro et al. 2001 is a later synonym of Vibrio mediterranei Pujalte and Garay 1986

The coral bleaching Vibrio shiloi LMG 19703T was characterized by means of Fluorescent Amplified Fragment Length Polymorphism (FAFLP), DNA-DNA hybridisation, mol% G+C content, fatty acids methyl ester (FAME) analysis and phenotypical tests. Numerical analysis of the FAFLP band patterns indicated that the type strain of V. shiloi in fact belongs to the species V. mediterranei. The type strains of both species shared 77% DNA similarity, as determined by DNA-DNA hybridisation experiments at stringent conditions. Moreover, V. shiloi and V. mediterranei showed almost identical fatty acid composition and phenotypical features. Collectively, the genotypic and phenotypic data presented in this study suggest that V. shiloi Kushmaro et al. 2001 should be considered a later synonym of V. mediterranei Pujalte and Garay 1986. The involvement of V. mediterranei in coral bleaching was unknown until now.     

Reclassification of Methylarcula marina Doronina et al. 2000 as Paracoccus methylarcula nom. nov.

Microbiology - Phylogenetic analysis of the 16S rRNA gene sequences showed that the type species of the genus Methylarcula, Methylarculamarina h1T was closely related to Paracoccus saliphilus DSM...     

Examination into the taxonomic position of Bacillus thermotolerans Yang et al., 2013, proposal for its reclassification into a new genus and species Quasibacillus thermotolerans gen. nov., comb. nov. and reclassification of B. encimensis Dastager et al., 2015 as a later heterotypic synonym of B. badius

Two novel Gram-staining positive, rod-shaped, moderately halotolerant, endospore forming bacterial strains 5.5LF 38TD and 5.5LF 48TD were isolated and taxonomically characterized from a landfill in Chandigarh, India. The analysis of 16S rRNA gene sequences of the strains confirmed their closest identity to Bacillus thermotolerans SgZ-8T with 99.9% sequence similarity. A comparative phylogenetic analysis of strains 5.5LF 38TD, 5.5LF 48TD and B. thermotolerans SgZ-8^T confirmed their separation into a novel genus with B. badius and genus Domibacillus as the closest phylogenetic relatives. The major fatty acids of the strains are iso-C_15:0 and iso-C_16:0 and MK-7 is the only quinone. The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The digital DNA-DNA hybridization (DDH) and ortho average nucleotide identity (ANI) values calculated through whole genome sequences indicated that the three strains showed low relatedness with their phylogenetic neighbours. Based on evidences from phylogenomic analyses and polyphasic taxonomic characterization we propose reclassification of the species B. thermotolerans into a novel genus named Quasibacillus thermotolerans gen. nov., comb. nov with the type strain SgZ-8^T (= CCTCC AB2012108^T = KACC 16706^T). Further our analyses also revealed that B. encimensis SGD-V-25^T is a later heterotypic synonym of Bacillus badius DSM 23^T.     

Caenimonas terrae sp. nov., isolated from a soil sample in Korea, and emended description of the genus Caenimonas Ryu et al. 2008

A white-coloured bacterium, SGM1-15^T, was isolated from a paddy soil sample from Suwon, Republic of Korea. The cells were strictly aerobic, Gram-negative and curved rod-shaped. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SGM1-15^T was closely related to Curvibacter delicatus LMG 4328^T (97.6% similarity) and Caenimonas koreensis EMB320^T (97.5% similarity). The major respiratory quinone system was Q-8 and the predominant cellular fatty acids were C_16:0 (39.9%), summed feature 3 (C_16:1 ω7c and/or iso-C_15:0 2-OH; 24.3%) and C_17:0 cyclo (22.7%). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major polyamines were 2-hydroxypurescine, purescine and spermidine. The DNA G+C content was 68.7 mol%. On the basis of the phylogenetic, physiologicl and chemotaxonomic data, stain SGM1-15^T represents a novel species of the genus Caenimonas, for which the name Caenimonas terrae sp. nov. is proposed. The type strain of Caenimonas terrae is SGM1-15^T (=KACC 13365^T =NBRC 106341^T).     

DNA relatedness among some thermophilic members of the genus Methanobacterium: emendation of the species Methanobacterium thermoautotrophicum and rejection of Methanobacterium thermoformicicum as a synonym of Methanobacterium thermoautotrophicum.

DNA reassociation was used to determine levels of relatedness among four thermophilic Methanobacterium strains that are able to use formate and between these organisms and two representative strains of Methanobacterium thermoautotrophicum, strain delta HT (= DSM 1053T = ATCC 29096T) (T = type strain) and strain Marburg (= DSM 2133). Three homology groups were delineated, and these groups coincided with the clusters identified by antigenic fingerprinting. The first group, which had levels of cross hybridization that ranged from 73 to 99%, included M. thermoautotrophicum delta HT, Methanobacterium thermoformicicum Z-245, Methanobacterium sp. strain THF, and Methanobacterium sp. strain FTF. The second and third groups were each represented by only one strain, Methanobacterium sp. strain CB-12 and M. thermoautotrophicum Marburg, respectively (cross-hybridization levels, 13 to 30 and 29 to 33%, respectively). Our results indicate that the name M. thermoformicicum should be rejected as it is a synonym of M. thermoautotrophicum. The taxonomic positions of strains Marburg and CB-12 need further investigation.     

Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources

During studies on the bacteriology of appendicitis in children, we often isolated from inflamed and non-inflamed tissue samples, an unusual bile-resistant pigment-producing strictly anaerobic gram-negative rod. Phenotypically this organism resembles members of Bacteroides fragilis group of species, as it is resistant to bile and exhibits a special-potency-disk pattern (resistance to vancomycin, kanamycin and colistin) typical for the B. fragilis group. However, the production of brown pigment on media containing haemolysed blood and a cellular fatty acid composition dominated by iso-C15:0, suggests that the organism most closely resembles species of the genus Porphyromonas. However, the unidentified organism differs from porphyromonads by being bile-resistant and by not producing butyrate as a metabolic end-product. Comparative 16S ribosomal RNA gene sequencing studies show the unidentified organism represents a distinct sub-line, associated with but distinct from, the miss-classified species Bacteroides putredinis. The clustering of the unidentified bacterium with Bacteroides putredinis was statistically significant, but they displayed > 4% sequence divergence with each other. Chromosomal DNA-DNA pairing studies further confirmed the separateness of the unidentified bacterium and Bacteroides putredinis. Based on phenotypic and phylogenetic considerations, it is proposed that Bacteroides putredinis and the unidentified bacterium from human sources be classified in a new genus Alistipes, as Alistipes putredinis comb. nov. and Alistipes finegoldii sp. nov., respectively. The type strain of Alistipes finegoldii is CCUG 46020(T) (= AHN243(T)).