A new aerobic alphaproteobacterium, strain SA-279T, was isolated from a water sample of a crater lake. The 16S rRNA gene sequence analysis revealed that strain SA-279T formed a distinct lineage within the family Ancalomicrobiaceae and shared the highest pairwise similarity values with Pinisolibacterravus E9T (96.4 %) and Ancalomicrobiumadetum NBRC 102456T (94.2 %). Cells of strain SA-279T were rod-shaped, motile, oxidase and catalase positive, and capable of forming rosettes. Its predominant fatty acids were C18 : 1ω7c (69.0 %) and C16 : 1ω7c (22.7 %), the major respiratory quinone was Q-10, and the main polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified aminophospholipid and an unidentified lipid. The G+C content of the genomic DNA of strain SA-279T was 69.2 mol%. On the basis of the phenotypic, chemotaxonomic and molecular data, strain SA-279T is considered to represent a new genus and species within the family Ancalomicrobiaceae, for which the name Siculibacillus lacustris gen. nov., sp. nov. is proposed. The type strain is SA-279T (=DSM 29840T=JCM 31761T).

An inventory of culturable yeasts from the soil and water of natural CO2 springs (mofettes) in northeast Slovenia is presented. In mofettes, CO2 of geological origin reaches the soil surface causing temporarily and spatially stable hypoxic environments in soil and water. In total, 142 yeast strains were isolated and identified from high CO2 and control meadow soil, meadow ground-water, forest pond and stream water. All water locations showed below-ground CO2 release. They were assigned to six basidiomycetous yeast genera (six species) and 11 ascomycetous genera (18 species). All ascomycetous yeasts, with the exception of Debaryomyces hansenii, were able to grow under elevated CO2 and fermented glucose. Candida sophiae-reginae, Pichia fermentans and Candida vartiovaarae were the dominating species in meadow and forest high CO2 exposed water. Meyerozyma guilliermondii and Wickerhamomyces anomalus predominated in high CO(2 )exposed soils. Using high dilution plating of a mofette soil sample, four strains of an unknown basidiomycetous species were isolated and are here newly described as Occultifur mephitis based on molecular phylogenetic and phenotypic criteria. The type strain of Occultifur mephitis is EXF-6436(T)[CBS 14611=PYCC 7049, LT594852 (D1/D2), KX929055 (ITS)]. An additional three isolated strains are EXF-6437 (LT594853, KX929056), EXF-6473 (LT594863, KX929057) and EXF-6482 (LT594867, KX929054), as well as a strain reported from previous studies isolated from a leaf of Cistus albidus in Portugal (CBS 10223=PYCC 6067), EU002842 (D1/D2), KY308183 (ITS).

The genus Macrococcus is a close relative of the genus Staphylococcus. Whilst staphylococci are widespread as human pathogens, macrococci have not yet been reported from human clinical specimens. Here we investigated Gram-positive and catalase-positive cocci recovered from human clinical material and identified as Macrococcus sp. by a polyphasic taxonomic approach and by comparative genomics. Relevant phenotypic, genotypic and chemotaxonomic methods divided the analyzed strains into two separate clusters within the genus Macrococcus. Comparative genomics of four representative strains revealed enormous genome structural plasticity among the studied isolates. We hypothesize that high genomic variability is due to the presence of a com operon, which plays a key role in the natural transformation of bacilli and streptococci. The possible uptake of exogenous DNA by macrococci can contribute to a different mechanism of evolution from staphylococci, where phage-mediated horizontal gene transfer predominates. The described macrococcal genomes harbor novel plasmids, genomic islands and islets, as well as prophages. Capsule gene clusters, intracellular protease, and a fibronectin-binding protein enabling opportunistic pathogenesis were found in all four strains. Furthermore, the presence of a CRISPR-Cas system with 90 spacers in one of the sequenced genomes corresponds with the need to limit the burden of foreign DNA. The highly dynamic genomes could serve as a platform for the exchange of virulence and resistance factors, as was described for the methicillin resistance gene, which was found on the novel composite SCCmec-like element containing a unique mec gene complex that is considered to be one of the missing links in SCC evolution. The phenotypic, genotypic, chemotaxonomic and genomic results demonstrated that the analyzed strains represent one novel subspecies and three novel species of the genus Macrococcus, for which the names Macrococcus caseolyticus subsp. hominis subsp. nov. (type strain CCM 7927T = DSM 103682T), Macrococcus goetzii sp. nov. (type strain CCM 4927T = DSM 103683T), Macrococcus epidermidis sp. nov. (type strain CCM 7099T = DSM 103681T), and Macrococcus bohemicus sp. nov. (type strain CCM 7100T = DSM 103680T) are proposed. Moreover, a formal description of Macrococcus caseolyticus subsp. caseolyticus subsp. nov. and an emended description of the genus Macrococcus are provided.

A Gram-stain-positive, flagellated, catalase- and cytochrome c oxidase-positive bacterial strain, designated S20-100T, was isolated from alpine forest soil. Growth occurred at a temperature range of 0-30 °C, at pH 6-9 and in the presence of 0-1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain S20-100T was related to the genus Marmoricola and had the highest 16S rRNA gene sequence similarity to Marmoricola ginsengisoli Gsoil 097T (98.4 %) and Marmoricola solisilvae KIS18-7T (98.3 %). The cell-wall peptidoglycan of strain S20-100T contained ll-diaminopimelic acid (ll-Dpm) as the diagnostic diamino acid and was of the type A3γ ll-Dpm - Gly. The strain contained MK-8(H4) as the predominant isoprenoid quinone and diphosphatidylglycerol, phosphatidylglycerol, four unidentified phospholipids and three unidentified lipids in lower amounts. The major cellular fatty acids (>10 %) were iso-C16 : 0, C17 : 1ω6c and C18 : 1ω9c. The genomic DNA G+C content was 66.2 mol%. Combined data of phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strain S20-100T represents a novel species of the genus Marmoricola, for which the name Marmoricola silvestris sp. nov. is proposed. The type strain is S20-100T (=DSM 104694T=LMG 30008T).

Roseoflavin is the only known riboflavin (vitamin B2) analog with antibiotic properties. It is actively taken up by many microorganisms and targets flavinmononucleotide riboswitches and flavoproteins. It is described as the product of the tentatively named 'Streptomyces davawensis' JCM 4913. Taxonomic analysis of this strain with a polyphasic approach showed that it is very closely related to Streptomyces cinnabarinus (DSM 40467). The two Streptomyces isolates were obtained from different geographical locations (the Philippines and the Kamchatka Peninsula, respectively), their genomes have been sequenced and the question was whether or not the two isolates were representatives of the same species. As we also worked with another isolate of Streptomyces cinnabarinus JS 360, the producer of the cinnabaramides, we wanted to clarify the taxonomic position of the three isolates by using a polyphasic approach. After analysis of the 16S rRNA gene sequence, we found in total 23 species of the genus Streptomyces that showed a similarity higher than 98.5% to the three strains. We showed that 'S. davawensis' JCM 4913 and S. cinnabarinus DSM 40467 were very closely related but belong to two different species. Hence, we validate 'S. davawensis' as Streptomyces davaonensis sp. nov. with the type strain JCM 4913(T) (=DSM 101723(T)). In addition, the cinnabaramide producer can be clearly differentiated from S. davaonensis and this isolate is described as Streptomyces cinnabarigriseus sp. nov. with strain JS360(T) (=NCCB 100590(T) = DSM 101724(T)) as the type strain.

The novel strain IHBB 11108(T) was a psychrotolerant and alkaliphilic bacterium isolated from the subsurface water of Chandra Tal Lake in the Lahaul-Spiti valley located in the Indian trans-Himalayas. Cells were Gram-stain-positive, aerobic, non-motile, catalase-positive and oxidase-negative. The strain grew at 5-37 degrees C (optimum 28 degrees C), pH 5.0-12.0 (optimum pH 7.0) and with up to 8% NaCl (optimum 1 %). The 16S rRNA gene sequence analysis revealed the highest relatedness of strain IHBB 11108(T) with Psychromicrobium silvestre DSM 102047(T) (97.5 %), Arthrobacter russicus DSM 14555(T) (97.4 %) and Renibacterium salmoninarum ATCC 33209(T) (97.4 %). The strain contained a quinone system with 57.2% MK-9(H-2), 39.1% MK-10(H-2), 3.0% MK-8(H-2) and 0.7% MK-7(H-2). The polar lipids detected were diphosphatidylglycerol, dimannosylglyceride, phosphatidylinositol, phosphatidylglycerol, monogalactosyldiacylglycerol, one unidentified glycolipid and four unidentified lipids. The cell-wall peptidoglycan structure type was A3 alpha L-Lys-L-Thr-L-Ala with substitution of the alpha-carboxyl group of D-Glu by alanine amide. Anteiso-C-15:0, iso-C-16:0 and anteiso-C-17:0 were the predominant fatty acids. The genomic DNA G+C content was 59.0 mol%. The DNA-DNA relatedness of strain IHBB 11108(T) was 46.7 +/- 2.2, 43.1 +/- 2.5 and 19.1 +/- 2.4% with P. silvestre DSM 102047(T), A. russicus DSM 14555(T) and R. salmoninarum ATCC 33209(T), respectively. On the basis of the results of the phenotypic, chemotaxonomic and phylogenetic analyses, IHBB 11108(T) is considered to represent a novel species of the genus Psychromicrobium for which the name Psychromicrobium lacuslunae sp. nov. is proposed. The type strain is IHBB 11108(T) (=MTCC 12460(T) = MCC 2780(T) = JCM 31143(T) = KACC 19070(T)).

A novel strain belonging to the genus Promicromonospora, designated HM 533T, was isolated from soil in Kerman Province, Iran. It produced long and branched hyphae on ISP 2 medium that developed into a large number of irregular-shaped spores. It showed optimal growth at 25-30 °C and pH 5.0-8.0 with 0-4 % (w/v) NaCl. The peptidoglycan type of strain HM 533T was A4α l-Lys-l-Ala-d-Glu. Whole-cell hydrolysates of strain HM 533T contained the sugars ribose, glucose and galactose. The main phospholipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, two unknown glycolipids and an unknown phospholipid. MK-9(H4) and MK-9(H2) were the predominant menaquinones. The fatty acids pattern was mainly composed of the saturated branched-chain acids anteiso-C15 : 0 and iso-C15 : 0. The 16S rRNA gene sequence analysis showed the highest pairwise sequence identity (99.5-97.1 %) with the members of the genus Promicromonospora. Based on phenotypic and genotypic features, strain HM 533T is considered to represent a novel species of the genus Promicromonospora, for which the name Promicromonospora kermanensis is proposed with strain HM 533T (=DSM 45485T=UTMC 00533T=CECT 8709T) as the type strain.

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-8T 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-C15:0 and iso-C16:0 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-8T (=CCTCC AB2012108T=KACC 16706T). Further our analyses also revealed that B. encimensis SGD-V-25T is a later heterotypic synonym of Bacillus badius DSM 23T.

Heavy contamination of soils by crude oil is omnipresent in areas of oil recovery and exploitation. Bioremediation by indigenous plants in cooperation with hydrocarbon degrading microorganisms is an economically and ecologically feasible means to reclaim contaminated soils. To study the effects of indigenous soil bacteria capable of utilizing oil hydrocarbons on biomass production of plants growing in oil-contaminated soils eight bacterial strains were isolated from contaminated soils in Kazakhstan and characterized for their abilities to degrade oil components. Four of them, identified as species of Gordonia and Rhodococcus turned out to be effective degraders. They produced a variety of organic acids from oil components, of which 59 were identified and 7 of them are hitherto unknown acidic oil metabolites. One of them, Rhodococcus erythropolis SBUG 2054, utilized more than 140 oil components. Inoculating barley seeds together with different combinations of these bacterial strains restored normal growth of the plants on contaminated soils, demonstrating the power of this approach for bioremediation. Furthermore, we suggest that the plant promoting effect of these bacteria is not only due to the elimination of toxic oil hydrocarbons but possibly also to the accumulation of a variety of organic acids which modulate the barley's rhizosphere environment.

Strain RP1T, a Gram-stain-positive, non-motile, non-spore-forming, coccus-shaped bacterium, was isolated from drainage of India Pesticides Limited, a lindane-producing unit situated at Chinhat, Lucknow, India. 16S rRNA gene sequence analysis revealed that strain RP1T belongs to the family Propionibacteriaceae and was closely related to the members of the genus Tessaracoccus with a similarity range of 95.4-97.6%. Strain RP1T was facultatively anaerobic, oxidase-negative, catalase-positive and capable of nitrate reduction. Strain RP1T contained peptidoglycan type A3γ', with ll-diaminopimelic acid as the diagnostic diamino acid and glycine at position 1 of the peptide subunit. The major cellular fatty acid of strain RP1T was anteiso-C15 : 0 but a significant amount of iso-C14:0 was also detected. MK-9(H4) was the major respiratory quinone and polyamines detected were spermine and spermidine. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids and two unknown phospholipids. The G+C content of the DNA was 66.7 mol%. The levels of DNA-DNA relatedness between RP1T and Tessaracoccus lubricantis KSS-17SeT, Tessaracoccus oleiagri SL014B-20A1T and Tessaracoccus flavescens SST-39T were 49.8, 34.8 and 23.5%, respectively. Based on the phenotypic and phylogenetic data presented, strain RP1T can be differentiated from previously described species of the genus Tessaracoccus, and thus represents a novel species, for which the name Tessaracoccus flavus sp. nov. is proposed. The type strain is RP1T (=DSM 100159T=MCC 2769T=KCTC 39686T).

A Gram-stain-positive staining, motile, endospore forming and moderately halophilic bacterium, designated as strain AS8T, was isolated from a microbial mat deposited at thermal discharges of Manikaran hot spring (with surface water temperature ~95 °C) located in Himachal Pradesh, India. 16S rRNA gene sequence based phylogenetic analysis revealed that strain AS8T belonged to the genus Fictibacillus with the highest sequence similarity to Fictibacillus nanhaiensis DSM 23009T (99.9 %) and Fictibacillus phosphorivorans Ca7T (99.9 %), followed by Fictibacillus barbaricus V2-BIII-A2T (99.1 %) and Fictibacillus arsenicus Con a/3T (97.4 %). The polar lipids fraction consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cell-wall peptidoglycan was of the type A1γ based on directly cross-linked meso-diaminopimelic acid. The DNA G+C content of strain AS8T was found to be 46.9 mol%. The quinone system of strain AS8T consisted of MK-7 predominantly, and the polyamine pattern primarily contained spermidine and spermine. The major cellular fatty acids in strain AS8T were iso-C15:0, anteiso-C15:0 and iso-C16:0. The strain showed DNA-DNA relatedness of 52.7 % with F. nanhaiensis DSM 23009T, 50.7 % with F. phosphorivorans Ca7T, 34.8 % with F. barbaricus V2-BIII-A2T and 38.0 % with F. arsenicus Con a/3T. In spite of the high 16S rRNA gene sequence similarities, the DNA-DNA hybridization and gyr B gene sequencing results (≤87 %) supported by physiological and biochemical tests demonstrated that strain AS8T is a representative of a novel species, for which the name Fictibacillus halophilus sp. nov. is proposed. The type strain is AS8T (=MCC 2765T=DSM 100124T=KCTC 33758T).

Due to its separate position within the genus Arthrobacter in many published phylogenetic trees and its incomplete chemotaxonomic characterization, the type strain of Arthrobacter sanguinis was subjected to analysis of its chemotaxonomic traits including quinone system, polar lipid profile, peptidoglycan structure and fatty acid profile. The fatty acid profile consisted of the major compounds (> 10 %) iso-C-15:0, anteiso-C-15:0 and anteiso-C-17:0. It showed a quinone system with the predominating menaquinone MK-9(H-2). Both, fatty acid profile and quinone system are in line with the description of the genus Arthrobacter. The peptidoglycan type was L-Lys-L-Ala-Gly (A11.50) which is unique within the genus Arthrobacter sensu lato and also among species of the genus Arthrobacter recently reclassified in the genera Sinomonas, Paenarthrobacter and Pseudarthrobacter. The polar lipid profile was very complex and unique among the group of taxa in containing relatively high proportions of several unidentified lipids. In conclusion from the phylogenetic position and chemotaxonomic distinguishability from related taxa, the reclassification of Arthrobacter sanguinis in a new genus and species, Haematomicrobium sanguinis gen. nov., comb. nov., is proposed. The type strain of the type species is 741 T (= CCUG 46407(T) = DSM 21259 (T)).

During the course of a screening programme for new taxa of actinobacteria, a strain designated ACD1(T), was isolated from a Saharan soil in the Hoggar region (Algeria). The taxonomic position of this strain was determined using a polyphasic taxonomic approach. The strain was observed to form extensively branched, non-fragmenting substrate mycelium, and aerial mycelium with straight to flexuous, hooked and irregular spirals (1-2 turns) forming short chains of spores. The diamino acid present in the cell wall is meso-diaminopimelic acid. Galactose, glucose, madurose, mannose and ribose occur in whole-cell hydrolysates. The diagnostic phospholipids detected were diphosphatidylglycerol and phosphatidylinositol. The major menaquinones were identified as MK-9 (H4) and MK-9 (H2). The major fatty acids were found to be C16:0, C18:1 cis9, iso-C16:0 and 10-methyl C18:0. Phylogenetic analysis based on the 16S rRNA gene showed that the strain belongs to the genus Actinomadura, and is closely related to Actinomadura sediminis DSM 45500(T) (98.5 % similarity) and Actinomadura cremea subsp. cremea DSM 43676(T) (98.3 % similarity). However, DNA-DNA hybridization revealed only 48.0 % relatedness with A. sediminis DSM 45500(T) and 33.2 % relatedness with A. cremea subsp. cremea DSM 43676(T). The combined phenotypic and genotypic data showed that the strain represents a novel species of the genus Actinomadura, for which the name Actinomadura algeriensis sp. nov. is proposed, with the type strain ACD1(T) (= DSM 46744(T) = CECT 8841(T)).

An aerobic, mildly acidophilic actinobacterium was isolated from the Ochre Beds bog in Kootenay National Park, Canada. Cells of isolate OB1T were Gram-stain-positive, non-motile, pink- to purple-pigmented filaments. The pH range for growth was pH 3.5-6.5 (optimum pH 5.5), and the temperature range was 13-30°C. The major cellular fatty acids were i-C16 : 0 (28.5 %), i-C15 : 0 (14.6 %) and ai-C15 : 0 (14.3 %), and the major polar lipid was phosphohexose. The major quinone was menaquinone-11 (MK-11), and the peptidoglycan type was A1γ. The DNA G+C content was 70.2 %. Along with growth on complex media including yeast extract, proteose peptone, casamino acids and tryptic soy broth, growth occured on mono- and disaccharides (glucose, sucrose, galactose and xylose) and polysaccharides (starch, gellan, pectin, xylan and alginate). Anaerobic growth was not observed. The cells did not fix atmospheric nitrogen. On the basis of comparative 16S rRNA gene sequence analysis, this isolate belonged to the family Actinospicaceae, in the suborder Catenulisporineae of the order Actinomycetales. The most closely related species was Actinospica robiniae. However, the 16S rRNA gene sequence identity to this bacterium was low (92.8 %) and there were several chemotaxonomic differences from this species. We therefore propose a novel genus and species, Actinocrinis puniceicyclus gen. nov., sp. nov., with strain OB1T (=DSM 45618T=ATCC BAA-2771T) as the type strain.

A bacterial strain with the ability to transform bisphenol A (BPA) and other so-called “new-generation bisphenols” like bisphenol C (BPC), bisphenol E (BPE), bisphenol F (BPF) and bisphenol Z (BPZ) was isolated from sewage sludge and identified as Bacillus amyloliquefaciens. We investigated the biotransformation of bisphenols and analyzed the toxicity and estrogenicity of the products formed compared to the parent compounds. During the incubation of this bacterial strain with different bisphenols one major metabolite was detected in each case by HPLC but its formation was partly reversible. Highest transformation rate of 77% of the initial concentration applied was determined for BPA and BPE. Mass spectrometric and nuclear magnetic resonance spectroscopic analyses as well as deconjugation experiments proofed the formation of phosphate conjugates with each bisphenol. The conjugates formed were considerably less toxic and less estrogenically active than their parent bisphenols.

An investigation into the taxonomic position of Bacillus isronensis MTCC 7902T revealed that the strain shares a common phylogenetic lineage with Solibacillus silvestris MTCC 10789T. It displays considerable overlap in phenotypic properties with the genus Solibacillus, including endospore shape and position, oxidase and catalase activities, presence of iso-C15 : 0, C16 : 1ω7c alcohol and iso-C17 : 1ω7c as major cellular fatty acids, A4α-type cell-wall peptidoglycan, polar lipids and menaquinone pattern. These features reinforce the findings of molecular phylogenetic analyses based on 16S rRNA gene, gyrB gene and 16S-23S internal transcribed spacer (ITS) region sequences and, in line with the recommendations of Kämpfer et al. [Int J Syst Evol Microbiol 56 (2006), 781-786], provide justification for the transfer of Bacillus isronensis from the genus Bacillus to Solibacillus as Solibacillus isronensis comb. nov. The type strain is B3W22T ( = MTCC 7902T = DSM 21046T = JCM 13838T). An emended description of the genus Solibacillus is also provided.

A novel actinomycete, designated HM 537T, was isolated from soil in Hamedan Province, Iran. Cell-wall hydrolysates of strain HM 537T contained meso-diaminopimelic acid, and whole-cell hydrolysates contained ribose, glucose, galactose, rhamnose and traces of mannose. The main phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and an unknown phospholipid. MK-9(H4), an unknown MK and MK-10(H4) were the predominant menaquinones. The major fatty acids included iso-C16 : 0, iso-C15 : 0, iso-C16 : 1 G and 9(?)-methyl C16 : 0. Strain HM 537T had the highest 16S rRNA gene sequence similarity to Saccharothrix hoggarensis DSM 45457T (99.5 %) and Saccharothrix saharensis DSM 45456T (99.0 %). DNA-DNA hybridization studies showed relatedness values of 13.8 ± 3.3 % with S. hoggarensis DSM 45457T and 16.3 ± 3.5 % with S. saharensis DSM 45456T. Based on the results of phenotypic and genotypic studies, strain HM 537T represents a novel species of the genus Saccharothrix, for which the name Saccharothrix ecbatanensis sp. nov. is proposed. The type strain is HM 537T ( = DSM 45486T = UTMC 00537T = CCUG 63021T).

The arrangement of content follows a phylogenetic framework or road map based largely on analyses of nucleotide sequences of the ribosomal small subunit RNA rather than on phenotypic data. Implicit in the use of the road map are the convictions that prokaryotes have a phylogeny and that phylogeny matters. However, phylogenies, like other experimentally derived hypotheses, are not static but may change whenever new data and/or improved methods of analysis become available. Thus, the large increases in data have led to a re‐evaluation of the road map. Not surprisingly, the taxonomic hierarchy has been modified or newly interpreted for a number of taxonomic units.