Fourteen novel lipomycetaceous yeast species isolated from soil in Japan and transfer of Dipodascopsis anomala to the genus Babjevia based on ascospore production phenotype.

Fourteen novel lipomycetaceous yeasts species were isolated from soil samples collected from the Hokkaido, Chiba and Okinawa prefectures of Japan. Phylogenetic analyses of the D1/D2 domains of the large subunit rRNAs and translation elongation factor 1 alpha genes (TEF1-α) revealed that five strains of two species from the soil in Furano-shi, Hokkaido were related to Dipodascopsis anomala and 29 strains representing 12 species from soils in Kamogawa-shi, Chiba and Iriomote Island, Okinawa were in the Myxozyma clade. The two species of Dipodascopsis form globose or ellipsoid ascospores in their sac-like ascus and pseudohyphae. Furthermore, these species produce ascospores in their pseudohyphae and do not produce an acicular ascus, which is common among the three species including D. anomala. Therefore, we propose transferring D. anomala to the genus Babjevia and amending Babjevia. Two novel species were described and included in the genus Babjevia: Babjevia hyphoforaminiformans sp. nov. (holotype NBRC 111233; MycoBank no. MB 829051) and Babjevia hyphasca sp. nov. (holotype NBRC 112965; MycoBank no. MB 829053). The 12 species in the Myxozyma clade produce neither ascospores nor pseudohyphae and have different characteristics in assimilating several carbon sources from each other. Thus, we propose that the novel species of Lipomyces be classified as forma asexualis (f.a.). From Kamogawa-shi, Chiba (19 strains representing five species): Lipomyces melibiosiraffinosiphilus f.a., sp. nov. (holotype NBRC 111411; MycoBank no. MB 829034), Lipomyces kiyosumicus f.a., sp. nov. (holotype NBRC 111424; MycoBank no. MB 829035), Lipomyces chibensis f.a., sp. nov. (holotype NBRC 111413; MycoBank no. MB 829036), Lipomyces kamogawensis f.a., sp. nov. (holotype NBRC 112967; MycoBank no. MB 829037), Lipomyces amatsuensis f.a., sp. nov. (holotype NBRC 111420; MycoBank no. MB 829041). From Iriomote island, Okinawa (10 strains representing seven species): Lipomyces taketomicus f.a., sp. nov. (holotype NBRC 112966; MycoBank no. MB 829042), Lipomyces yaeyamensis f.a., sp. nov. (holotype NBRC 110433; MycoBank no. MB 829050), Lipomyces iriomotensis f.a., sp. nov. (holotype NBRC 110436; MycoBank no. MB 829045), Lipomyces haiminakanus f.a., sp. nov. (holotype NBRC 110435; MycoBank no. MB 829046), Lipomyces komiensis f.a., sp. nov. (holotype NBRC 110440; MycoBank no. MB 829047), Lipomyces nakamensis f.a., sp. nov. (holotype NBRC 110434; MycoBank no. MB 829048), Lipomyces sakishimensis f.a., sp. nov. (holotype NBRC 110439; MycoBank no. MB 829049).

Adenine Addition Restores Cell Viability and Butanol Production in Clostridium saccharoperbutylacetonicum N1-4 (ATCC 13564) Cultivated at 37°C.

We have developed butanol-producing consolidated bioprocessing from cellulosic substrates through coculture of cellulolytic clostridia and butanol-producing Clostridium saccharoperbutylacetonicum strain N1-4. However, the butanol fermentation by strain N1-4 (which has an optimal growth temperature of 30°C) is sensitive to the higher cultivation temperature of 37°C; the nature of this deleterious effect remains unclear. Comparison of the intracellular metabolites of strain N1-4 cultivated at 30°C and 37°C revealed decreased levels of multiple primary metabolites (notably including nucleic acids and cofactors) during growth at the higher temperature. Supplementation of the culture medium with 250 mg/liter adenine enhanced both cell growth (with the optical density at 600 nm increasing from 4.3 to 10.2) and butanol production (increasing from 3.9 g/liter to 9.6 g/liter) at 37°C, compared to those obtained without adenine supplementation, such that the supplemented 37°C culture exhibited growth and butanol production approaching those observed at 30°C in the absence of adenine supplementation. These improved properties were based on the maintenance of cell viability. We further showed that adenine supplementation enhanced cell viability during growth at 37°C by maintaining ATP levels and inhibiting spore formation. This work represents the first demonstration (to our knowledge) of the importance of adenine-related metabolism for clostridial butanol production, suggesting a new means of enhancing target pathways based on metabolite levels.IMPORTANCE Metabolomic analysis revealed decreased levels of multiple primary metabolites during growth at 37°C, compared to 30°C, in C. saccharoperbutylacetonicum strain N1-4. We found that adenine supplementation restored the cell growth and butanol production of strain N1-4 at 37°C. The effects of adenine supplementation reflected the maintenance of cell viability originating from the maintenance of ATP levels and the inhibition of spore formation. Thus, our metabolomic analysis identified the depleted metabolites that were required to maintain cell viability. Our strategy, which is expected to be applicable to a wide range of organisms, permits the identification of the limiting metabolic pathway, which can serve as a new target for molecular breeding. The other novel finding of this work is that adenine supplementation inhibits clostridial spore formation. The mechanism linking spore formation and metabolomic status in butanol-producing clostridia is expected to be the focus of further research.

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

Genome analysis-based reclassification of Streptomyces endus and Streptomyces sporocinereus as later heterotypic synonyms of Streptomyces hygroscopicus subsp. hygroscopicus.

The aim of this study was to reclarify the taxonomic relationship among Streptomyces hygroscopicus subsp. hygroscopicus, Streptomyces endus and Streptomyces sporocinereus. Whole genome shotgun sequencing was performed for the type strains of these three taxa. Average nucleotide identity and digital DNA-DNA hybridization values among the three taxa were greater than the thresholds for bacterial species delineation, indicating that they belong to the same genomospecies. In addition, the phenotypic data previously reported also support the synonymy. Therefore, S. endus and S. sporocinereus should be reclassified as later heterotypic synonyms of S. hygroscopicus subsp. hygroscopicus.

Pseudactinotalea terrae gen. nov., sp. nov., isolated from greenhouse soil, and reclassification of Actinotalea suaedae as Pseudactinotalea suaedae comb. nov.

A bacterial strain, designated 5GHs33-3T, was isolated from greenhouse soil collected from Yongin region, Gyeonggi province, South Korea. The strain was an aerobic, Gram-stain-positive, flagellated, rod-shaped bacterium. Strain 5GHs33-3T grew at 4-37 °C (optimally at 28-30 °C), pH 6.0-10.0 (optimally at pH 7.0) and with 0-7 % (w/v) NaCl (optimally with 0 %). The 16S rRNA gene sequence analysis revealed that strain 5GHs33-3T had high sequence similarity with Actinotalea suaedae EGI 60002T (98.4 %), Actinotalea ferrariae CF5-4T (96.4 %) and Actinotalea fermentans DSM 3133T (96.2 %), and less than 95.5 % sequence similarity against all the other species with validly published names. The phylogenetic tree revealed that strain 5GHs33-3T formed a robust independent monophyletic line with Actinotalea suaedae EGI 60002T. The predominant fatty acids of strain 5GHs33-3T were anteiso-C15 : 0 and iso-C14 : 0. The only quinone was MK-8(H4). Polar lipids were diphosphatidylglycerol, phosphatidylinositol, an unknown phosphoglycolipid and unknown lipids. The peptidoglycan type was A4ß, with ornithine as the diagnostic diamino acid and an interpeptide bridge comprising l-Glu. The DNA G+C content is 69.0 mol%. Based on phylogenetic evidence and the results of phenotypic, genotypic and chemotaxonomic analyses, strain 5GHs33-3T represents a novel species of a new genus of the family Cellulomonadaceae, for which the name Pseudactinotalea terrae gen. nov., sp. nov. is proposed. The type strain of the type species is 5GHs33-3T (=KACC 16542T=NBRC 111006T). We also propose the reclassification of Actinotalea suaedae as Pseudactinotalea suaedae comb. nov. (type strain EGI 60002T=JCM 19624T=KACC 17839T=KCTC 29256T).

Cellulosimicrobium marinum sp. nov., an actinobacterium isolated from sea sediment.

A novel Gram stain positive actinobacterium, designated RS-7-4(T), was isolated from a sea sediment sample collected in Indonesia, and its taxonomic position was investigated using a polyphasic approach. Strain RS-7-4(T) was observed to form vegetative hyphae in the early phase of growth, but the hyphae eventually fragmented into short rods to coccoid cells. Growth occurred at 15-37 °C, pH 6.0-11.0 and in the presence of 0-7 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain RS-7-4(T) was closely related to the members of the genus Cellulosimicrobium, with a similarity range of 98.08-99.10 %. The peptidoglycan type of strain RS-7-4(T) was found to be A4α L-Lys-L-Thr-D-Asp. The predominant menaquinone was MK-9(H4), and the major fatty acids were anteiso-C15:0, iso-C15:0 and anteiso-C17:0. The DNA G+C content was 75.6 mol%. These chemotaxonomic features corresponded to those of the genus Cellulosimicrobium. Meanwhile, the results of DNA-DNA hybridization, and physiological and biochemical tests revealed that strain RS-7-4(T) was different from the recognized species of the genus Cellulosimicrobium. Therefore, strain RS-7-4(T) represents a novel species of the genus Cellulosimicrobium, for which the name Cellulosimicrobium marinum sp. nov. is proposed. The type strain is RS-7-4(T) (=NBRC 110994(T) =InaCC A726(T)).

Halobium palmae gen. nov., sp. nov., an extremely halophilic archaeon isolated from a solar saltern.

A novel and extremely halophilic archaeon, designated strain 2a_47_2T, was isolated from a solar saltern sample collected in Indonesia. Cells of the strain were Gram-stain-negative, non-motile and pleomorphic and formed orange-red pigmented colonies. Strain 2a_47_2T grew at 20-48 °C (optimum 38-41 °C), pH 6.0-8.5 (optimum pH 7.5), >1.7 M NaCl (optimum 2.6 M) and <0.5 M MgCl2 (optimum 0.3 M). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two phospholipids and sulfated diglycosyl diether. The cells mainly contained menaquinone-8. The G+C content in the genomic DNA of the strain was 67.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 2a_47_2T represents a member of the family Halorubraceae and is different from any other known halophilic archaea. This finding was also demonstrated by phylogenetic analyses based on deduced RpoB' amino acid sequences. Collectively, these results show that strain 2a_47_2T represents a novel genus and species in the family Halorubraceae, and the name Halobium palmae gen. nov., sp. nov. is proposed. The type strain is 2a_47_2T (=NBRC 111368T=InaCC Ar34T).

Haloarchaeobius baliensis sp. nov., isolated from a solar saltern.

A novel halophilic archaeon, designated strain 2b_61_3T, was isolated from a solar saltern in Indonesia. Cells of the strain were Gram-stain-negative, motile, pleomorphic rods that formed orange-red-pigmented colonies on solid medium. The isolate grew optimally at 42-44 °C, pH 6.5-7.0, and with 2.6 M NaCl, and MgCl2 was required for growth. Strain 2b_61_3T had two differential 16S rRNA genes (rrnA and rrnB), and phylogenetic analysis revealed that the strain belonged to the genus Haloarchaeobius. The rrnA and rrnB sequence similarities between strain 2b_61_3T and species of the genus Haloarchaeobius were 98.4-99.2 % and 98.5-98.8 %, respectively. The findings from the 16S rRNA gene analysis were supported by sequence analysis of rpoB', the B' subunit of RNA polymerase. On the basis of the phenotypic characteristics and phylogenetic analyses, as well as DNA-DNA hybridization experiments with Haloarchaeobius iranensis NBRC 110930T, strain 2b_61_3T represents a novel species of the genus Haloarchaeobius, for which the name Haloarchaeobius baliensis sp. nov. is proposed. The type strain is 2b_61_3T ( = NBRC 110517T = InaCC Ar2T).

Friedmanniella aerolata sp. nov., isolated from air.

A novel bacterium, strain 7515T-26T, was isolated from an air sample collected in Taean region, Republic of Korea. Cells were aerobic, Gram-stain-positive, non-flagellated cocci, growing in the temperature, pH and NaCl ranges of 10-33 °C, pH 5.0-9.0 and 0-2 % (w/v). It shared high 16S rRNA gene sequence similarity with Friedmanniella lacustris EL-17AT (97.6 %), Friedmanniella lucida FA2T (96.9 %) and Friedmanniella luteola FA1T (96.9 %), showing high sequence similarities of 96.5-97.6 % with members of the genus Friedmanniella. Phylogenetic trees based on 16S rRNA gene sequences showed that strain 7515T-26T and members of the genus Friedmanniella formed a compact cluster separable from other genera. The isolate contained anteiso-C15 : 0, iso-C14 : 0 3-OH and iso-C15 : 0 as the major cellular fatty acids, and MK-9(H4) as the predominant isoprenoid quinone. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unknown phospholipids and one unknown lipid, and the DNA G+C content was 73.1 mol%. The peptidoglycan type was A3γ. It showed DNA-DNA hybridization values of less than 70 % with F. lacustris EL-17AT. On the basis of the evidence from this polyphasic study, a novel species, Friedmanniella aerolata sp. nov., is proposed. The type strain is 7515T-26T ( = KACC 17306T = DSM 27139T).

Kocuria pelophila sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove.

A novel spherical actinobacterium, designated RS-2-3T, was isolated from the rhizosphere of a mangrove growing on Rambut Island, Indonesia, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain RS-2-3T was related to the members of the genus Kocuria. The highest 16S rRNA gene sequence similarity value was observed with Kocuria marina KMM 3905T (97.0 %). The peptidoglycan type of strain RS-2-3T was found to be A3α with an interpeptide bridge comprising l-Ala4-5. The predominant menaquinone was MK-7(H2) and the major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content was 71.8 mol%. These characteristics were consistent with those of members of the genus Kocuria. Meanwhile, physiological and biochemical characteristics revealed that strain RS-2-3T differed from the species of the genus Kocuria with validly published names. Therefore, strain RS-2-3T represents a novel species of the genus Kocuria, for which the name Kocuria pelophila sp. nov. is proposed. The type strain is RS-2-3T (=NBRC 110990T=InaCC A704T).

Thiogranum longum gen. nov., sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the family Ectothiorhodospiraceae isolated from a deep-sea hydrothermal field, and an emended description of the genus Thiohalomonas.

A novel, obligately chemolithoautotrophic, sulfur-oxidizing bacterial strain, designated strain gps52(T), was isolated from a rock sample collected near the hydrothermal vents of the Suiyo Seamount in the Pacific Ocean. The cells possessed a Gram-stain-negative-type cell wall and contained menaquinone-8(H4) and menaquinone-9(H4) as respiratory quinones, and C16 : 1ω7c, C16 : 0 and C18 : 1ω7c as major cellular fatty acids. Neither storage compounds nor extensive internal membranes were observed in the cells. Strain gps52(T) grew using carbon dioxide fixation and oxidation of inorganic sulfur compounds with oxygen as electron acceptor. Optimal growth was observed at 32 °C, pH 6.5 and with 3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain gps52(T) belongs to the family Ectothiorhodospiraceae and is different from any other known bacteria, with sequence similarities of less than 93 %. Based on phenotypic and phylogenetic findings, the isolate is considered to represent a novel genus and species in the family Ectothiorhodospiraceae, and the name Thiogranum longum gen. nov., sp. nov. is proposed. The type strain is gps52(T) ( = NBRC 101260(T) = DSM 19610(T)). An emended description of the genus Thiohalomonas is also proposed.

Isaria takamizusanensis is the anamorph of Cordyceps ryogamimontana, warranting a new combination, Purpureocillium takamizusanense comb. nov.

The entomogenous anamorphic fungus Isaria takamizusanensis has not been resolved clearly in its teleomorphic state. We succeeded in inducing ascostroma formation by incubating conidiomata of I. takamizusanensis on cicada adults in a moist chamber. We observed the ascostroma and conducted a phylogenetic analysis based on ITS rDNA and EF-1α genes. The morphology of the ascostroma was identical to that of Cordyceps ryogamimontana. In the phylogenetic tree inferred from EF-1α, the isolate from the partspores grouped with nine strains derived from conidia of I. takamizusanensis, which was distinct from a clade including Purpureocillium lilacinum. Moreover, a conidial structure identical to that of I. takamizusanensis was rediscovered on the holotype specimen of C. ryogamimontana. As a result, we propose a new name, Purpureocillium takamizusanense, which is a combination of the teleomorph-anamorph connection of C. ryogamimontana-I. takamizusanensis, in accordance with the 'one fungus, one name' concept of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN).

Serinibacter tropicus sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove, and emended description of the genus Serinibacter.

A novel Gram-stain-positive actinobacterium, designated PS-14-7(T), was isolated from the rhizosphere of a mangrove on Pramuka Island, Indonesia, and its taxonomic position was investigated using a polyphasic approach. The peptidoglycan type of strain PS-14-7(T) was A4α and lysine was the diagnostic diamino acid of the peptidoglycan. The predominant menaquinone was MK-8(H4) and the major fatty acids were anteiso-C(15 : 0), C(16 : 0) and iso-C(16 : 0). The DNA G+C content was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain PS-14-7(T) was closely related to Serinibacter salmoneus Kis4-28(T) (99.6%). However, DNA-DNA hybridization and phenotypic characteristics revealed that strain PS-14-7(T) differed from Serinibacter salmoneus . Therefore, strain PS-14-7(T) represents a novel species of the genus Serinibacter , for which the name Serinibacter tropicus sp. nov. is proposed. The type strain is PS-14-7(T) ( = NBRC 110108(T) = InaCC A 515(T)). An emended description of the genus Serinibacter is also proposed.

Proposal of nine novel species of the genus Lysinimicrobium and emended description of the genus Lysinimicrobium.

Thirteen novel Gram-stain-positive bacteria were isolated from various samples collected from mangrove forests in Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequence comparisons showed that the 13 isolates formed a single clade with Lysinimicrobium mangrovi HI08-69T, with a similarity range of 97.6-99.5 %. The peptidoglycan of the isolates was of the A4α type with an interpeptide bridge comprising Ser-Glu and an l-Ser residue at position 1 of the peptide subunit. The predominant menaquinone was demethylmenaquinone DMK-9(H4) and the major fatty acid was anteiso-C15 : 0. These chemotaxonomic characteristics corresponded to those of the genus Lysinimicrobium. On the basis of the phenotypic and phylogenetic data, along with average nucleotide identity values among the isolates, we concluded that the 13 isolates should be assigned to the following nine novel species of the genus Lysinimicrobium: Lysinimicrobium aestuarii sp. nov. (type strain HI12-104T = NBRC 109392T = DSM 28144T), Lysinimicrobium flavum sp. nov. (type strain HI12-45T = NBRC 109391T = DSM 28150T), Lysinimicrobium gelatinilyticum sp. nov. (type strain HI12-44T = NBRC 109390T = DSM 28149T), Lysinimicrobium iriomotense sp. nov. (type strain HI12-143T = NBRC 109399T = DSM 28146T), Lysinimicrobium luteum sp. nov. (type strain HI12-123T = NBRC 109395T = DSM 28147T), Lysinimicrobium pelophilum sp. nov. (type strain HI12-111T = NBRC 109393T = DSM 28148T), Lysinimicrobium rhizosphaerae sp. nov. (type strain HI12-135T = NBRC 109397T = DSM 28152T), Lysinimicrobium soli sp. nov. (type strain HI12-122T = NBRC 109394T = DSM 28151T) and Lysinimicrobium subtropicum sp. nov. (type strain HI12-128T = NBRC 109396T = DSM 28145T). In addition, an emended description of the genus Lysinimicrobium is proposed.

Oryzobacter terrae gen. nov., sp. nov., isolated from paddy soil.

A bacterial strain, PSGM2-16(T), was isolated from a pot of paddy soil grown with rice in Suwon region, Republic of Korea, and was characterized as having aerobic, Gram-stain-positive, short-rod-shaped cells with one polar flagellum. The 16S rRNA gene sequence of strain PSGM2-16(T) revealed the highest sequence similarities with Knoellia locipacati DMZ1T (97.4%), Fodinibacter luteus YIM C003(T) (97.2%) and Lapillicoccus jejuensis R-Ac013(T) (97.0%), and the phylogenetic tree showed that strain PSGM2-16(T) formed a subgroup with Ornithinibacter aureus HB09001(T) and F. luteus YIM C003(T) within the family Intrasporangiaceae. The major fatty acids (>10% of the total fatty acids) of strain PSGM2-16(T) were iso-C16 : 0, C17 : 1ω8c and iso-C14 : 0. The predominant menaquinone was MK-8(H4). The polar lipids present were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, three aminophospholipids and two phospholipids. The peptidoglycan was type A4γ with meso-diaminopimelic acid as the diagnostic diamino acid. DNA-DNA hybridization values between strain PSGM2-16(T) and closely related taxa were much less than 70%. The genomic DNA G+C content of strain PSGM2-16(T) was 70.0 mol%. On the basis of the evidence presented, it is concluded that strain PSGM2-16(T) represents a novel species of a new genus in the family Intrasporangiaceae, for which the name Oryzobacter terrae gen. nov., sp. nov. is proposed. The type strain of the type species is PSGM2-16(T) ( = KACC 17299(T)= DSM 27137(T)= NBRC 109598(T)).

Lactobacillus plajomi sp. nov. and Lactobacillus modestisalitolerans sp. nov., isolated from traditional fermented foods.

Three Lactobacillus-like strains, NB53T, NB446T and NB702, were isolated from traditional fermented food in Thailand. Comparative 16S rRNA gene sequence analysis indicated that these strains belong to the Lactobacillus plantarum group. Phylogenetic analysis based on the dnaK, rpoA, pheS and recA gene sequences indicated that these three strains were distantly related to known species present in the L. plantarum group. DNA-DNA hybridization with closely related strains demonstrated that these strains represented two novel species; the novel strains could be differentiated based on chemotaxonomic and phenotypic characteristics. Therefore, two novel species of the genus Lactobacillus, Lactobacillus plajomi sp. nov. (NB53T) and Lactobacillus modestisalitolerans sp. nov. (NB446T and NB702), are proposed with the type strains NB53T ( = NBRC 107333T = BCC 38054T) and NB446T ( = NBRC 107235T = BCC 38191T), respectively.

Jatrophihabitans soli sp. nov., isolated from soil.

One bacterial strain, designated KIS75-12T, isolated from a soil sample collected from Wonsando island located in Boryeong city, Republic of Korea, was characterized as aerobic, Gram-stain-positive, non-flagellated and a short rod. It grew between temperatures of 15-37 °C, pH 4-9 and 0-3.0 % (w/v) NaCl. The 16S rRNA gene analysis showed the strain was moderately related to Jatrophihabitans endophyticus S9-650T (97.7 %) and revealed low sequence similarity (≤94.7 %) with all the other species with validly published names. Its major fatty acid was iso-C16 : 0. The predominant menaquinone of strain KIS75-12T was MK-9(H4). The polar lipids consisted of diphosphatidylglycerol and several small amounts of phosphatidylinositol, aminolipids and glycolipid. The peptidoglycan contained meso-A2pm as diagnostic diamino acid and the peptidoglycan type is A4γ. The genomic DNA G+C content of the type strain was 72.1 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain KIS75-12T could be clearly distinguished from the only member of the genus Jatrophihabitans,J. endophyticus. Therefore, the results of this study indicate the existence of a representative of a novel species of the genus Jatrophihabitans, for which we propose the name Jatrophihabitans soli sp. nov., with strain KIS75-12T ( = KACC 17298T = DSM 45908T  = NBRC 109658T) as the type strain. An emended description of the genus Jatrophihabitans is also given.

Marmoricola solisilvae sp. nov. and Marmoricola terrae sp. nov., isolated from soil and emended description of the genus Marmoricola.

Two strains of species of the genus Marmoricola, designated KIS18-7T and JOS5-1T, were isolated from soil samples in Korea. The 16S rRNA gene sequence of strain KIS18-7T showed highest similarities with Marmoricola scoriae Sco-D01T (97.8 %), Marmoricola aequoreus SST-45T (97.6 %) and Marmoricola aurantiacus BC 361T (97.3 %), and strain JOS5-1T had highest sequence similarities with M. aequoreus SST-45T (97.5 %) and Marmoricola bigeumensis MSL-05T (97.3 %). The sequence similarity between KIS18-7T and JOS5-1T was 98.1 %. Phylogenetic analysis showed that these strains grouped with species of the genus Marmoricola. The major fatty acids of strain KIS18-7T were iso-C16 : 0 and C17 : 1ω8c, and C17 : 1ω8c, C18 : 0 10-methyl (TBSA), C18 : 1ω9c, C17 : 0 10-methyl and C16 : 0 2-OH for strain JOS5-1T. Strain KIS18-7T contained the polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylcholine, while strain JOS5-1T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown aminolipid and two unknown phospholipids. The peptidoglycan of both strains contained ll-diaminopimelic acid as the diagnostic diamino acid and a single glycine residue as the interpeptide bridge (type A3γ). The major menaquinone of both strains was MK-8(H4). The G+C contents of the DNA of strains KIS18-7T and JOS5-1T were 68.0 mol% and 62.9 mol%, respectively. These data demonstrate that strains KIS18-7T and JOS5-1T are representatives of two novel species of the genus Marmoricola, for which the names Marmoricola solisilvae sp. nov. (type strain KIS18-7T = KACC 17307T = DSM 27140T = NBRC 109601T) and Marmoricola terrae sp. nov. (type strain JOS5-1T = KACC 17308T = DSM 27141T = NBRC 109602T) are proposed.

Tropicihabitans flavus gen. nov., sp. nov., a new member of the family Cellulomonadaceae.

Two novel Gram-stain positive actinobacteria, designated PS-14-16(T) and RS-7-1, were isolated from the rhizosphere of a mangrove and sea sediment, respectively, and their taxonomic positions were investigated by a polyphasic approach. Both strains were observed to form vegetative hyphae in the early phase of growth but the hyphae eventually fragment into short rods to coccoid cells. The peptidoglycan type of both strains was found to be A4α. Their predominant menaquinone was identified as MK-9(H4) and the major fatty acid as anteiso-C(15:0). The DNA G+C content was determined to be 68.4-68.5 mol%. 16S rRNA gene sequencing revealed that strains PS-14-16(T) and RS-7-1 were related to members of the family Cellulomonadaceae. Their nearest phylogenetic neighbour was found to be Sediminihabitans luteus, which is currently the only species of the genus Sediminihabitans, with a similarity of 97.94%. However, strains PS-14-16(T) and RS-7-1 were distinguishable from the members of the genus Sediminihabitans and the other genera within the family Cellulomonadaceae in terms of chemotaxonomic characteristics and phylogenetic relationship. The results of DNA-DNA hybridization experiments indicated that strains PS-14-16(T) and RS-7-1 belong to the same species. Strains PS-14-16(T) and RS-7-1 are concluded to represent a novel genus and species of the family Cellulomonadaceae, for which the name Tropicihabitans flavus gen. nov., sp. nov. is proposed. The type strain of T. flavus is PS-14-16(T) (=NBRC 110109(T) = IanCC A 516(T)). [corrected].

Genome based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in seven strains of five representative Nocardia species.

BACKGROUND: Actinobacteria of the genus Nocardia usually live in soil or water and play saprophytic roles, but they also opportunistically infect the respiratory system, skin, and other organs of humans and animals. Primarily because of the clinical importance of the strains, some Nocardia genomes have been sequenced, and genome sequences have accumulated. Genome sizes of Nocardia strains are similar to those of Streptomyces strains, the producers of most antibiotics. In the present work, we compared secondary metabolite biosynthesis gene clusters of type-I polyketide synthase (PKS-I) and nonribosomal peptide synthetase (NRPS) among genomes of representative Nocardia species/strains based on domain organization and amino acid sequence homology. RESULTS: Draft genome sequences of Nocardia asteroides NBRC 15531(T), Nocardia otitidiscaviarum IFM 11049, Nocardia brasiliensis NBRC 14402(T), and N. brasiliensis IFM 10847 were read and compared with published complete genome sequences of Nocardia farcinica IFM 10152, Nocardia cyriacigeorgica GUH-2, and N. brasiliensis HUJEG-1. Genome sizes are as follows: N. farcinica, 6.0 Mb; N. cyriacigeorgica, 6.2 Mb; N. asteroides, 7.0 Mb; N. otitidiscaviarum, 7.8 Mb; and N. brasiliensis, 8.9 - 9.4 Mb. Predicted numbers of PKS-I, NRPS, and PKS-I/NRPS hybrid clusters ranged between 4-11, 7-13, and 1-6, respectively, depending on strains, and tended to increase with increasing genome size. Domain and module structures of representative or unique clusters are discussed in the text. CONCLUSION: We conclude the following: 1) genomes of Nocardia strains carry as many PKS-I and NRPS gene clusters as those of Streptomyces strains, 2) the number of PKS-I and NRPS gene clusters in Nocardia strains varies substantially depending on species, and N. brasiliensis strains carry the largest numbers of clusters among the species studied, 3) the seven Nocardia strains studied in the present work have seven common PKS-I and/or NRPS clusters, some of whose products are yet to be studied, and 4) different N. brasiliensis strains have some different gene clusters of PKS-I/NRPS, although the rest of the clusters are common within the N. brasiliensis strains. Genome sequencing suggested that Nocardia strains are highly promising resources in the search of novel secondary metabolites.