Genetic diversity of rhizobia isolated from nodules of the relic species Vavilovia formosa (Stev.) Fed.

Sixteen bacterial strains were isolated from root nodules of Vavilovia formosa plants originated from the North Ossetian State Natural Reserve (Caucasus, Russia). Phylogenetic analysis of these strains was performed using partial 16S rRNA gene and internally transcribed spacer (ITS) sequences. The results showed that the isolates belong to three families of root nodule bacteria. Twelve of them were related to the genus Rhizobium (family Rhizobiaceae) but four strains can be most probably identified as Phyllobacterium-related (family Phyllobacteriaceae), Bosea- and Rhodopseudomonas-related (family Bradyrhizobiaceae). Amplified fragment length polymorphism clustering was congruent with ITS phylogeny but displayed more variability for Rhizobium isolates, which formed a single group at the level of 30 % similarity. We expect that the isolates obtained can belong to new taxa at genus, species or subspecies levels. The results of PCR amplification of the nodulation genes nodC and nodX showed their presence in all Rhizobium isolates and one Rhodopseudomonas-related isolate. The nodC gene sequences of V. formosa isolates were closely related to those of the species Rhizobium leguminosarum bv. viciae but formed separate clusters and did not intermingle with any reference strains. The presence of the nodX gene, which is necessary for nodulation of Afghan peas (Pisum sativum L.) originated from the Middle East, allows the speculation that these wild-type pea cultivars may be the closest existing relatives of V. formosa. Thus, the studies of genetic diversity and symbiotic genes of V. formosa microsymbionts provide the primary information about their phylogeny and contribute to the conservation of this relict leguminous species.     

Arcobacter molluscorum sp. nov., a new species isolated from shellfish

Nineteen bacteria isolates recovered from shellfish samples (mussels and oysters) showed a new and specific 16S rDNA-RFLP pattern with an Arcobacter identification method designed to recognize all species described up to 2008. These results suggested that they could belong to a new species. ERIC-PCR revealed that the 19 isolates belonged to 3 different strains. The sequence of the 16S rRNA gene of a representative strain (F98-3^T) showed 97.6% similarity with the closest species Arcobacter marinus followed by Arcobacter halophilus (95.6%) and Arcobacter mytili (94.7%). The phylogenetic analysis with the16S rRNA, rpoB, gyrB and hsp60 genes placed the shellfish strains within the same cluster as the three species mentioned (also isolated from saline habitats) but they formed an independent phylogenetic line. The DDH results between strain F98-3^T and A. marinus (54.8% ± 1.05), confirmed that it represents a new species. Several biochemical tests differentiated the shellfish isolates from all other Arcobacter species. Although the new species was different from A. mytili, they shared not only the same habitat (mussels) but also the characteristic of being so far the only Arcobacter species that are simultaneously negative for urea and indoxyl acetate hydrolysis. All results supported the classification of the shellfish strains as a new species, for which the name Arcobacter molluscorum sp. nov. with the type strain F98-3^T is proposed (=CECT 7696^T = LMG 25693^T).     

Rhizobium croatiense sp. nov. and Rhizobium redzepovicii sp. nov., two new species isolated from nodules of Phaseolus vulgaris in Croatia

Phaseolus vulgaris is a legume indigenous to America which is nodulated by strains of genus Rhizobium in Croatia. Four of these strains, 13T^T, 9T, 18T^T and 8Z are phylogenetically close to the species from the Rhizobium leguminosarum phylogenetic complex in the 16S rRNA gene analysis. The results of both the analyses of the concatenated recA and atpD genes and whole genomes revealed that the strains 13T^T and 9T clustered with Rhizobium sophoriradicis CCBAU 03470^T and the strains 18T^T and 8Z with Rhizobium ecuadorense CNPSO 671^T. Whole genome average nucleotide identity blast (ANIb) and dDDH values between the strains 13T^T and the type strain of R. sophoriradicis and between the strains 18T^T and the type strain of R. ecuadorense were lower than 95% and 70%, respectively, which are the threshold values recommended for bacterial species differentiation. These results combined with those of chemotaxonomic and phenotypic analyses support the affiliation of these strains to two novel species within the genus Rhizobium for which we propose the names Rhizobium croatiense sp. nov. 13T^T (=LMG 32397^T, = HAMBI 3740^T) as type strain and Rhizobium redzepovicii sp. nov. 18T^T (=LMG 32398^T, = HAMBI 3741^T) as type strain.     

Coprobacillus catenaformis gen. nov., sp. nov., a new genus and species isolated from human feces

Three strains of Eubacterium-like isolates from human feces were characterized by biochemical tests and 16S rDNA analysis. The phenotypic characteristics of the three strains resembled those of the genus Collinsella transferred from the genus Eubacterium recently. However, Eubacterium-like strains were phylogenetically members of the Clostridium subphylum of gram-positive bacteria, and these showed a specific phylogenetic association with Clostridium ramosum and C. spiroforme. C. ramosum and C. spiroforme are gram-positive, anaerobic, spore-forming bacteria that belong to the genus Clostridium, and the G + C contents are 26.0 and 27.4 mol%, respectively. However, the three Eubacterium-like strains had G + C contents of 32.1 to 33.1 mol% and were non-spore-forming rods. Based on phenotypic characteristics, we can differentiate these species, and furthermore, a 16S rDNA sequence divergence of greater than 9% with a new related genus, Coprobacillus, is proposed for the three strains, with one species, Coprobacillus catenaformis. The type strain of C. catenaformis is JCM 10604T.     

Arcobacter bivalviorum sp. nov. and Arcobacter venerupis sp. nov., new species isolated from shellfish

A group of ten Arcobacter isolates (Gram negative, slightly curved motile rods, oxidase positive) was recovered from mussels (nine) and from clams (one). These isolates could not be assigned to any known species using the molecular identification methods specific for this genus (16S rDNA-RFLP and m-PCR). The aim of this study is to establish the taxonomic position of these isolates. The 16S rRNA gene sequence similarity of mussel strain F4(T) to the type strains of all other Arcobacter species ranged from 91.1% to 94.8%. The species most similar to the clams' strain F67-11(T) were Arcobacter defluvii (CECT 7697(T), 97.1%) and Arcobacter ellisii (CECT 7837(T), 97.0%). On the basis of phylogenetic analyses with 16S rRNA, rpoB, gyrB and hsp60 genes, the mussel and clam strains formed two different, new lineages within the genus Arcobacter. These data, together with their different phenotypic characteristics and MALDI-TOF mass spectra, revealed that these strains represent two new species, for which the names Arcobacter bivalviorum (type strain F4(T)=CECT 7835(T)=LMG 26154(T)) and Arcobacter venerupis (type strain F67-11(T)=CECT 7836(T)=LMG 26156(T)) are proposed.     

Leucobacter kyeonggiensis sp. nov., a new species isolated from dye waste water

A Gram-positive, aerobic, non-motile bacterium designated F3-P9^T, was isolated from dye waste water in Korea and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain F3-P9^T belongs to genus Leucobacter. The 16S rRNA gene sequence similarities among strain F3-P9^T and validated representatives of the genus Leucobacter ranged from 95.9–97.4%. Strain F3-P9^T exhibited DNA-DNA relatedness values below 48% with respect to Leucobacter species. The G+C content of the genomic DNA was 67.5 mol%. F3-P9^T contained MK-11 as the major respiratory quinone. The major fatty acids were anteiso-C_15:0 (48.5%), anteiso-C_17:0 (22.7%), and iso-C_16:0 (14.5%). The peptidoglycan was composed of L-2,4-diaminbutyric acid, alanine, glycine, and glutamic acid. The polar lipid profile showed a major amount of diphosphatidylglycerol (DPG), a moderate amount of phosphatidylglycerol (PG), and two unknown glycolipids. On the basis of its phenotypic and genotypic properties and its phylogenetic distinctiveness, strain F3-P9^T (KEMC 211-128^T =KACC 16572^T =JCM 17539^T) should be classified in the genus Leucobacter as the type strain of a novel species, for which the name Leucobacter kyeonggiensis sp. nov. is proposed.     

Halomonas borealis sp. nov. and Halomonas niordiana sp. nov., two new species isolated from seawater

Two Gram-negative strains obtained from tank water in a scallop hatchery in Norway, were phenotypically and genotypically characterized in order to clarify their taxonomic position. On the basis of 16S rRNA gene sequence analysis, these isolates, ATF 5.2^T and ATF 5.4^T, were included in the genus Halomonas, being their closest relatives H. smyrnensis and H. taeanensis, with similarities of 98.9% and 97.7%, respectively. Sequence analysis of the housekeeping genes atpA, ftsZ, gyrA, gyrB, mreB, rpoB, rpoD, rpoE, rpoH, rpoN and rpoS clearly differentiated the isolates from the currently described Halomonas species, and the phylogenetic analysis using concatenated sequences of these genes located them in two robust and independent branches. DNA–DNA hybridization (eDDH) percentage, together with average nucleotide identity (ANI), were calculated using the complete genome sequences of the strains, and demonstrate that the isolates constitute two new species of Halomonas, for which the names of Halomonas borealis sp. nov. and Halomonas niordiana sp. nov. are proposed, with type strains ATF 5.2^T (=CECT 9780^T = LMG 31367^T) and ATF 5.4^T (=CECT 9779^T = LMG 31227^T), respectively.     

Mycobacterium valentiae sp. nov., a new species of the genus Mycobacterium isolated from soil

One strain of rapidly growing scotochromogenic mycobacteria was isolated. This study comprises 101 biochemical, cultural and morphological characteristics and reports the behavior towards several concentrations of the most commonly used antituberculous drugs. The organism is considered to belong to a new species of the genus Mycobacterium and has been deposited in the American Type Culture Collection, Rockville, Maryland, USA (ATCC 29356) and in the Czechoslovak Collection of Microorganisms, Czechoslovak National Collection of Type Cultures, Institute of Hygiene and Epidemiology, Srobárova 48, 100 42 Prague 10 under the My 220/77.     

Flavobacterium oncorhynchi sp. nov., a new species isolated from rainbow trout (Oncorhynchus mykiss)

Eighteen isolates of a Gram-negative, catalase and oxidase-positive, rod-shaped bacterium, recovered from diseased rainbow trout (Oncorhynchus mykiss), were characterized, using a polyphasic taxonomic approach. Studies based on comparative 16S rRNA gene sequence analysis showed that that the eighteen new isolates shared 99.2-100% sequence similarities. Phylogenetic analysis revealed that isolates from trout belonged to the genus Flavobacterium, showing the highest sequence similarities to F. chungangense (98.6%), F. frigidimaris (98.1%), F. hercynium (97.9%) and F. aquidurense (97.8%). DNA-DNA reassociation values between the trout isolates (exemplified by strain 631-08(T)) and five type strains of the most closely related Flavobacterium species exhibited less than 27% similarity. The G+C content of the genomic DNA was 33.0 mol%. The major respiratory quinone was observed to be menaquinone 6 (MK-6) and iso-C(15:0), C(15:0) and C(16:1) ω7c the predominant fatty acids. The polar lipid profile of strain 631-08(T) consisted of phosphatidylethanolamine, unknown aminolipids AL1 and AL3, lipids L1, L2, L3 and L4 and phospholipid PL1. The novel isolates were differentiated from related Flavobacterium species by physiological and biochemical tests. On the basis of the evidence from this polyphasic study, it is proposed that the isolates from rainbow trout be classified as a new species of the genus Flavobacterium, Flavobacterium oncorhynchi sp. nov. The type strain is 631-08(T) (= CECT 7678(T) = CCUG 59446(T)).     

Ensifer shofinae sp. nov., a novel rhizobial species isolated from root nodules of soybean (Glycine max)

Two bacterial strains isolated from root nodules of soybean were characterized phylogenetically as members of a distinct group in the genus Ensifer based on 16S rRNA gene comparisons. They were also verified as a separated group by the concatenated sequence analyses of recA, atpD and glnII (with similarities ≤93.9% to the type strains for defined species), and by the average nucleotide identities (ANI) between the whole genome sequence of the representative strain CCBAU 251167^T and those of the closely related strains in Ensifer glycinis and Ensifer fredii (90.5% and 90.3%, respectively). Phylogeny of symbiotic genes (nodC and nifH) grouped these two strains together with some soybean-nodulating strains of E. fredii, E. glycinis and Ensifer sojae. Nodulation tests indicated that the representative strain CCBAU 251167^T could form root nodules with capability of nitrogen fixing on its host plant and Glycine soja, Cajanus cajan, Vigna unguiculata, Phaseolus vulgaris and Astragalus membranaceus, and it formed ineffective nodules on Leucaena leucocephala. Strain CCBAU 251167^T contained fatty acids 18:1 ω9c, 18:0 iso and 20:0, differing from other related strains. Utilization of l-threonine and d-serine as carbon source, growth at pH 6.0 and intolerance of 1% (w/v) NaCl distinguished strain CCBAU 251167^T from other type strains of the related species. The genome size of CCBAU 251167^T was 6.2 Mbp, comprising 7,581 predicted genes with DNA G+C content of 59.9 mol% and 970 unique genes. Therefore, a novel species, Ensifer shofinae sp. nov., is proposed, with CCBAU 251167^T (=ACCC 19939^T = LMG 29645^T) as type strain.     

Fellomyces horovitziae sp. nov., a new basidiomycetous yeast species isolated from aXenasmatella basidiocarp

A new species of the genusFellomyces, F. horovitziae, was isolated from aXenasmatella basidiocarp. It differs from other accepted species in its carbon assimilation pattern, mol% G+C and low DNA-DNA homology. The delimiting characters are discussed and a key to the genus is provided.     

Novosphingobium hassiacum sp. nov., a new species isolated from an aerated sewage pond

The taxonomy of two strains W-51T and W-52 isolated from a wastewater treatment plant was investigated in a polyphasic approach. The yellow pigmented gram-negative organism contained a quinone system with mainly ubiquinone Q-10, and the polar lipid profile contained a sphingoglycolipid suggesting that both strains belonged to the the alpha-4 subclass of the Proteobacteria. The polar lipid profile consisted furthermore of phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylcholine and of minor amounts of phosphatidylglycerol and phosphatidylmonomethylethanolamine. Sequencing of the 16S rRNA gene supported the allocation into the genus Novosphingobium, together with the type strains of N. subterraneum, N. aromaticivorans, N. stygium, and N. capsulatum, showing similarities of 97.3%, 97.0%, 95.7% and 96.2%, respectively. This allocation was supported by the polyamine profile, which consisted mainly of spermidine. The analysis of the fatty acids revealed 2-OH 13:0, 2-OH 14:0 and 2-OH 15:0, with 2-OH 15:0 as predominant hydroxylated fatty acid. W-51T and W-52 were almost identical with respect to their phenotypic including the majority of the chemotaxonomic properties, identical in their 16S rRNA sequences, and showed 86% DNA-DNA similarity. Both strains were able to reduce nitrate and on the basis of further physiological features, a clear differentiation from all other Novosphingobium species was possible. The DNA-DNA similarities of W-51T to the type strains of N. subterraneum, N. aromaticivorans, and N. capsulatum were below 56%. For these reasons, it is proposed to create a new species with the name Novosphingobium hassiacum sp. nov.     

Spatial patterns and intraspecific diversity of the glacial relict legume species <Emphasis Type="Italic">Vavilovia formosa</Emphasis> (Stev.) Fed. in Eurasia

Vavilovia formosa is one of five genera in tribe Fabeae, (Fabaceae, Leguminosae) with close phylogenetic relationships to Pisum. It grows in subalpine and alpine levels in Armenia, Azerbaijan, Georgia, Iran, Iraq, Lebanon, Russia and Turkey and is recognized as an endangered and protected plant. This study was conducted to reveal its intraspecific variability, as well as to predict the past, extant and future species distribution range. We analysed 51 accessions with common phylogenetic markers (trnF-trnL, trnS-trnG, matK, rbcL, psbA-trnH and ITS). These represent in total up to 2551 bp of chloroplast and 664 bp of nuclear sequences per sample. Two populations from Turkey and Armenia were analysed for genetic diversity by AFLP. Leaf morphometry was conducted on 1457 leaflets from 43 specimens. Extracted bioclimatic parameters were used for niche-modelling approach. Analysis of cpDNA revealed two haplotypes, 12 samples from Armenia, Daghestan, Nakhichevan and Iran belonged to H1 group, while 39 samples of all Turkish and part of Armenian were in H2 group. The mean intrapopulation diversity based on AFLP was low (H _E = 0.088) indicating limited outcrossing rate. A significantly positive correlation between geographical latitude and leaf area (\(\rho\) = 0.527, p < 0.05) was found. Niche modelling has shown temporal variation of predicted occurrence across the projected time periods. Vavilovia formosa has suffered a range reduction following climate warming after last glacial maximum, which classify this species as cold-adapted among the Fabeae species as well as a glacial relict.     

Leucobacter chromiireducens sp. nov, and Leucobacter aridicollis sp. nov., two new species isolated from a chromium contaminated environment

Two strains designated strains L-1^T and L-9^T were isolated from activated sludge of a treatment plant that receives wastewater from the tannery industry contaminated with chromium. Phylogenetic analysis showed that the organisms represented two new species of the genus Leucobacter. Strains L-1^T and L-9^T could be distinguished from the type strain of L. komagatae and from the type strain of “L. albus” by the B-type peptidoglycan composition, fatty acid composition, several phenotypic and physiological characteristics. The major fatty acids of the organisms were iso- and anteiso-branched C15:0 and C17:0, straight-chain C16:0 was also found in relatively high proportions. The organisms were halotolerant, grew in medium containing 9% NaCl, and all strains, including the type strain of L. komagatae grew in medium containing 5 mM Cr(VI). On the basis of the distinct peptidoglycan composition, 16S ribosomal DNA sequence analysis, percentage of DNA-DNA reassociation values, and phenotypic characteristics we are of the opinion that strain L-1^T represents a new species of the genus Leucobacter for which we propose the name Leucobacter chromiireducens and that strain L-9^T represents an additional new species of the same genus for which we propose the name Leucobacter aridicollis.     

Three new species of the genus Peptostreptococcus isolated from humans: Peptostreptococcus vaginalis sp. nov., Peptostreptococcus lacrimalis sp. nov., and Peptostreptococcus lactolyticus sp. nov.

We describe three new species of the genus Peptostreptococcus which were isolated from human specimens and were tentatively identified as Peptostreptococcus prevotii. These three organisms were not homologous with previously described type strains of the genus Peptostreptococcus. A total of 12 strains that were identified biochemically as P. prevotii were divided into five independent DNA similarity groups; 10 of these strains were divided into three similarity groups which exhibited significant phenotypic differences from previously described species. Therefore, we propose the following new species: Peptostreptococcus vaginalis for group 1 strains, Peptostreptococcus lacrimalis for group 2 strains, and Peptostreptococcus lactolyticus for group 3 strains. The type strain of P. vaginalis is strain GIFU 12669 (= JCM 8138), the type strain of P. lacrimalis is strain GIFU 7667 (= JCM 8139), and the type strain of P. lactolyticus is strain GIFU 8586 (= JCM 8140).     

Rhizobium ruizarguesonis sp. nov., isolated from nodules of Pisum sativum L

Four strains, coded as UPM1132, UPM1133^T, UPM1134 and UPM1135, and isolated from nodules of Pisum sativum plants grown on Ni-rich soils were characterised through a polyphasic taxonomy approach. Their 16S rRNA gene sequences were identical and showed 100% similarity with their closest phylogenetic neighbors, the species included in the ‘R. leguminosarum group’: R. laguerreae FB206^T, R. leguminosarum USDA 2370^T, R. anhuiense CCBAU 23252^T, R. sophoreae CCBAU 03386^T, R. acidisoli FH13^T and R. hidalgonense FH14^T, and 99.6% sequence similarity with R. esperanzae CNPSo 668^T. The analysis of combined housekeeping genes recA, atpD and glnII sequences showed similarities of 92-95% with the closest relatives. Whole genome average nucleotide identity (ANI) values were 97.5-99.7% ANIb similarity among the four strains, and less than 92.4% with closely related species, while digital DNA-DNA hybridization average values (dDDH) were 82-85% within our strains and 34-52% with closely related species. Major fatty acids in strain UPM1133^T were C18:1 ω7c / C18:1 ω6c in summed feature 8, C14:0 3OH/ C16:1 iso I in summed feature 2 and C18:0. Colonies were small to medium, pearl-white coloured in YMA at 28 °C and growth was observed in the ranges 8-34 °C, pH 5.5-7.5 and 0-0.7% (w/v) NaCl. The DNA G + C content was 60.8 mol %. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strains UPM1132, UPM1133^T, UPM1134 and UPM1135 into a novel species of Rhizobium, for which the name Rhizobium ruizarguesonis sp. nov. is proposed. The type strain is UPM1133^T (=CECT 9542^T = LMG 30526^T).     

Saccharopolyspora pathumthaniensis sp. nov., a novel actinomycetes isolated from termite guts (Speculitermes sp.)

Morphological and chemotaxonomic characterization of actinomycete strain S582 isolated from the gut of a termite (Speculitermes sp.) in Pathum Thani Province, Thailand, clearly demonstrated that this strain is a member of the genus Saccharopolyspora. 16S rDNA sequence analysis for the strain supported the assignment of the strain to the genus Saccharopolyspora. The similarity value of sequences between this strain and the closely related species Saccharopolyspora endophytica was 99.5%. The DNA G+C content was 70.2 mol%. DNA-DNA hybridization results (53.3%) and some physiological and biochemical properties indicated that strain S582(T) was distinguished from the phylogenetically closest relatives. Based on these genotypic and phenotypic data, strain S582(T) should be a new species in the genus Saccharopolyspora and the name Saccharopolyspora pathumthaniensis sp. nov. is proposed for the strain. The type strain is S582(T) (=NBRC 104112(T) =BCC 28624(T)).     

Hymenobacter properus sp. nov., Hymenobacter ruricola sp. nov., and Hymenobacter jeongseonensis sp. nov., three new species isolated from mountain and beach soil in South Korea

Antonie van Leeuwenhoek - Three Gram-stain-negative, aerobic, circular, convex, red-colored and rod-shaped bacterial strains, designated BT439T, BT662T and BT683T were obtained from soil collected...