Proposal of Ensifer psoraleae sp. nov., Ensifer sesbaniae sp. nov., Ensifer morelense comb. nov. and Ensifer americanum comb. nov

In a survey of rhizobia associated with the native legumes in Yunnan Province, China, seven and nine strains isolated from the root nodules of Psoralea corylifolia, Sesbania cannabina and Medicago lupulina were respectively classified into the novel genomic species groups I and II in the genus Ensifer (former Sinorhizobium) based on the sequence analyses of the 16S rRNA gene. Analyses of concatenated housekeeping genes (atpD, recA and glnII) further revealed that they were distinct lineages in the genus, and group I was most similar to Ensifer terangae and Ensifer garamanticus (both with 94.2% similarity), while group II was most similar to Ensifer adhaerens (94.0%). These groups could be distinguished from closely related species by DNA–DNA relatedness, MALID-TOF MS, cellular fatty acid profiles and a series of phenotypic characters. Therefore, two novel species were proposed: Ensifer psoraleae sp. nov. (seven strains, type strain CCBAU 65732^T = LMG 26835^T = HAMBI 3286^T) and Ensifer sesbaniae sp. nov. (nine strains, type strain CCBAU 65729^T = LMG 26833^T = HAMBI 3287^T). They had a DNA G + C mol% (T_m) of 58.9 and 60.4, respectively. Both of the type strains formed effective nodules on common bean (Phaseolus vulgaris) and their hosts of origin. In addition, the previously described species Sinorhizobium morelense and Sinorhizobium americanum were renamed as Ensifer morelense comb. nov. and Ensifer americanum comb. nov. according to the accumulated data from different studies.     

Achromobacter animicus sp. nov., Achromobacter mucicolens sp. nov., Achromobacter pulmonis sp. nov. and Achromobacter spiritinus sp. nov., from human clinical samples

The phenotypic and genotypic characteristics of fourteen human clinical Achromobacter strains representing four genogroups which were delineated by sequence analysis of nusA, eno, rpoB, gltB, lepA, nuoL and nrdA loci, demonstrated that they represent four novel Achromobacter species. The present study also characterized and provided two additional reference strains for Achromobacter ruhlandii and Achromobacter marplatensis, species for which, thus far, only single strains are publicly available, and further validated the use of 2.1% concatenated nusA, eno, rpoB, gltB, lepA, nuoL and nrdA sequence divergence as a threshold value for species delineation in this genus. Finally, although most Achromobacter species can be distinguished by biochemical characteristics, the present study also highlighted considerable phenotypic intraspecies variability and demonstrated that the type strains may be phenotypically poor representatives of the species. We propose to classify the fourteen human clinical strains as Achromobacter mucicolens sp. nov. (with strain LMG 26685^T [=CCUG 61961^T] as the type strain), Achromobacter animicus sp. nov. (with strain LMG 26690^T [=CCUG 61966^T] as the type strain), Achromobacter spiritinus sp. nov. (with strain LMG 26692^T [=CCUG 61968^T] as the type strain), and Achromobacter pulmonis sp. nov. (with strain LMG 26696^T [=CCUG 61972^T] as the type strain).     

Tepidamorphus gemmatus gen. nov., sp. nov., a slightly thermophilic member of the Alphaproteobacteria

Two isolates, with an optimum growth temperature of about 45–50 °C and an optimum pH for growth between 7.5 and 8.5, were recovered from a hot spring in the Furnas area on the Island of São Miguel in the Azores. Strains form irregular rod-shaped cells are motile and stain Gram negative. The cells multiply by budding. These strains are non-pigmented, strictly aerobic, catalase and oxidase positive. These organisms assimilated carbohydrates, organic acids and amino acids. The major fatty acids are 19:0_{cyclo ω8c} and 18:0. Ubiquinone 10 is the major respiratory quinone. The major polar lipids are diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine in addition to one unidentified aminolipid and one unidentified glycolipid. Bacteriochlorophyll a, puf genes and RuBisCo genes were not detected. Analysis of the 16S rRNA gene shows the strains to cluster with species of the genera Afifella, Rhodobium, Anderseniella and Amorphus to which they have sequence similarity in the range 93–94%. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics we describe a new species of a novel genus represented by strain CB-27A^T (=DSM 19345^T=LMG 24113^T) for which we propose the name Tepidamorphus gemmatus.     

Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov.

Four strains (M15∅_3, M17^T, M49 and R37^T) were isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. Together with an older preserved isolate (strain 2OM6) from cultured oysters at Vinaroz, Castellón, Spain, the strains were thoroughly characterized in a polyphasic study and were placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae. Highest 16S rRNA sequence similarities of the five strains to the types of any established species corresponded to Tropicibacter multivorans (95.8–96.4%), Phaeobacter inhibens (95.9–96.3%) and Phaeobacter gallaeciensis (95.9–96.2%). On the other hand, whole genome (ANI) and protein fingerprinting (MALDI-TOF) data proved: (i) non clonality among the strains, and (ii) the existence of two genospecies, one consisting of strains M15∅_3, M17^T, M49 and 2OM6 and another one consisting of strain R37^T. Phenotypic traits determined allow differentiating both genospecies from each other and from closely related taxa. In view of all data collected we propose to accommodate these isolates in two species as members of the genus Tropicibacter, Tropicibacter mediterraneus sp. nov. (type strain M17^T = CECT 7615^T = KCTC 23058^T) and Tropicibacter litoreus sp. nov. (type strain R37^T = CECT 7639^T = KCTC 23353^T).     

Four new species of Chryseobacterium from the rhizosphere of coastal sand dune plants, Chryseobacterium elymi sp. nov., Chryseobacterium hagamense sp. nov., Chryseobacterium lathyri sp. nov. and Chryseobacterium rhizosphaerae sp. nov.

The taxonomic positions of five Gram-negative, non-spore-forming and non-motile bacterial strains isolated from the rhizosphere of sand dune plants were examined using a polyphasic approach. The analysis of the 16S rRNA gene sequence indicated that all of the isolates fell into four distinct phylogenetic clusters belonging to the genus Chryseobacterium of the family Flavobacteriaceae. The 16S rRNA gene sequence similarities of isolates to mostly related type strains of Chryseobacterium ranged from 97.5% to 98.5%. All strains contained MK-6 as the predominant menaquinone, and iso-C_15:0, iso-C_17:0 3-OH and a summed feature of iso-C_15:0 2-OH and/or C_16:1 ω7c as the dominant fatty acids. Combined phenotypic, genotypic and chemotaxonomic data supported that they represented four novel species in the genus Chryseobacterium, for which the names Chryseobacterium hagamense sp. nov. (type strain RHA2-9^T=KCTC 22545^T=NBRC 105253^T), Chryseobacterium elymi sp. nov. (type strain RHA3-1^T=KCTC 22547^T=NBRC 105251^T), Chryseobacterium lathyri sp. nov. (type strain RBA2-6^T=KCTC 22544^T=NBRC 105250^T), and Chryseobacterium rhizosphaerae sp. nov. (type strain RSB3-1^T=KCTC 22548^T=NBRC 105248^T) are proposed.     

Kocuria uropygioeca sp. nov. and Kocuria uropygialis sp. nov., isolated from the preen glands of Great Spotted Woodpeckers (Dendrocopos major)

Two new species of Gram-positive cocci were isolated from the uropygial glands of wild woodpeckers (Dendrocopos major) originating from different locations in Germany. A polyphasic approach confirmed the affiliation of the isolates to the genus Kocuria. Phylogenetic analysis based on the 16S rRNA gene showed high degree of similarity to Kocuria koreensis DSM 23367^T (99.0% for both isolates). However, low ANIb values of <80% unequivocally separated the new species from K. koreensis. This finding was further corroborated by DNA fingerprinting and analysis of polar lipid profiles. Furthermore, growth characteristics, biochemical tests, MALDI-TOF MS analysis, and G + C contents clearly differentiated the isolates from their known relatives. Besides, the woodpecker isolates significantly differed from each other in their whole-cell protein profiles, DNA fingerprints, and ANIb values. In conclusion, the isolated microorganisms constitute members of two new species, for which the names Kocuria uropygioeca sp. nov. and Kocuria uropygialis sp. nov. are proposed. The type strains are 36^T (DSM 101740^T = LMG 29265^T) and 257^T (=DSM 101741^T = LMG 29266^T) for K. uropygialis sp. nov. and K. uropygioeca sp. nov., respectively.     

Description of Brenneria roseae sp. nov. and two subspecies, Brenneria roseae subspecies roseae ssp. nov and Brenneria roseae subspecies americana ssp. nov. isolated from symptomatic oak

Gram-negative, facultatively anaerobic bacteria were isolated from symptomatic oak tissue in the UK and USA. Partial gyrB sequencing placed ten strains in the genus Brenneria, with B. goodwinii as the closest phylogenetic relative. The strains were investigated further using a polyphasic approach including MLSA (based on partial gyrB, rpoB, infB and atpD gene sequences), 16S rRNA gene sequencing, DNA–DNA relatedness studies and both phenotypic and chemotaxonomic assays. The MLSA and 16S rRNA gene analyses separated the strains into two groups based on origin, suggesting that they belong to Brenneria as two novel species. However, the DNA–DNA relatedness values revealed a closer relationship between the groups and indicated that they should belong to the same species. As the two groups of strains from the UK and USA can be differentiated from each other phenotypically and by ERIC PCR fingerprints, it is proposed to classify them as novel subspecies of a novel Brenneria species. The name Brenneria roseae sp. nov. (FRB 222^T = LMG 27714^T = NCPPB 4581^T) is proposed, with Brenneria roseae subsp. roseae ssp. nov. (FRB 222^T = LMG 27714^T = NCPPB 4581^T) for the strains from the UK and Brenneria roseae subsp. americana ssp. nov. (FRB 223^T = LMG 27715^T = NCPPB 4582^T) for the strains from the USA.     

Acetobacter oryzifermentans sp. nov., isolated from Korean traditional vinegar and reclassification of the type strains of Acetobacter pasteurianus subsp. ascendens (Henneberg 1898) and Acetobacter pasteurianus subsp. paradoxus (Frateur 1950) as Acetobacter ascendens sp. nov., comb. nov.

Twelve Acetobacter pasteurianus-related strains with publicly available genomes in GenBank shared high 16S rRNA gene sequence similarity (>99.59%), but average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values and multilocus sequence- and genome-based relatedness analyses suggested that they were divided into four different phylogenetic lineages. Relatedness analyses based on multilocus sequences, 1,194 core genes and whole-cell MALDI-TOF profiles supported that strains LMG 1590^T and LMG 1591 (previously classified as the type strains of A. pasteurianus subsp. ascendens and paradoxus, respectively) and strain SLV-7^T do not belong to A. pasteurianus. Strain SLV-7^T, isolated from Korean traditional vinegar, shared low ANI (<91.0%) and in silico DDH (44.2%) values with all other Acetobacter type strains analyzed in this study, indicating that strain SLV-7^T represents a new Acetobacter species. The phenotypic and chemotaxonomic analyses confirmed these results and therefore a new species named Acetobacter oryzifermentans sp. nov. is proposed with SLV-7^T (= KACC 19301^T = JCM 31096^T) as the type strain. Strains LMG 1590^T and LMG 1591 shared high ANI (99.4%) and in silico DDH (96.0%) values between them, but shared low ANI (<92.3%) and in silico DDH (<49.0%) values with other type strains analyzed in this study, indicating that strains LMG 1590^T and LMG 1591 should be reclassified into a new single species that should be named Acetobacter ascendens sp. nov., comb. nov., with LMD 51.1^T (= LMG 1590^T = NCCB 51001^T) as its type strain.     

Classification of Achromobacter genogroups 2, 5, 7 and 14 as Achromobacter insuavis sp. nov., Achromobacter aegrifaciens sp. nov., Achromobacter anxifer sp. nov. and Achromobacter dolens sp. nov., respectively

The phenotypic and genotypic characteristics of seventeen Achromobacter strains representing MLST genogroups 2, 5, 7 and 14 were examined. Although genogroup 2 and 14 strains shared a DNA–DNA hybridization level of about 70%, the type strains of both genogroups differed in numerous biochemical characteristics and all genogroup 2 and 14 strains could by distinguished by nitrite reduction, denitrification and growth on acetamide. Given the MLST sequence divergence which identified genogroups 2 and 14 as clearly distinct populations, the availability of nrdA sequence analysis as a single locus identification tool for all Achromobacter species and genogroups, and the differential phenotypic characteristics, we propose to formally classify Achromobacter genogroups 2, 5, 7 and 14 as four novel Achromobacter species for which we propose the names Achromobacter insuavis sp. nov. (with strain LMG 26845^T [= CCUG 62426^T] as the type strain), Achromobacter aegrifaciens sp. nov. (with strain LMG 26852^T [= CCUG 62438^T] as the type strain), Achromobacter anxifer sp. nov. (with strain LMG 26857^T [= CCUG 62444^T] as the type strain), and Achromobacter dolens sp. nov. (with strain LMG 26840^T [= CCUG 62421^T] as the type strain).     

Seminibacterium arietis gen. nov., sp. nov., isolated from the semen of rams

Two gram-negative, catalase- and oxidase-positive, bacillus-shaped bacterial strains were isolated from the semen of two rams. 16S rRNA gene sequencing demonstrated that both isolates represented a distinct subline within the family Pasteurellaceae with <95% sequence similarity to any recognized member of this family. Sequencing of rpoB and infB genes confirmed this finding with the semen isolates representing a new sub-line within the family Pasteurellaceae. The main cell fatty acids of strain DICM-00342^T were C_14:0, C_16:0, C_18:1ω7c and summed feature 3 (C_16:1ω7c/iso-C_15:0 2OH). Ubiquinone Q-8 was the major quinone and 1,3-diaminopropane was the predominat polyamine. Major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The new genus can be phenotypically distinguished from currently described genera of this family based on physiological traits and a combination of signature amino acids in the RpoB protein sequence. On the basis of these results we describe a new genus and species for which we propose the name of Seminibacterium arietis gen. nov., sp. nov. (DICM11-00342^T = CCUG 61707^T = CECT 8033^T).     

Arcobacter cloacae sp. nov. and Arcobacter suis sp. nov., two new species isolated from food and sewage

Three strains recovered from mussels (F26), sewage (SW28-13^T) and pork meat (F41^T) were characterized as Arcobacter. They did not appear to resemble any known species on the basis of their 16S rDNA-RFLP patterns and the rpoB gene analyses. However, strains F26 and SW28-13^T appeared to be the same species. The 16S rRNA gene sequence similarity of strains SW28-13^T and F41^T to the type strains of all other Arcobacter species ranged from 94.1% to 99.6% and 93.4% to 98.8%, respectively. Phenotypic characteristics and the DNA–DNA hybridization (DDH) results showed that they belonged to 2 new Arcobacter species. A multilocus phylogenetic analysis (MLPA) with the concatenated sequences of 5 housekeeping genes (gyrA, atpA, rpoB, gyrB and hsp60) was used for the first time in the genus, showing concordance with the 16S rRNA gene phylogenetic analysis and DDH results. The MALDI-TOF mass spectra also discriminated these strains as two new species. The names proposed for them are Arcobacter cloacae with the type strain SW28-13^T (=CECT 7834^T = LMG 26153^T) and Arcobacter suis with the type strain F41^T (=CECT 7833^T = LMG 26152^T).     

New insights into skeletal morphology of the oldest known silicoflagellates: Variramus, Cornua and Gleserocha gen. nov.

Two of the oldest known silicoflagellate-bearing sediments, lower Albian at Ocean Drilling Program Site 693 in the Weddell Sea of Antarctica and Santonian in the Devon Island sequence of the Canadian Archipelago, are re-examined with a focus on silicoflagellate genera Variramus, Cornua, and Gleserocha that lack basal rings, a feature appearing during late Santonian/early Campanian time within the genus Corbisema. The extraordinary variability of Variramus aculeifera is studied, and a new genus Gleserocha is proposed for taxa with apical structures made of three struts, but without pikes. This new genus includes previously described Variramus wisei and Cornua tapiae and new species G. harrisonii, and is here proposed as a genus transitional between Variramus and Cornua. Two unusual new species of Cornua, C. deflandrei and C. witkowskiana, are also described and a revised terminology is proposed for the skeletal components of Cornua and closely related genera.     

Evidence for the existence of two new members of the family Chlamydiaceae and proposal of Chlamydia avium sp. nov. and Chlamydia gallinacea sp. nov.

The family Chlamydiaceae with the recombined single genus Chlamydia currently comprises nine species, all of which are obligate intracellular organisms distinguished by a unique biphasic developmental cycle. Anecdotal evidence from epidemiological surveys in flocks of poultry, pigeons and psittacine birds have indicated the presence of non-classified chlamydial strains, some of which may act as pathogens. In the present study, phylogenetic analysis of ribosomal RNA and ompA genes, as well as multi-locus sequence analysis of 11 field isolates were conducted. All independent analyses assigned the strains into two different clades of monophyletic origin corresponding to pigeon and psittacine strains or poultry isolates, respectively. Comparative genome analysis involving the type strains of currently accepted Chlamydiaceae species and the designated type strains representing the two new clades confirmed that the latter could be classified into two different species as their average nucleotide identity (ANI) values were always below 94%, both with the closest relative species and between themselves.     

Staphylococcus petrasii sp. nov. including S. petrasii subsp. petrasii subsp. nov. and S. petrasii subsp. croceilyticus subsp. nov., isolated from human clinical specimens and human ear infections

Thirteen coagulase-negative, oxidase-negative, and novobiocin-susceptible staphylococci were isolated from human clinical specimens. The isolates were differentiated from known staphylococcal species on the basis of 16S rRNA, hsp60, rpoB, dnaJ, tuf, and gap gene sequencing, automated ribotyping, (GTG)₅-PCR fingerprinting, and MALDI-TOF MS analysis. Phylogenetic analysis based on the 16S rRNA gene sequence indicated phylogenetic relatedness of the analyzed strains to Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus devriesei, and Staphylococcus lugdunensis. DNA–DNA hybridization experiments between representative strains CCM 8418^T, CCM 8421^T, and the closest phylogenetic neighbors confirmed that the isolates represent novel Staphylococcus species, for which the name Staphylococcus petrasii sp. nov. is proposed. Genotypic and phenotypic analyses unambiguously split the strains into two closely related subclusters. Based on the results, two novel subspecies S. petrasii subsp. petrasii subsp. nov. and S. petrasii subsp. croceilyticus subsp. nov. are proposed, with type strains CCM 8418^T (=CCUG 62727^T) and CCM 8421^T (=CCUG 62728^T), respectively.     

Pancreatonema torriensis gen. nov., sp. nov. (Nematoda: Rhabdochonidae) from the pancreatic duct of Raja naevus

A new genus and species of nematode, Pancreatonema torriensis, from the pancreatic duct of Raja naevus caught off Aberdeen and north-west Scotland is described and aspects of its biology are discussed. According to the classification of Skrjabin, Sobolev & Ivashkin (1967) [Spirurata of animals and man and the diseases caused by them (4). Essentials of Nematodology, Vol. 16 (I.P.S.T. Translation No. 5904, Jerusalem, 1971)]it belongs to the family Rhabdochonidae, sub-family Prosungulonematinae, and is closely related to the genus Johnstonmawsonia. The taxonomy of the Prosungulonematinae is confused but it is suggested that Johnstonmawsonia should at present be restricted to those species of the genus described from marine teleosts, and that the species from freshwater teleosts should be included in the genus Prosungulonema.