Thermus amyloliquefaciens sp. nov., isolated from a hot spring sediment sample.

A Gram-stain-negative, aerobic bacterium, designated strain YIM 77409T, was isolated from the Niujie hot spring in the Eryuan county of Dali, Yunnan province, south-west China. Cells of the strain were rod-shaped and colonies were yellow and circular. The strain grew at pH 6.0-8.0 (optimum, pH 7.0) and 50-70°C (optimum, 60-65°C). The predominant menaquinone was MK-8 and the DNA G+C content was 66.4 mol%. Major fatty acids (>10 %) were iso-C15 : 0 and iso-C17 : 0.The polar lipids consisted of one aminophospholipid, one phospholipid and two glycolipids. 16S rRNA gene sequence analysis showed that strain YIM 77409T formed a cluster with Thermus scotoductus DSM 8553T, Thermus antranikianii DSM 12462T, Thermus caliditerrae YIM 77925T and Thermus tengchongensis YIM 77924T, with highest 16S rRNA gene sequence similarity to T. scotoductus DSM 8553T (97.57%). However, DNA-DNA hybridization indicated that strain YIM 77409T should be viewed as a representative of a novel species, as there was only 30.6 ± 1.6% reassociation with T. scotoductus DSM 8553T. On the basis of the morphological and chemotaxonomic characteristics, as well as the genotypic data, it is proposed that strain YIM 77409T represents a novel species of the genus Thermus, with the name Thermus amyloliquefaciens sp. nov. The type strain is YIM 77409T ( = DSM 25898T = KCTC 32024T).

Genome-wide identification, domain architectures and phylogenetic analysis provide new insights into the early evolution of shikimate pathway in prokaryotes.

Despite intense scrutiny from researchers in the fields of biochemistry and metabolism, our understanding of the evolutionary history of the key anabolic shikimate pathway remains limited. To shed light on the early evolutionary events leading to the assembly of the pathway, we investigated the distributions, domain architectures and phylogenies of component enzymes using a bioinformatic procedure based on Hidden Markov Model profiles. The aro genes for the canonical shikimate pathway had most wider distribution in prokaryotes; and the variant pathway coordinated by 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid (ADH) synthase and type II 3-dehydroquinate (DHQ) synthase could be identified in most of archaeal species. In addition, the ancient bidirectional horizontal gene transfer events had happened between two prokaryotic domains: Bacteria and Archaea. Besides 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, the phylogenetically distinct subfamilies of 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase and chorismate synthase had ever emerged in the evolutionary history of shikimate pathway. These findings provide new insight into the early evolution of the shikimate pathway and advance our understanding of the evolution of metabolic pathways.

The futalosine pathway played an important role in menaquinone biosynthesis during early prokaryote evolution.

Menaquinone (MK) is an important component of the electron-transfer system in prokaryotes. One of its precursors, 1,4-dihydroxy-2-naphthoate, can be synthesized from chorismate by the classical MK pathway. Interestingly, in some bacteria, chorismate can also be converted to 1,4-dihydroxy-6-naphthoate by four enzymes encoded by mqnABCD in an alternative futalosine pathway. In this study, six crucial enzymes belonging to these two independent nonhomologous pathways were identified in the predicted proteomes of prokaryotes representing a broad phylogenetic distribution. Although the classical MK pathway was found in 32.1% of the proteomes, more than twice the proportion containing the futalosine pathway, the latter was found in a broader taxonomic range of organisms (18 of 31 phyla). The prokaryotes equipped with the classical MK pathway were almost all aerobic or facultatively anaerobic, but those with the futalosine pathway were not only aerobic or facultatively anaerobic but also anaerobic. Phylogenies of enzymes of the classical MK pathway indicated that its genes in archaea were probably acquired by an ancient horizontal gene transfer from bacterial donors. Therefore, the organization of the futalosine pathway likely predated that of the classical MK pathway in the evolutionary history of prokaryotes.

Meiothermus terrae sp. nov., isolated from a geothermally heated soil sample.

A Gram-negative, aerobic bacterium, designated strain YIM 77755(T), was isolated from a geothermally heated soil sample collected at Rehai National Park, Tengchong, Yunnan province, south-west China. Cells of the strain were rod-shaped and colonies were yellow and circular. Growth occurred in 0-1 % (w/v) NaCl, at pH 6.0-8.0 (optimum, pH 7.0) and at 35-55 °C (optimum, 50 °C). The predominant menaquinone was MK-8 and the DNA G+C content was 68.9 mol%. Major fatty acids (>10 %) were anteiso-C15 : 0 and iso-C15 : 0. The polar lipids consisted of an uncharacterized phospholipid and four glycolipids. Based on 16S rRNA gene sequence analysis, strain YIM 77755(T) formed a cluster with Meiothermus chliarophilus ALT-8(T) and showed the highest 16S rRNA gene sequence similarity to M. chliarophilus ALT-8(T) (98.23 %). DNA-DNA relatedness between YIM 77755(T) and M. chliarophilus DSM 9957(T) was 54.9±4.1 %. On the basis of the morphological and chemotaxonomic characteristics as well as genotypic data, it is proposed that strain YIM 77755(T) represents a novel species of the genus Meiothermus, named Meiothermus terrae sp. nov. The type strain is YIM 77755(T) ( = DSM 26712(T) = CCTCC AB 2012942(T)).

Vulcaniibacterium tengchongense gen. nov., sp. nov. isolated from a geothermally heated soil sample, and reclassification of Lysobacter thermophilus Wei et al. 2012 as Vulcaniibacterium thermophilum comb. nov.

A thermotolerant Gram-staining negative and aerobic bacterium, designated strain YIM 77520(T), was isolated from a geothermally heated soil sample collected at Rehai National Park, Tengchong, Yunnan Province, South-West China. Cells of the strain were found to be rod-shaped and colonies were light beige and circular. The strain was found to grow in the presence of 0-2 % (w/v) total salts (optimum, 0 %), at pH 6.0-8.0 (optimum, pH 7.0) and 25-55 °C (optimum, 45 °C). The only quinone detected was Q-8 and the genomic DNA G+C content was determined to be 66.9 mol%. The major fatty acids (>10 %) were identified as iso-C16:0 and iso-C15:0. The phospholipids were found to consist of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, five unknown phospholipids and three aminophospholipids. Based on the 16S rRNA gene sequence analysis, strain YIM 77520(T) was found to form a cluster with Lysobacter thermophilus YIM 77875(T) and showed the highest 16S rRNA gene sequence similarity to L. thermophilus YIM 77875(T) (96.0 %). These two strains formed a distinct lineage of the family 'Xanthomonadaceae'. On the basis of the morphological and chemotaxonomic characteristics, as well as genotypic data, a new genus, Vulcaniibacterium gen. nov. is proposed with Vulcaniibacterium tengchongense sp. nov. as the type species. The type strain of V. tengchongense sp. nov. is strain YIM 77520(T) (=DSM 25623(T) = CCTCC AB 2011152(T)). Furthermore we propose that L. thermophilus Wei et al. 2012 is reclassified in the new genus as Vulcaniibacterium thermophilum comb. nov. (type strain YIM 77875(T) = CCTCC AB 2012064(T) = KCTC 32020(T)) based on polyphasic data.

Rehaibacterium terrae gen. nov., sp. nov. isolated from a geothermally heated soil sample.

A thermotolerant, alkalitolerant, Gram-stain-negative and strictly aerobic bacterium, designated strain YIM 77974(T), was isolated from a geothermally heated soil sample collected at Rehai National Park, Tengchong, Yunnan province, south-west China. Cells of the strain were rod-shaped and colonies were light brown and circular. The strain grew in the presence of 0-3 % (w/v) NaCl (optimum, 0-1 %) and at pH 7.0-10.0 (optimum, pH 8.0) and 30-55 °C (optimum, 45 °C). The only quinone was Q-8 and the genomic DNA G+C content was 68.3 mol%. Major fatty acids (>10 %) were iso-C16 : 0, iso-C17 : 0, iso-C15 : 0 and iso-C11 : 0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminophospholipid, three unidentified phospholipids and two unidentified polar lipids. On the basis of the morphological and chemotaxonomic characteristics as well as genotypic data, it is proposed that this strain should be classified as a representative of a novel genus and species, Rehaibacterium terrae gen. nov., sp. nov., in the family Xanthomonadaceae. The type strain is strain YIM 77974(T) ( = DSM 25897(T) = CCTCC AB 2012062(T)).

Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium.

Two novel isolates of rapidly growing, Gram-stain-positive, non-chromogenic species of the genus Mycobacterium, strain YIM M13028(T) from a sediment sample collected from the South China Sea (19° 30.261' N 111° 0.247' E) at a depth of 42 m and strain YIM 121001(T) from a coastal zone sand sample collected in Dubai, United Arab Emirates, were obtained in our laboratory. Their taxonomic positions were determined by a polyphasic approach. Good growth of the two strains was observed at 28 °C and pH 7.0 with 0-2 % NaCl on tryptic soy agar medium. Both strains formed round orange-red colonies, strain YIM M13028(T) had a rough surface, while YIM 121001(T) was smooth. Cellular fatty acids, whole-cell protein profiles and TLC analysis of their mycolic acids show significant differences from reference stains. Phenotypic characteristics and multilocus sequence analysis (MLSA) of 16S rRNA gene, hsp65, rpoB and 16S-23S internal transcribed spacer (ITS) sequences indicated that both strains YIM M13028(T) and YIM 121001(T) belong to the genus Mycobacterium. DNA-DNA hybridization values revealed a low relatedness (<70 %) of the two isolates with the type strains Mycobacterium neoaurum DSM 44074(T) and Mycobacterium hodleri DSM 44183(T). The low DNA-DNA hybridization values (40.4±3.5 %) between strains YIM M13028(T) and YIM 121001(T) and phenotypic distinctiveness indicated that the two strains were representatives of different novel species of the genus Mycobacterium. The names proposed for these novel species are Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., and the type strains are YIM M13028(T) ( = DSM 45643(T) = KCTC 19999(T)) and YIM 121001(T) ( = DSM 45768(T) = JCM 18538(T)), respectively.

Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.

The genus Nocardiopsis, a widespread group in phylum Actinobacteria, has received much attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array of bioactive metabolites. Its high environmental adaptability might be attributable to its genome dynamics, which can be estimated through comparative genomic analysis targeting microorganisms with close phylogenetic relationships but different phenotypes. To shed light on speciation, gene content evolution, and environmental adaptation in these unique actinobacteria, we sequenced draft genomes for 16 representative species of the genus and compared them with that of the type species N. dassonvillei subsp. dassonvillei DSM 43111(T). The core genome of 1,993 orthologous and paralogous gene clusters was identified, and the pan-genomic reservoir was found not only to accommodate more than 22,000 genes, but also to be open. The top ten paralogous genes in terms of copy number could be referred to three functional categories: transcription regulators, transporters, and synthases related to bioactive metabolites. Based on phylogenomic reconstruction, we inferred past evolutionary events, such as gene gains and losses, and identified a list of clade-specific genes implicated in environmental adaptation. These results provided insights into the genetic causes of environmental adaptability in this cosmopolitan actinobacterial group and the contributions made by its inherent features, including genome dynamics and the constituents of core and accessory proteins.

Thermus tengchongensis sp. nov., isolated from a geothermally heated soil sample in Tengchong, Yunnan, south-west China.

A Gram-stain negative aerobic bacterium, designated YIM 77924(T), was isolated from a geothermally heated soil sample collected at Rehai National Park, Tengchong, Yunnan province, south-west China. Growth was found to occur from 55 to 75 °C (optimum 65 °C), pH 6.0-8.0 (optimum pH 7.0) and 0-1 % NaCl (w/v). Cells were observed to be rod-shaped and the colonies convex, circular, smooth, yellow and non-transparent. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 77924(T) belongs to the genus Thermus. The 16S rRNA gene sequence similarity values between strain YIM 77924(T) and other species of the genus Thermus were all below 97 %. The polar lipids of strain YIM 77924(T) were determined to be aminophospholipid, phospholipid and glycolipid. The predominant respiratory quinone was determined to be MK-8 and the G+C content was 66.64 mol%. The major fatty acids identified were iso-C(16:0), iso-C(15:0), iso-C(17:0) and C(16:0). On the basis of the morphological and chemotaxonomic characteristics as well as genotypic data, strain YIM 77924(T) is proposed to represent a novel species, Thermus tengchongensis sp. nov., in the genus Thermus. The type strain is YIM 77924(T) (=KCTC 32025(T) = CCTCC AB2012063(T)).

Lihuaxuella thermophila gen. nov., sp. nov., isolated from a geothermal soil sample in Tengchong, Yunnan, south-west China.

A novel filamentous bacterium, designated YIM 77831(T), was isolated from a geothermal soil sample collected at Rehai National Park, Tengchong, Yunnan province, south-west China. Growth occurred from 28 to 65 °C (optimum 50 °C), pH 6.0-8.0 (optimum pH 7.0). The strain formed branched substrate mycelia, endospores were produced on the substrate mycelium and aerial mycelium was not produced on any of the growth media tested. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YIM 77831(T) was affiliated with the family Thermoactinomycetaceae. The stain YIM 77831(T) contained meso-diaminopimelic acid in the cell wall. Whole-cell hydrolysates contained glucose, galactose, mannose, ribose and rhamnose. The polar lipids were phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid and four unknown phospholipids. The only menaquinone was MK-7. Major fatty acids were iso-C(15:0), anteiso-C(15:0) and anteiso-C(17:0). The G+C content was 55.6 mol%. On the basis of the morphological and chemotaxonomic characteristics as well as genotypic data, strain YIM 77831(T) represents a novel genus and species, Lihuaxuella thermophila gen. nov., sp. nov., in the family Thermoactinomycetaceae. The type strain is YIM 77831(T) (CCTCC AA 2011024(T) = JCM 18059(T)).

Lysobacter thermophilus sp. nov., isolated from a geothermal soil sample in Tengchong, south-west China.

A Gram-negative and aerobic bacterium, designated YIM 77875(T), was isolated from a geothermal soil sample collected at Rehai National Park, Tengchong, Yunnan Province, south-west China. Bacterial growth occurred from 37 to 65 °C (optimum 50 °C), pH 6.0-8.0 (optimum pH 7.0) and 0-1 % NaCl (w/v). Cells were rod-shaped and colonies were convex, circular, smooth, yellow and non-transparent. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 77875(T) belongs to the genus Lysobacter. The 16S rRNA gene sequence similarity values between strain YIM 77875(T) and other species of the genus Lysobacter were all below 94.7 %. The polar lipids of strain YIM 77875(T) were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and five unknown phospholipids. The predominant respiratory quinone was Q-8 and the G+C content was 68.8 mol%. Major fatty acids were iso-C(16:0), iso-C(15:0) and iso-C(11:0). On the basis of the morphological and chemotaxonomic characteristics, as well as genotypic data, strain YIM 77875(T) represents a novel species, Lysobacter thermophilus sp. nov., in the genus Lysobacter. The type strain is YIM 77875(T) (CCTCC AB 2012064(T) = KCTC 32020(T)).