- Volume 60, Issue 8, 2010

Two Gram-stain-positive, mycelium-forming actinobacteria (strains 14-Be-013T and 02-Gi-014) were isolated from walls colonized with moulds and studied taxonomically. The isolates formed yellowish-pigmented substrate mycelium showing no fragmentation. Comparative analysis of 16S rRNA gene sequences showed that these bacteria are most closely related to genera within the family Nocardiopsaceae, but form a separate lineage within this family. Highest sequence similarities were to the type strains of Marinactinospora thermotolerans (96.0 % to 14-Be-013T), Nocardiopsis dassonvillei subsp. albirubida and Nocardiopsis lucentensis (both 95.3 % to 14-Be-013T). Whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid of the cell wall and no diagnostic sugars. Mycolic acids were absent. The major menaquinones were MK-10(H4), MK-11(H4) and MK-12(H2). The polar lipid profile consisted of phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown lipids. Major fatty acids iso-C16 : 0, anteiso-C17 : 0 and C18 : 1 ω9c supported the affiliation of these isolates to the family Nocardiopsaceae. Phenotypic analysis (including chemotaxonomy) further differentiated strains 14-Be-013T and 02-Gi-014 from the most closely related members of the genera Marinactinospora and Nocardiopsis. Since the two strains form a distinct lineage in the 16S rRNA gene sequence-based phylogenetic tree, the novel genus Murinocardiopsis gen. nov. with the type species Murinocardiopsis flavida sp. nov. is proposed. The type strain of Murinocardiopsis flavida is 14-Be-013T (=DSM 45312T =CCM 7612T).

A novel actinobacterium, designated RS-15T, was isolated from rhizosphere soil of a plant (Peucedanum japonicum Thunb.) on Mara Island, Jeju, Republic of Korea. Cells were strictly aerobic, Gram-stain-positive, oxidase-negative, catalase-positive, non-motile, irregular, short rods. The peptidoglycan in the cell wall was of the B2β type with ornithine as the diagnostic diamino acid. The major menaquinone was MK-8; small amounts of MK-9 and MK-7 were also present. The polar lipids contained phosphatidylglycerol, five unknown glycolipids, three unknown phospholipids and two unknown lipids. Mycolic acids were not present. The predominant fatty acids were summed feature 7 (one or more of C18 : 1 ω9c, C18 : 1 ω12t and C18 : 1 ω7c), anteiso-C15 : 0 and C14 : 0 2-OH. The DNA G+C content was 68.3 mol%. 16S rRNA gene sequence analysis showed that strain RS-15T belonged to the family Microbacteriaceae and formed a tight phylogenetic cluster with Frondihabitans australicus E1HC-02T (98.5 % sequence similarity). The DNA–DNA relatedness between strain RS-15T and Frondihabitans australicus DSM 17894T was 17.2 % (17.1 %, duplicate measurements). On the basis of the physiological, chemotaxonomic and DNA–DNA hybridization data, strain RS-15T is considered to represent a novel species of the genus Frondihabitans, for which the name Frondihabitans peucedani sp. nov. is proposed. The type strain is RS-15T (=KCTC 13435T =DSM 22180T). An emended description of the genus Frondihabitans is also presented.

A novel actinomycete, designated strain OU-63T, was isolated from garden soil collected on the campus of Osmania University in Hyderabad, southern India. The strain was found to have morphological and chemotaxonomic characteristics typical of the genus Streptomyces. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus Streptomyces, and was related most closely to Streptomyces chartreusis NBRC 12753T (98.6 % similarity). However, the mean level of DNA–DNA relatedness between the two strains was only 25±1.73 %. Based on DNA–DNA relatedness, morphological and phenotypic data, strain OU-63T could be distinguished from the type strains of phylogenetically related species. It is therefore considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces osmaniensis sp. nov. is proposed. The type strain is OU-63T (=CCTCC AA209025T =PCM 2690T).

An actinomycete, designated MS426T, the culture broth of which showed potent antimicrobial activity, was isolated from a deep-sea sediment sample of the South China Sea. An almost-complete sequence of the 16S rRNA gene of strain MS426T was determined and aligned with those of representatives of the family Micromonosporaceae available in public databases. Phylogenetic trees were inferred by using three algorithms. Strain MS426T formed a branch adjacent to Verrucosispora lutea YIM 013T in a distinct cluster occupied only by strains of the genus Verrucosispora. Strain MS426T was distinguishable from the type strains of the two described Verrucosispora species by using a combination of chemical and morphological markers and by DNA–DNA relatedness. On the basis of these genotypic and phenotypic differences, the novel antimicrobial strain with pharmaceutical potential represents a novel species, for which the name Verrucosispora sediminis sp. nov. is proposed. The type strain is MS426T (=CGMCC 4.3550T =JCM 15670T).

A novel, aerobic, Gram-positive actinomycete strain, designated XMU15T, was isolated from an ocean sediment collected from Zhaoan Bay in the East China Sea and was subjected to a polyphasic approach to determine its taxonomic position. The isolate grew optimally at 28 °C and at pH 7.0 in the presence of 3 % (w/v) NaCl on ISP medium 2. Gelatin liquefaction, milk coagulation and nitrate reduction were positive. Cellulose and starch hydrolysis, hydrogen sulfide and melanin production, and catalase, urease and oxidase activities were negative. The predominant menaquinone of the isolate was MK-9 (H4), and meso-diaminopimelic acid was the diagnostic amino acid in the cell wall. The phospholipids of the isolate comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and a minor amount of phosphatidylethanolamine. The major fatty acids of the strain were iso-C16 : 0 (26.36 %), C17 : 1 ω6c (16.80 %), C15 : 0 (16.2 %), C16 : 0 (8.90 %), C17 : 1 ω8c (7.69 %) and iso-C16 : 1 H (5.95 %). The DNA G+C content of the genomic DNA was 68.1 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that the isolate fell within the evolutionary radiation encompassed by the genus Saccharomonospora and showed the highest 16S rRNA gene sequence similarity (96.7 %) to Saccharomonospora xinjiangensis DSM 44391T. Based on the results of 16S rRNA gene sequence analysis and phenotypic and genotypic characterization, strain XMU15T (=KCTC 19701T =CCTCC AA 209048T) represents a novel species of the genus Saccharomonospora, for which the name Saccharomonospora marina sp. nov. is proposed.

Two bacterial strains, DNG5T and V3M1T, isolated from forest soil of the Changbai mountains in China, were characterized using a polyphasic approach. Analysis of their 16S rRNA gene sequences indicated that strains DNG5T and V3M1T were phylogenetically related to members of the genus Agrococcus (96.0–98.4 % similarity) and Micrococcus (96.7–98.0 % similarity), respectively, within the order Actinomycetales. Strains DNG5T and V3M1T were Gram-stain-positive and strictly aerobic and formed yellow colonies on LB agar. Cells of strain DNG5T were short, non-motile rods, 0.4–0.5×0.8–1.0 μm. Strain DNG5T contained MK-10 and MK-11 as the major respiratory quinones and anteiso-C15 : 0 (49.2 %) and iso-C16 : 0 (22.4 %) as the major fatty acids. The diamino acid in the peptidoglycan of strain DNG5T was 2,4-diaminobutyric acid and the murein was of the acetyl type. Cells of strain V3M1T were cocci, 0.6–0.7 μm in diameter. The cell-wall peptidoglycan of strain V3M1T contained the amino acids lysine, glutamic acid, alanine and glycine. Strain V3M1T contained MK-7, MK-7(H2), MK-8 and MK-8(H2) as respiratory quinones and anteiso-C15 : 0 (78.2 %) and iso-C15 : 0 (13.1 %) as the major cellular fatty acids. The DNA G+C contents of strains DNG5T and V3M1T were 75.9 and 67.2 mol%, respectively. The DNA–DNA relatedness of strain DNG5T to Agrococcus jejuensis DSM 22002T, A. jenensis JCM 9950T, A. baldri JCM 12132T and A. citreus JCM 12398T was 58.3, 43.9, 36.1 and 54.1 %, respectively. The DNA–DNA relatedness of strain V3M1T to Micrococcus luteus CGMCC 1.2299T, M. antarcticus CGMCC 1.2373T and M. lylae CGMCC 1.2300T was 57.5, 45.4 and 39.0 %, respectively. Combining phenotypic and genotypic traits, strain DNG5T represents a novel species of the genus Agrococcus, for which the name Agrococcus terreus sp. nov. is proposed, with DNG5T (=CGMCC 1.6960T =NBRC 104260T) as the type strain. Strain V3M1T represents a novel species of the genus Micrococcus, for which the name Micrococcus terreus sp. nov. is proposed, with V3M1T (=CGMCC 1.7054T =NBRC 104258T) as the type strain.

The taxonomic position of a rhizosphere soil isolate, designated strain SR8.15T, was determined by using a polyphasic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence of the strain showed that it formed a well-separated sub-branch within the radiation encompassing the genus Saccharopolyspora. Highest levels of 16S rRNA gene sequence similarity were found between strain SR8.15T and Saccharopolyspora shandongensis CGMCC 4.3530T (98.9 %) and Saccharopolyspora spinosa DSM 44228T (98.5 %). However, these strains shared low levels of DNA–DNA relatedness (<26 %). Strain SR8.15T had chemical characteristics consistent with its classification in the genus Saccharopolyspora. It contained meso-diaminopimelic acid as the diagnostic diamino acid. Whole-cell hydrolysates contained arabinose and galactose. The diagnostic phospholipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The main menaquinone was MK-9(H4). No mycolic acid was detected. The predominant cellular fatty acid was iso-C16 : 0. The G+C content of the genomic DNA of strain SR8.15T was 70.3 mol%. Strain SR8.15T had a phenotypic profile that readily distinguished it from recognized representatives of the genus Saccharopolyspora. It is evident from its combined genotypic and phenotypic properties that strain SR8.15T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora phatthalungensis sp. nov. is proposed. The type strain is SR8.15T (=TISTR 1921T=BCC 35844T=NRRL B-24798T).

A taxonomic study was performed on strain D7015T, which was isolated from coastal sediment close to a coal-fired power station in Qingdao, China. Cells of strain D7015T were Gram-positive, non-motile, diphtheroid rods that grew in the presence of 0–8 % (w/v) NaCl and at 4–37 °C, with optimum growth at 1 % (w/v) NaCl and 30–32 °C. The DNA G+C content was 65.0 mol%. The major fatty acids were C18 : 1 ω9c (56.18 %), C16 : 0 (38.02 %), C16 : 1 ω7c (4.45 %), C18 : 0 (1.0 %) and C14 : 0 (0.35 %). On the basis of morphological, physiological and phylogenetic characteristics, strain D7015T was classified in the genus Corynebacterium. It exhibited a 16S rRNA gene sequence similarity of 95.9 % and a DNA–DNA relatedness value of 20.4 % with Corynebacterium halotolerans DSM 44683T. Strain D7015T was sufficiently different from recognized species of the genus Corynebacterium to be considered to represent a novel species. The name Corynebacterium marinum sp. nov. is proposed, with strain D7015T (=CGMCC 1.6998T=NRRL B-24779T) as the type strain.

Two novel haloalkaliphilic archaea, strains CG-6T and CG-4, were isolated from sediment of the hypersaline Lake Chagannor in Inner Mongolia, China. Cells of the two strains were pleomorphic, non-motile and strictly aerobic. They required at least 2.5 M NaCl for growth, with optimum growth at 3.4 M NaCl. They grew at pH 8.0–11.0, with optimum growth at pH 9.0. Hypotonic treatment with less than 1.5 M NaCl caused cell lysis. The two strains had similar polar lipid compositions, possessing C20C20 and C20C25 derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. No glycolipids were detected. Comparison of 16S rRNA gene sequences and morphological features placed them in the genus Natronorubrum. 16S rRNA gene sequence similarities to strains of recognized species of the genus Natronorubrum were 96.2–93.8 %. Detailed phenotypic characterization and DNA–DNA hybridization studies revealed that the two strains belong to a novel species in the genus Natronorubrum, for which the name Natronorubrum sediminis sp. nov. is proposed; the type strain is CG-6T (=CECT 7487T =CGMCC 1.8981T =JCM 15982T).

An extremely halophilic archaeon, strain RO5-8T, was isolated from a disused marine solar saltern in China. The cells were pleomorphic and flat. In static liquid medium, cells floated to the surface. Strain RO5-8T stained Gram-negative and colonies were pink-pigmented. It was able to grow at 30–50 °C (optimum 40 °C), at 2.6–4.3 M NaCl (optimum 3.1 M NaCl), at 0.03–0.5 M MgCl2 (optimum 0.03 M MgCl2) and at pH 5.5–7.5 (optimum pH 6.0–6.5). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 12 % (w/v). The major polar lipids of strain RO5-8T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and one major glycolipid chromatographically identical to the sulfated mannosyl glucosyl diether S-DGD-1. On the basis of 16S rRNA gene sequence analysis, strain RO5-8T was closely related to three strains of Haloplanus natans with similarities of 97.3–97.6 %. The DNA G+C content of strain RO5-8T was 62.1 mol%. The DNA–DNA hybridization value between strain RO5-8T and Haloplanus natans JCM 14081T was 51.6 %. It was concluded that strain RO5-8T represents a novel species of the genus Haloplanus, for which the name Haloplanus vescus sp. nov. is proposed. The type strain is RO5-8T (=CGMCC 1.8712T =JCM 16055T).

The taxonomic position of three bacterial strains, Asr22-19T, NBRC 101035 and NBRC 101041, isolated from shellfish in Japan, was determined by using a polyphasic taxonomic approach. The strains were facultatively anaerobic, motile by gliding and Gram-staining-negative slender rods. Their major respiratory quinone was menaquinone-7 and their predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH, C16 : 0 3-OH, and C16 : 0. The G+C content of the genomic DNA was 42.0–42.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains clustered with the genus Persicobacter in the family ‘Flammeovirgaceae’. DNA–DNA relatedness values were higher than 68 % among strains Asr22-19T, NBRC 101035 and NBRC 101041, and were lower than 28 % between strain Asr22-19T and Persicobacter diffluens NBRC 15940T. The three novel strains could be differentiated from Persicobacter diffluens by several phenotypic characteristics. On the basis of these results, the novel species Persicobacter psychrovividus sp. nov. (type strain Asr22-19T=NBRC 101262T=CIP 109100T) is proposed and emended descriptions are given for the genus Persicobacter and for Persicobacter diffluens.

A bacterial strain (CC-VM-7T), isolated from the faeces of the pill millipede Arthrosphaera magna Attems collected in India, was studied to determine its taxonomic allocation. Cells stained Gram-negative and were rod-shaped. Comparative analyses of the 16S rRNA gene sequence of the strain with those of the most closely related species clearly suggested allocation to the genus Chryseobacterium, with the highest sequence similarities of 99.2 % to Chryseobacterium gleum CCUG 14555T, 98.6 % to Chryseobacterium indologenes CCUG 14556T and 98.4 % to Chryseobacterium aquifrigidense KCTC 12894T. 16S rRNA gene sequence similarities to all other species of the genus Chryseobacterium were below 98 %. The major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 1 ω9c. DNA–DNA hybridization resulted in relatedness values of only 29.6 % (reciprocal 31.3 %) to Chryseobacterium gleum CCUG 14555T, 41.2 % (reciprocal 38.8 %) to C. indologenes CCUG 14556T and 35.4 % (reciprocal 38.5 %) to C. aquifrigidense KCTC 12894T. DNA–DNA relatedness, biochemical and chemotaxonomic properties clearly show that strain CC-VM-7T represents a novel species, for which the name Chryseobacterium arthrosphaerae sp. nov. is proposed. The type strain is CC-VM-7T (=CCUG 57618T =CCM 7645T).

Two aerobic, Gram-reaction-negative, non-spore-forming bacterial strains, 4M29T and 4M40T, were isolated from cotton composts. The two strains grew in the presence of 0–5 % (w/v) NaCl (optimum growth in the absence of NaCl), at pH 6.0–8.0 (optimum, pH 7.0) and at 15–45 °C (optimum, 30 °C). The strains shared 97.1 % 16S rRNA gene sequence similarity. Strains 4M29T and 4M40T showed the next highest levels of 16S rRNA gene sequence similarity to Parapedobacter koreensis Jip14T (95.6 and 94.4 %, respectively) and Parapedobacter soli DCY14T (95.2 and 93.8 %). The level of DNA–DNA relatedness between strains 4M29T and 4M40T was 38 %. The two strains contained iso-C15 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c) and iso-C17 : 0 3-OH as major fatty acids, MK-7 as the major respiratory quinone, homospermidine as the only polyamine and phosphatidylethanolamine as the major polar lipid. The DNA G+C contents of strains 4M29T and 4M40T were 47.6 and 48.6 mol%, respectively. On the basis of phylogenetic and phenotypic data, strains 4M29T and 4M40T are considered to represent two novel species of the genus Parapedobacter, for which the names Parapedobacter luteus sp. nov. (type strain 4M29T =KACC 10955T =JCM 15977T) and Parapedobacter composti sp. nov. (type strain 4M40T =KACC 10972T =JCM 15978T) are proposed.

The taxonomic position of the misclassified strains [Flexibacter] tractuosus KCTC 2958T and ‘[Microscilla] sericea’ LMG 13021 was studied using a polyphasic approach. The two strains shared 99.1 % 16S rRNA gene sequence similarity and 28 % DNA–DNA relatedness. On the basis of the phylogenetic evidence supported by genotypic and phenotypic data [Flexibacter] tractuosus KCTC 2958T and ‘[Microscilla] sericea’ LMG 13021 are classified as two distinct species in a novel genus, Marivirga, in the family ‘Flammeovirgaceae’, as Marivirga tractuosa comb. nov. and Marivirga sericea nom. rev., comb. nov., with strains KCTC 2958T (=ATCC 23168T =CIP 106410T =DSM 4126T =NBRC 15989T =NCIMB 1408T =VKM B-1430T) and LMG 13021T (=ATCC 23182T =NBRC 15983T =NCIMB 1403T), respectively, as the type strains. The type species is Marivirga tractuosa.

Three Gram-stain-negative, obligately anaerobic, non-spore-forming, rod-shaped bacteria (strains YIT 12056T, YIT 12057T and YIT 12058T) were isolated from human faeces. These strains were characterized by phylogenetic analyses based on 16S rRNA gene sequence and phenotypic tests. 16S rRNA gene sequence analyses revealed that strains YIT 12056T, YIT 12057T and YIT 12058T were most closely related to the type strains of Bacteroides gallinarum, Bacteroides uniformis and Bacteroides intestinalis with approximate similarity values of 96.6, 95.0 and 96.7 %, respectively. The DNA G+C contents of the novel strains were 45.3 (YIT 12056T), 45.2 (YIT 12057T) and 43.6 mol% (YIT 12058T) and the major respiratory quinones of all three isolates were menaquinones MK-10 and MK-11. These properties were typical for members of the genus Bacteroides. The results of the other phenotypic analyses also supported the affiliation of these strains to the genus Bacteroides. The 16S rRNA gene sequence analysis, analysis of the major cellular fatty acids and other biochemical tests enabled the genotypic and phenotypic differentiation of the three new strains. Based on these data, three novel species, Bacteroides clarus sp. nov., Bacteroides fluxus sp. nov. and Bacteroides oleiciplenus sp. nov. are proposed. The type strains of B. clarus, B. fluxus and B. oleiciplenus are YIT 12056T (=JCM 16067T=DSM 22519T), YIT 12057T (=JCM 16101T=DSM 22534T) and YIT 12058T (=JCM 16102T=DSM 22535T), respectively.

A Gram-staining-negative, yellow-pigmented, strictly aerobic bacterium, designated strain 1YB-R12T, was isolated from a soil sample in western Algeria. The novel isolate was heterotrophic, chemoorganotrophic, halotolerant and psychrotolerant. The temperature and pH optima for growth were 28–30 °C and pH 7.3–8. The bacterium tolerated up to 6 % (w/v) NaCl. Cells were non-motile, non-gliding and non-spore-forming, and were characterized by a variable morphological cycle. Flexirubin-type pigments were not detected. 16S rRNA gene sequence analysis showed that strain 1YB-R12T occupied a distinct lineage within the genus Chryseobacterium and shared highest sequence similarity with Chryseobacterium haifense LMG 24029T (96.5 %). The DNA G+C content of strain 1YB-R12T was 40.9 mol%. The predominant cellular fatty acids were anteiso-C15 : 0 (41.4 %) and iso-C15 : 0 (14.4 %). On the basis of phenotypic properties and phylogenetic distinctiveness, strain 1YB-R12T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium solincola sp. nov. is proposed. The type strain is 1YB-R12T (=DSM 22468T=CCUG 55604T).

A novel strain, designated KMM 6019T, was isolated from coastal seawater and subjected to taxonomic examination using a polyphasic approach. A comparative analysis of 16S rRNA gene sequences revealed that strain KMM 6019T formed a distinct phyletic line within the genus Winogradskyella, a member of the family Flavobacteriaceae, phylum Bacteroidetes. The 16S rRNA gene sequence similarity between the novel isolate and the type strains of the recognized species of the genus Winogradskyella was 94.0–97.8 %. Winogradskyella thalassocola KMM 3907T was the closest relative, with 97.8 % sequence similarity. The predominant fatty acids of strain KMM 6019T were iso-C15 : 0, iso-C15 : 1, anteiso-C15 : 0, iso-C15 : 0 3-OH, iso-C16 : 0 3-OH, C15 : 0, iso-C17 : 0 3-OH and summed feature 3 comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c, which are characteristic for members of the genus Winogradskyella. The DNA G+C content was 35.3 mol%. Strain KMM 6019T moved by gliding and grew with 1–5 % NaCl and at 4–30 °C. The novel strain degraded gelatin, casein and starch and produced acid from cellobiose, d-glucose and maltose. Strain KMM 6019T could clearly be differentiated from the other Winogradskyella species by the ability to utilize inositol and sorbitol and to produce hydrogen sulphide. On the basis of phylogenetic and phenotypic findings, strain KMM 6019T is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella pacifica sp. nov. is proposed. The type strain is KMM 6019T (=KCTC 22997T=LMG 22568T).

A novel strain of the genus Paenibacillus, KFC91T, was isolated from the Kafni glacier of the Himalayas. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KFC91T clustered with Paenibacillus antarcticus LMG 22078T (98.9 %) and Paenibacillus macquariensis LMG 6935T (98.7 %). The cell wall peptidoglycan contained meso-diaminopimelic acid as the diamino acid, anteiso-C15 : 0 as the predominant fatty acid and MK-7 as the major isoprenoid quinone. Based on the phylogenetic analysis, chemotaxonomic characteristics and other phenotypic traits, strain KFC91T was assigned to the genus Paenibacillus. DNA–DNA hybridization experiments of KFC91T with P. antarcticus and P. macquariensis showed reassociation values of 39 and 52 %, respectively. Thus, it is proposed that strain KFC91T should be assigned the status of a novel species of the genus Paenibacillus and the name proposed is Paenibacillus glacialis sp. nov., with KFC91T (=NCCB 100252T =DSM 22343T) as the type strain.