Two new species of the genus Micromonospora: Micromonospora chokoriensis sp. nov. and Micromonospora coxensis sp. nov., isolated from sandy soil

Two actinomycete strains, 2-19(6)(T) and 2-30-b(28)(T), which produced single, non-motile noduler to warty spore surfaces, were isolated from sandy soil in Chokoria, Cox's Bazar, Bangladesh. A polyphasic study was carried out to establish the taxonomic position of these strains. Morphological and chemotaxonomic characteristics of these strains coincided with those of the genus Micromonospora. Phylogenetic analysis using 16S rDNA sequences indicated that these strains should be classified in the genus Micromonospora. The 16S rDNA sequence of strain 2-19(6)(T )showed closest similarity to the type strains of M. mirobrigensis (98.9%) and M. carbonacea (98.8%), and the strain 2-30-b(28)(T) to the type strains of M. purpureochromogenes (99.4%), M. halophytica (99.3%) and M. aurantiaca (99.2%). Furthermore, a combination of DNA-DNA hybridization results and some differential physiological and biochemical properties indicated that these strains were distinguished from the phylogenetically closest relatives. These strains therefore represent two novel species, for which the name Micromonospora chokoriensis sp. nov. and Micromonospora coxensis sp. nov. are proposed. The type strains are 2-19(6)(T) (=JCM 13247(T) =MTCC 8535(T)) and 2-30-b(28)(T) (=JCM 13248(T)=MTCC 8093(T)).     

Micromonospora haikouensis sp. nov., isolated from mangrove soil

An actinomycete strain 232617^T was isolated from a composite mangrove sediment sample collected in Haikou, China. Phylogenetic analysis of the 16S rRNA gene sequence of strain 232617^T indicated the highest similarity with Micromonospora siamensis TT2-4^T (99.05%), Micromonospora krabiensis A-2^T (98.99%) and Micromonospora carbonacea DSM 43815^T (98.91%). The gyrB gene sequence analysis also indicated that 232617^T should be assigned to the genus Micromonospora. The cell wall contains meso-DAP and glycine. The major menaquinones were MK-10(H₄) and MK-10(H₆), with MK-9(H₄) as minor components. The characteristic whole-cell sugars are xylose, arabinose and glucose. The phospholipid profile comprises phosphatidylethanolamine, diphosphatidlglycerol and phosphatidylinositol mannoside. The DNA G+C content is 71.5 mol%. Furthermore, a combination of DNA–DNA relatedness and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from the closest related species. On the basis of these phenotypic and genotypic data, strain 232617^T represents a novel species of the genus Micromonospora, for which the name Micromonospora haikouensis sp. nov. is proposed. The type strain is 232617^T (= CCTCC AA 201112 ^T = DSM 45626 ^T).     

Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora

A novel actinomycete, designated strain NEAU-GRX11^T, was isolated from muddy soil collected from a stream of Jinlong Mountain in Harbin, north China. The organism was found to have morphological and chemotaxonomic characteristics typical of the genus Micromonospora. The 16S rRNA gene sequence of strain NEAU-GRX11^T showed highest similarity to Micromonospora zamorensis CR38^T (99.2 %), Micromonospora saelicesensis Lupac 09^T (99.0 %), Micromonospora chokoriensis 2-19/6^T (98.7 %), Micromonospora coxensis 2-30-b/28^T (98.5 %), Micromonospora aurantiaca ATCC 27029^T (98.4 %) and Micromonospora lupini lupac 14N^T (98.3 %). Phylogenetic analysis based on the 16S rRNA gene and gyrB gene demonstrated that strain NEAU-GRX11^T was a member of the genus Micromonospora and supported the closest phylogenetic relationship to M. zamorensis CR38^T, M. saelicesensis Lupac 09^T, M. chokoriensis 2-19/6^T and M. lupini lupac 14N^T. A combination of DNA–DNA hybridization and some phenotypic characteristics indicated that the novel strain could be readily distinguished from these closest phylogenetic relatives. Therefore, it is proposed that NEAU-GRX11^T represents a novel species of the genus Micromonospora, for which the name Micromonospora jinlongensis sp. nov. is proposed. The type strain is NEAU-GRX11^T (=CGMCC 4.7103^T=DSM 45876^T).     

Eight new species of the genus Micromonospora, Micromonospora citrea sp. nov., Micromonospora echinaurantiaca sp. nov., Micromonospora echinofusca sp. nov. Micromonospora fulviviridis sp. nov., Micromonospora inyonensis sp. nov., Micromonospora peucetia sp. nov., Micromonospora sagamiensis sp. nov., and Micromonospora viridifaciens sp. nov

A previous phylogenetic study on type strains of the genus Micromonospora and Micromonospora species bearing non-validly published names has pointed towards the species status of several of latter strains. Subsequent studies on morphological, cultural, chemotaxonomic, metabolic, and genomic properties, and on whole cell mass spectrometric analyses by matrix adsorbed laser desorption/ionization time-of-flight (MALDI-TOF) confirmed the species status, leading to the proposal of eight new Micromonospora species: Micromonospora citrea sp. nov., type strain DSM 43903T, Micromonospora echinaurantiaca sp. nov., type strain DSM 43904T, Micromonospora echinofusca sp. nov., type strain DSM 43913T, Micromonospora fulviviridis sp. nov., type strain DSM 43906T, Micromonospora inyonensis sp. nov., type strain DSM 46123T, Micromonospora peucetia sp. nov., type strain DSM 43363T, Micromonospora sagamiensis sp. nov., type strain DSM 43912T and Micromonospora viridifaciens sp. nov., type strain DSM 43909T.     

Occurrence of gentamicin-producing micromonosporae in Lake Balaton (W. Hungary)

The total number of platable bacteria in the wet mud material characterized by the predominant occurrence of high-magnesian calcite and protodolomite of the Lake Balaton fluctuates between 3.5 X 10(4) and 2.3 X 10(5) g-1. Actinomycetes constitute about 25-30 per cent of this mud-community and not more than half of them belong to the genus Micromonospora. The presence of 10 species of this genus was detected among the isolated and studied strains identified by means of conventional methods and computer aided numerical analysis in which 20 authentic, mostly type strains of Micromonospora spp. were also involved. All of the three species of gentamicin-producing Micromonospora (M. echinospora, M. purpurea and M. sagamiensis) known so far were found in mud samples. These three species form stable but less numerous populations (less than 0.5 per cent of the total platable microflora) in the Balaton's mud, the members of which are capable to produce gentamicins at about 40-50 micrograms ml-1 level at most.     

Description of a Novel Actinobacterium Microbacterium assamensis sp. nov., Isolated from Water Sample Collected from the River Brahmaputra, Assam, India

A Gram-positive, yellow pigmented actinobacterium, strain S2-48(T) was isolated from water sample collected from the river Brahmaputra, Assam, India and subjected to a polyphasic taxonomic study. Most of the physiological and biochemical properties, major fatty acids (C(15:0) Anteiso, iso C(16:0) and C(17:0) Anteiso), estimated DNA G+C content (70.2 mol%) and 16S rRNA gene sequence analysis showed that strain S2-48(T) belonged to the genus Microbacterium. Strain S2-48(T) exhibited highest 16S rRNA gene sequence similarity with Microbacterium testaceum (97.0%); however, the DNA-DNA relatedness value between strain S2-48(T) and M. testaceum was 9.1%. On the basis of differential phenotypic characteristics and genotypic distinctiveness, strain S2-48(T) should be classified within the genus Microbacterium as a novel species, for which the name Microbacterium assamensis is proposed. The type strain is S2-48(T) (=MTCC 10486(T) = DSM 23998(T)).     

Isolation and characterization of Methanoculleus receptaculi sp. nov. from Shengli oil field, China

Three strictly anaerobic, thermophilic methanogens (ZC-2T, ZC-3 and ZC-6) were isolated from Shengli oil field, China. The 16S rRNA gene sequences of the three strains were nearly identical, possessing > 99.8% sequence similarity. They also possessed high sequence similarity, 97.4%, to Methanoculleus palmolei strain INSLUZ(T) (97.4% and 97.5%, respectively), indicating that they represented a novel species within the genus Methanoculleus. Cells of strain ZC-2T were nonmotile cocci, 0.8-1.7 microm in diameter, and always occurred singly or in pairs. The three strains used H2/CO2 or sodium formate as substrates for methanogenesis but not sodium acetate, trimethylamine, monomethylamine, ethanol, dimethyl sulfide, isopropanol, isobutanol, butan-2-ol or H2/CO. Optimum growth of strain ZC-2T occurred in the presence of 0.2 M NaCl, pH 7.5-7.8 and temperature 50-55 degrees C with a specific growth rate of 0.084 h(-1). The mol% G+C content of the genomic DNA was 55.2 mol%. Based on these phenotypic and phylogenetic characteristics, strains ZC-2T, ZC-3 and ZC-6 are proposed to represent a novel species in the genus Methanoculleus and named Methanoculleus receptaculi sp. nov. The type strain is ZC-2T (CGMCC 1.5087T=DSM 18860T).     

Thalassobius aestuarii sp. nov., isolated from tidal flat sediment

A strictly aerobic, non-motile, ovoid-shaped Alphaproteobacteria, designated strain JC2049(T), was isolated from a tidal flat sediment sample. The results of 16S rRNA gene sequence analysis indicated that this isolate belonged to the genus Thalassobius, with a sequence similarity of 96.9-97.3% to other valid Thalassobius spp. The cells required 1-7% NaCl for growth (optimum 2%) and accumulated poly-beta-hydroxybutyrate. Nitrite was reduced to nitrogen, but nitrate was not reduced to nitrite. No genetic potential for aerobic anoxygenic photosynthesis was detected. The primary isoprenoid quinone (Ubiquinone-10), predominant cellular fatty acids (C(18:1)omega7c, 11 methyl C(18:1)omega7c and C(16:0)) and DNA G+C content (61 mol%) were all consistent with the assignment of this isolate to the genus Thalassobius. Several phenotypic characteristics clearly distinguished our isolate from other Thalassobius species. The degree of genomic relatedness between strain JC2049(T) and other Thalassobius species was in a range of 20-43%. The polyphasic data presented in this study indicates that our isolate should be classified as a novel species within the genus Thalassobius. The name Thalassobius aestuarii sp. nov. is therefore proposed for this isolate; the type strain is JC2049(T) (= IMSNU 14011(T) = KCTC 12049(T) = DSM 15283(T)).     

Marivita roseacus sp. nov., of the family Rhodobacteraceae, isolated from a temperate estuary and an emended description of the genus Marivita

A gram-negative, non-motile, pigmented, rod-shaped and strictly aerobic bacterium (CB1052(T)) was isolated from a temperate estuary. On the basis of 16S rRNA gene sequence similarity, strain CB1052(T) belongs to the α-3 subclass of the Proteobacteria, within the family Rhodobacteraceae, having the highest similarity to members of the genus Marivita (97.8%) of the Roseobacter lineage. Pylogenetic analysis showed CB1052(T) to be a distinct sister clade to M. litorea and M. cryptomonadis and DNA-DNA relatedness was quite low amongst the strains (< 35%). Strain CB1052(T) cells are non-motile and display a needle-like filamentous form, where individual cells can become quite elongated (up to 15 μm). Similar to M. litorea and M. cryptomonadis, CB1052(T) harbors aerobic anoxygenic photosynthesis genes. However, in contrast to other described Marivita species, strain CB1052(T) actively produces bacteriochlorophyll a. Further physiological features, including antibiotic sensitivities, differentiate strain CB1052(T) from the other members of the genus. Therefore, strain CB1052(T) is considered to represent a novel species of the genus Marivita, for which the name Marivita roseacus sp. nov. is proposed, with the type strain CB1052(T) (=DSM 23118(T) =ATCC BAA 1914(T)).     

Marinomonas aquamarina sp. nov., isolated from oysters and seawater

The characterization of three bacterial strains isolated from cultured oysters and seawater at the Spanish Mediterranean coast has been performed. Strains were phenotypically and genetically characterized and the results led us to identify them as members of the genus Marinomonas. A phylogenetic analysis based on the almost complete 16S rDNA sequences clustered all three strains together (with sequence similarities around 99.8%) in the vicinity of M. communis and M. vaga sequences and distantly related to the other four species of the genus. The most closely related species was M. communis that shared 97.4-97.6% with the Mediterranean strains. DNA-DNA hybridizations were performed to clarify the taxonomic position of our isolates and the results confirmed their specific isolation, with interspecific binding ratios below 59%. We propose the bacteria to constitute a new Marinomonas species, i.e. M. aquamarina and strain 11SM4T (CECT 5080T, CIP 108405T, CCUG 49439T) as the type strain.     

Micromonospora maoerensis sp. nov., isolated from a Chinese pine forest soil

A novel actinomycete, designated strain NEAU-MES19^T, was isolated from pine forest soil in Heilongjiang province, China. A polyphasic study was carried out to establish the taxonomic position of this strain. The organism was found to have morphological and chemotaxonomic characteristics typical of the genus Micromonospora. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain NEAU-MES19^T was most closely related to Micromonospora matsumotoense IMSNU 22003^T. However, phylogenetic analysis based on the gyrB gene sequence showed that the isolate was more closely related to Micromonospora cremea CR30^T than M. matsumotoense IMSNU 22003^T. The low level of DNA–DNA relatedness allowed the isolate to be differentiated from M. matsumotoense IMSNU 22003^T and M. cremea CR30^T. Moreover, strain NEAU-MES19^T could also be distinguished from its closest phylogenetic relatives by morphological, physiological and biochemical characteristics. Therefore, it is proposed that strain NEAU-MES19^T represents a novel species of the genus Micromonospora, for which the name Micromonospora maoerensis sp. nov. is proposed. The type strain is NEAU-MES19^T (=CGMCC 4.7091^T = DSM 45884^T).     

Micromonospora violae sp. nov., isolated from a root of Viola philippica Car

A novel actinomycete, designated strain NEAU-zh8^T, was isolated from a root of Viola philippica Car collected in China and characterized using a polyphasic approach. 16S rRNA gene sequence similarity studies showed that strain NEAU-zh8^T belongs to the genus Micromonospora, being most closely related to Micromonospora chokoriensis 2-9(6)^T (99.9 %), Micromonospora saelicesensis Lupac 09^T (99.3 %) and Micromonospora lupini Lupac 14N^T (99.0 %). gyrB gene analysis also indicated that strain NEAU-zh8^T should be assigned to the genus Micromonospora. The cell-wall peptidoglycan consisted of meso-diaminopimelic acid and glycine. The major menaquinones were MK-10(H₄), MK-10(H₂) and MK-10(H₆). The phospholipid profile contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major fatty acids were iso-C_15:0, C_16:0 and C_17:0 10-methyl. A combination of DNA–DNA hybridization results and some physiological and biochemical properties indicated that strain NEAU-zh8^T could be readily distinguished from the closest phylogenetic relatives. Therefore, it is proposed that strain NEAU-zh8^T represents a novel Micromonospora species, for which the name Micromonospora violae sp. nov. is proposed. The type strain is NEAU-zh8^T (=CGMCC 4.7102^T=DSM 45888^T).     

Transfer of Methanolobus siciliae to the genus Methanosarcina, naming it Methanosarcina siciliae, and emendation of the genus Methanosarcina

A sequence analysis of the 16S rRNA of Methanolobus siciliae T4/M(T) (T = type strain) showed that this strain is closely related to members of the genus Methanosarcina, especially Methanosarcina acetivorans C2A(T). Methanolobus siciliae T4/M(T) and HI350 were morphologically more similar to members of the genus Methanosarcina than to members of the genus Methanolobus in that they both formed massive cell aggregates with pseudosarcinae. Thus, we propose that Methanolobus siciliae should be transferred to the genus Methanosarcina as Methanosarcina siciliae.     

Micromonospora taraxaci sp. nov., a novel endophytic actinomycete isolated from dandelion root (Taraxacum mongolicum Hand.-Mazz.)

A novel actinomycete, designated strain NEAU-P5^T, was isolated from dandelion root (Taraxacum mongolicum Hand.-Mazz.). Strain NEAU-P5^T showed closest 16S rRNA gene sequence similarity to Micromonospora chokoriensis 2–19/6^T (99.5 %), and phylogenetically clustered with Micromonospora violae NEAU-zh8^T (99.3 %), M. saelicesensis Lupac 09^T (99.0 %), M. lupini Lupac 14N^T (98.8 %), M. zeae NEAU-gq9^T (98.4 %), M. jinlongensis NEAU-GRX11^T (98.3 %) and M. zamorensis CR38^T (97.9 %). Phylogenetic analysis based on the gyrB gene sequence also indicated that the isolate clustered with the above type strains except M. violae NEAU-zh8^T. The cell-wall peptidoglycan consisted of meso-diaminopimelic acid and glycine. The major menaquinones were MK-9(H₈), MK-9(H₆) and MK-10(H₂). The phospholipid profile contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major fatty acids were C_16:0, iso-C_15:0 and C_17:0. Furthermore, some physiological and biochemical properties and low DNA–DNA relatedness values enabled the strain to be differentiated from members of closely related species. Therefore, it is proposed that strain NEAU-P5^T represents a novel species of the genus Micromonospora, for which the name Micromonospora taraxaci sp. nov. is proposed. The type strain is NEAU-P5^T (=CGMCC 4.7098^T = DSM 45885^T).     

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)).     

Halomonas alkalitolerans sp. nov., a novel moderately halophilic bacteriun isolated from soda meadow saline soil in Daqing, China

A moderately halophilic bacterial strain 15-13(T), which was isolated from soda meadow saline soil in Daqing City, Heilongjiang Province, China, was subjected to a polyphasic taxonomic study. The cells of strain 15-13 were found to be Gram-negative, rod-shaped, and motile. The required growth conditions for strain 15-13(T) were: 1-23% NaCl (optimum, 7%), 10-50°C (optimum, 35°C), and pH 7.0-11.0 (optimum, pH 9.5). The predominant cellular fatty acids were C(18:1) ω7c (60.48%) and C(16:0) (13.96%). The DNA G+C content was 67.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain 15-13(T) clustered within a branch comprising species of the genus Halomonas. The closest phylogenetic neighbor of strain 15-13(T) was Halomonas pantelleriensis DSM 9661(T) (98.9% 16S rRNA gene sequence similarity). The level of DNA-DNA relatedness between the novel isolated strain and H pantelleriensis DSM 9661(T) was 33.8%. On the basis of the phenotypic and phylogenetic data, strain 15-13(T) represents a novel species of the genus Halomonas, for which the name Halomonas alkalitolerans sp. nov. is proposed. The type strain for this novel species is 15-13(T) (=CGMCC 1.9129(T) =NBRC 106539(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)).     

Mycobacterium kumamotonense Sp. Nov. recovered from clinical specimen and the first isolation report of Mycobacterium arupense in Japan: Novel slowly growing, nonchromogenic clinical isolates related to Mycobacterium terrae complex

Three mycobacterium strains isolated from clinical specimens in Japan were provisionally assigned to the genus Mycobacterium based on their phenotypical characteristics. These isolates were further investigated to determine their specific taxonomic statuses. Mycolic acid analysis and 16S rRNA gene, rpoB, and hsp65 sequence data for the isolates showed that they are most similar to M. terrae complex. DNA-DNA hybridization studies indicated that the three strains were of two species and were distinguishable from M. terrae, M. nonchromogenicum, and M. hiberniae. Therefore, these strains represent two novel species within the genus Mycobacterium. However, one potential new species should have been considered as M. arupense with the 16S rRNA gene and hsp65 sequences similarities of 99.8% and 100% respectively; it was isolated from human specimens in the United States and was proposed in June 2006 as a new species. This report describes the first isolation of M. arupense in Japan, suggesting that the organism is clinically relevant. In addition, we propose the novel species designation Mycobacterium kumamotonense sp. nov. The type strain is CST 7247(T) (=GTC 2729(T), =JCM 13453(T), =CCUG 51961(T)).     

Diversity of Micromonospora strains isolated from nitrogen fixing nodules and rhizosphere of Pisum sativum analyzed by multilocus sequence analysis

It was recently reported that Micromonospora inhabits the intracellular tissues of nitrogen fixing nodules of the wild legume Lupinus angustifolius. To determine if Micromonospora populations are also present in nitrogen fixing nodules of cultivated legumes such as Pisum sativum, we carried out the isolation of this actinobacterium from P. sativum plants collected in two man-managed fields in the region of Castilla and León (Spain). In this work, we describe the isolation of 93 Micromonospora strains recovered from nitrogen fixing nodules and the rhizosphere of P. sativum. The genomic diversity of the strains was analyzed by amplified ribosomal DNA restriction analysis (ARDRA). Forty-six isolates and 34 reference strains were further analyzed using a multilocus sequence analysis scheme developed to address the phylogeny of the genus Micromonospora and to evaluate the species distribution in the two studied habitats. The MLSA results were evaluated by DNA-DNA hybridization to determine their usefulness for the delineation of Micromonospora at the species level. In most cases, DDH values below 70% were obtained with strains that shared a sequence similarity of 98.5% or less. Thus, MLSA studies clearly supported the established taxonomy of the genus Micromonospora and indicated that genomic species could be delineated as groups of strains that share > 98.5% sequence similarity based on the 5 genes selected. The species diversity of the strains isolated from both the rhizosphere and nodules was very high and in many cases the new strains could not be related to any of the currently described species.