Light-inducible carotenoid production controlled by a MarR-type regulator in Corynebacterium glutamicum.

Carotenoid production in some non-phototropic bacteria occurs in a light-dependent manner to protect cells from photo-oxidants. Knowledge regarding the transcriptional regulator involved in the light-dependent production of carotenoids of non-phototrophic bacteria has been mainly confined to coenzyme B12-based photo-sensitive regulator CarH/LitR family proteins belonging to a MerR family transcriptional regulator. In this study, we found that bacteria belonging to Micrococcales and Corynebacteriales exhibit light-dependent carotenoid-like pigment production including an amino acid-producer Corynebacterium glutamicum AJ1511. CrtR is a putative MarR family transcriptional regulator located in the divergent region of a carotenoid biosynthesis gene cluster in the genome of those bacteria. A null mutant for crtR of C. glutamicum AJ1511 exhibited constitutive production of carotenoids independent of light. A complemented strain of the crtR mutant produced carotenoids in a light-dependent manner. Transcriptional analysis revealed that the expression of carotenoid biosynthesis genes is regulated in a light-dependent manner in the wild type, while the transcription was upregulated in the crtR mutant irrespective of light. In vitro experiments demonstrated that a recombinant CrtR protein binds to the specific sequences within the intergenic region of crtR and crtE, which corresponds to -58 to -7 for crtE, and +26 to -28 for crtR with respect to the transcriptional start site, and serves as a repressor for crtE transcription directed by RNA polymerase containing SigA. Taken together, the results indicate that CrtR light-dependently controls the expression of the carotenoid gene cluster in C. glutamicum and probably closely related Actinobacteria.

Promomycin, a polyether promoting antibiotic production in Streptomyces spp.

Widespread interspecific stimulation of antibiotic production occurs in strains of Streptomyces owing to the activity of diffusible substances, as previously determined in our investigations of the cross-feeding effect. In this study, we newly isolated a substance produced by a Streptomyces strain closely related to Streptomyces scabrisporus, based on the observation that this substance induced the production of an unknown antibiotic in another strain related to Streptomyces griseorubiginosus. This substance, named promomycin, is a polyether structurally related to lonomycin. Promomycin itself had an antibiotic activity, but it stimulated antibiotic production in multiple Streptomyces strains at sub-inhibitory concentrations. Evidence implies that this stimulation effect is widespread within this group of bacteria.

Cohnella fontinalis sp. nov., a xylanolytic bacterium isolated from fresh water.

A novel xylan-degrading bacterium, YT-1101(T), was isolated from fresh water. The isolate was a Gram-reaction-negative, aerobic, motile, endospore-forming and rod-shaped bacterium. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain YT-1101(T) belonged to the genus Cohnella, sharing sequence similarities of less than 94 % with the type species. The genomic G+C content was 58.6 mol%. The predominant menaquinone was MK-7. The major fatty acids were anteiso-C(15 : 0), iso-C(16 : 0) and iso-C(15 : 0). Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of morphological, physiological and phylogenetic properties, strain YT-1101(T) represents a novel species of the genus Cohnella, for which the name Cohnella fontinalis sp. nov. is proposed. The type strain is YT-1101(T) (=NBRC 104957(T) =DSM 21753(T)).

Bartonella japonica sp. nov. and Bartonella silvatica sp. nov., isolated from Apodemus mice.

Two bacterial strains, Fuji 18-1(T) and Fuji 23-1(T), were isolated from the blood of the small Japanese field mouse (Apodemus argenteus) and the large Japanese field mouse (Apodemus speciosus), respectively, specimens of which were captured in the forest of Mount Fuji, Japan. Phenotypic characterization (growth conditions, incubation periods, biochemical properties and cell morphologies), DNA G+C contents (40.1 mol% for strain Fuji 18-1(T) and 40.4 mol% for strain Fuji 23-1(T)) and sequence analyses of the 16S rRNA genes indicated that both strains were members of the genus Bartonella. Using rpoB and gltA sequencing analysis, the highest sequence similarities between strains Fuji 18-1(T), Fuji 23-1(T) and other recognized species of the genus Bartonella showed values considerably lower than 91.4 % and 89.9 % in the rpoB gene and 89.1 % and 90.4 % in the gltA gene, respectively. It is known that similarities of 95.4 % for the rpoB gene and 96.0 % for the gltA gene can be applied as cut-off values for the designation of novel species of the genus Bartonella. In a phylogenetic tree based on the merged set of concatenated sequences of seven loci [16S rRNA, ftsZ, gltA, groEL, ribC and rpoB genes and the intergenic spacer region (ITS)], strains Fuji 18-1(T) and Fuji 23-1(T) formed a distinct clade from other recognized species of the genus Bartonella. These data support the classification of strains Fuji 18-1(T) and Fuji 23-1(T) as novel species of the genus Bartonella. The names Bartonella japonica sp. nov. and Bartonella silvatica sp. nov. are proposed for these novel species. The type strains of Bartonella japonica sp. nov. and Bartonella silvatica sp. nov. are Fuji 18-1(T) (=JCM 15567(T)=CIP 109861(T)) and Fuji 23-1(T) (=JCM 15566(T)=CIP 109862(T)), respectively.

Clostridium clariflavum sp. nov. and Clostridium caenicola sp. nov., moderately thermophilic, cellulose-/cellobiose-digesting bacteria isolated from methanogenic sludge.

Two novel anaerobic, moderately thermophilic and cellulose-/cellobiose-digesting bacteria, EBR45(T) and EBR596(T), were isolated from anaerobic sludge of a cellulose-degrading methanogenic bioreactor. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belonged to cluster III within the low-G+C-content Gram-positive bacteria. The close relatives of EBR45(T) were Clostridium straminisolvens DSM 16021(T) (sequence identity, 94.6 %) and Clostridium thermocellum DSM 1237(T) (93.4 %). The closest relative of EBR596(T) was Clostridium stercorarium DSM 8532(T) (95.9 %). Both isolates were rod-shaped sporulators, growing optimally at 60 degrees C. EBR45(T) was Gram-staining-reaction-variable and non-motile, formed bright-yellow colonies on solid media, and grew on a relatively narrow range of carbohydrates including cellulose and cellobiose. EBR596(T) was Gram-staining-reaction-negative and motile, formed glossy white colonies and grew on cellobiose and various carbohydrates except cellulose. Major fatty acid compositions were 16 : 0 iso, 16 : 0 and 16 : 0 dimethylacetal (strain EBR45(T)) and 15 : 0 iso, 16 : 0 iso, 15 : 0 anteiso and 17 : 0 anteiso (strain EBR596(T)). The DNA G+C contents were 36.9 mol% (EBR45(T)) and 51.1 mol% (EBR596(T)). Based on the phenotypic and phylogenetic data and genomic distinctiveness, strains EBR45(T) and EBR596(T) represent two novel species, for which the names Clostridium clariflavum sp. nov. (type strain EBR45(T) =DSM 19732(T) =NBRC 101661(T)) and Clostridium caenicola sp. nov. (type strain EBR596(T) =DSM 19027(T) =NBRC 102590(T)) are proposed.

Filimonas lacunae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from fresh water.

A Gram-negative, strictly aerobic, motile, filamentous and viscous exopolymer-producing bacterium, designated strain YT21(T), was isolated from fresh water. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain YT21(T) lies within a cluster containing the established genera Segetibacter, Terrimonas, Niastella and Chitinophaga in the phylum Bacteroidetes. However, the isolate represented a lineage distinct from these genera, with sequence similarities ranging from 88.9 to 91.8 %. The genomic G+C content was 45.2 mol%. The predominant isoprenoid quinone was MK-7. The major fatty acids were 15 : 0 iso, 17 : 0 iso 3-OH and 15 : 1 iso G. On the basis of morphological features and phenotypic and phylogenetic data, strain YT21(T) represents a novel genus and species, for which the name Filimonas lacunae gen. nov., sp. nov. is proposed. The type strain of Filimonas lacunae is strain YT21(T) (=NBRC 104114(T) =DSM 21054(T)).

Isolation of bacteria whose growth is dependent on high levels of CO2 and implications of their potential diversity.

Although some bacteria require an atmosphere with high CO(2) levels for their growth, CO(2) is not generally supplied to conventional screening cultures. Here, we isolated 84 bacterial strains exhibiting high-CO(2) dependence. Their phylogenetic affiliations imply that high-CO(2) culture has potential as an effective method to isolate unknown microorganisms.

Lutispora thermophila gen. nov., sp. nov., a thermophilic, spore-forming bacterium isolated from a thermophilic methanogenic bioreactor digesting municipal solid wastes.

A novel anaerobic, moderately thermophilic, spore-forming, rod-shaped bacterium (strain EBR46T) was isolated from an enrichment culture derived from an anaerobic thermophilic (55 degrees C) methanogenic bioreactor treating artificial solid wastes. Phylogeny based on 16S rRNA gene sequence analysis placed strain EBR46T within a distinct lineage between Clostridium clusters II and III. The closest recognized relative of strain EBR46T was Gracilibacter thermotolerans DSM 17427T (85.3 % 16S rRNA gene sequence similarity). The DNA G+C content of strain EBR46T was 36.2 mol%. The novel strain grew optimally at 55-58 degrees C and at pH 7.5-8.0 and was able to grow on peptone, tryptone, Casamino acids, casein hydrolysate, methionine, threonine, tryptophan, cysteine, lysine and serine in the presence of 0.2 % yeast extract. Carbohydrates were not utilized. The main products from tryptone utilization were acetate, iso-butyrate, propionate and iso-valerate. Strain EBR46T produced hydrogen sulfide from cysteine. The major fatty acids were iso-C15 : 0, C14 : 0, C16 : 0 DMA (dimethyl acetal) and iso-C15 : 0 DMA. Based on its unique phylogenetic and physiological features, strain EBR46T is considered to represent a novel species of a new genus, for which the name Lutispora thermophila gen. nov., sp. nov. is proposed. The type strain of the type species is EBR46T (=NBRC 102133T=DSM 19022T).

Isolation and characterization of a new Clostridium sp. that performs effective cellulosic waste digestion in a thermophilic methanogenic bioreactor.

A methanogenic bioreactor that utilized wastepaper was developed and operated at 55 degrees C. Microbial community structure analysis showed the presence of a group of clostridia that specifically occurred during the period of high fermentation efficiency. To isolate the effective cellulose digester, the sludge that exhibited high fermentation efficiency was inoculated into a synthetic medium that contained cellulose powder as the sole carbon source and was successively cultivated. A comprehensive 16S rRNA gene sequencing study revealed that the enriched culture contained various clostridia that had diverse phylogenetic positions. The microorganisms were further enriched by successive cultivation with filter paper as the substrate, as well as the bait carrier. A resultant isolate, strain EBR45 (= Clostridium sp. strain NBRC101661), was a new member of the order Clostridiales phylogenetically and physiologically related to Clostridium thermocellum and Clostridium straminisolvens. Specific PCR-based monitoring demonstrated that strain EBR45 specifically occurred during the high fermentation efficiency period in the original methanogenic sludge. Strain EBR45 effectively digested office paper in its pure cultivation system with a synthetic medium.