Deinococcus ficus sp. nov., isolated from the rhizosphere of Ficus religiosa L

Deinococcus aquatilis sp. nov., isolated from water

A pale-pink strain (CCUG 53370(T)) from water was investigated by a polyphasic taxonomic approach. The cells stained Gram-positive and were rod-shaped and non-spore-forming. Analyses using the 16S rRNA gene sequence of the isolate showed that the organism belongs to the genus Deinococcus, with the highest sequence similarities to the type strains of Deinococcus ficus (94.4 %), Deinococcus navajonensis (94.3 %) and Deinococcus mumbaiensis (94.3 %). Chemotaxonomic data revealed that CCUG 53370(T) contains exclusively menaquinone MK-8 as the respiratory quinone and a complex polar lipid profile consisting of different unidentified glycolipids and polar lipids, two unknown phospholipids and three unknown phosphoglycolipids. As in other deinococci, one of these phosphoglycolipids was predominant in the profile, and it was identified in Deinococcus radiodurans as 2'-O-(1,2-diacyl-sn-glycero-3-phospho)-3'-O-(alpha-galactosyl)-N-D-glyceroyl alkylamine. Predominant fatty acids were C(16 : 1)omega7c, C(17 : 1)omega8c and C(17 : 1)omega9c. Biochemical and chemotaxonomic properties demonstrate that strain CCUG 53370(T) represents a novel species, for which the name Deinococcus aquatilis sp. nov. is proposed. The type strain is CCUG 53370(T) (=CCM 7524(T)).

Deinococcus aquaticus sp. nov., isolated from fresh water, and Deinococcus caeni sp. nov., isolated from activated sludge

The taxonomic positions of two environmental isolates from South Korea were established using a combination of genotypic and phenotypic data. The organisms, designated PB314(T) and Ho-08(T), were Gram-negative, rod-shaped and non-spore-forming and had chemotaxonomic properties consistent with their classification in the genus Deinococcus 16S rRNA gene tree, the highest sequence similarities being shown to the type strains of Deinococcus grandis (96.3-96.7 %) and Deinococcus indicus (96.3-96.4 %). The isolates shared relatively high 16S rRNA gene sequence similarity (98.1 %) but had a DNA-DNA relatedness value of only 22 %. Chemotaxonomic data revealed that both strains possess quinone system MK-8 as the predominant compound, C(16 : 1)omega7c and C(16 : 0) as major fatty acids and ornithine as a diamino acid in the peptidoglycan structure, corroborating our assignment of the strains to the genus Deinococcus. The results of phylogenetic analyses based on 16S rRNA gene sequences, DNA-DNA relatedness values and physiological and biochemical tests clearly demonstrated that the two strains represent distinct species. On the basis of these data, two novel species, Deinococcus aquaticus sp. nov. (type strain PB314(T) =KCTC 12552(T) =NBRC 101311(T)) and Deinococcus caeni sp. nov. (type strain Ho-08(T) =KCTC 12553(T) =NBRC 101312(T)), are proposed.

Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus

The crystal structure of the DFA0005 protein complexed with alpha-ketoglutarate (AKG) from an alkali-tolerant bacterium Deinococcus ficus has been determined to a resolution of 1.62 A. The monomer forms an incomplete alpha7/beta8 barrel with a protruding alpha8 helix that interacts extensively with another subunit to form a stable dimer of two complete alpha8/beta8 barrels. The dimer is further stabilized by four glycerol molecules situated at the interface. One unique AKG ligand binding pocket per subunit is detected. Fold match using the DALI and SSE servers identifies DFA0005 as belonging to the isocitrate lyase/phosphoenolpyruvate mutase (ICL/PEPM) superfamily. However, further detailed structural and sequence comparison with other members in this superfamily and with other families containing AKG ligand indicate that DFA0005 protein exhibits considerable distinguishing features of its own and can be considered a novel member in this ICL/PEPM superfamily.

Description of four novel psychrophilic, ionizing radiation-sensitive Deinococcus species from alpine environments

Five psychrophilic bacterial strains were isolated from soil samples collected above the treeline of alpine environments. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these organisms represent four novel species of the genus Deinococcus; levels of sequence similarity to the type strains of recognized Deinococcus species were in the range 89.3-94.7 %. Strains PO-04-20-132T, PO-04-20-144, PO-04-19-125T, ME-04-01-32T and ME-04-04-52T grew aerobically, with optimum growth at 10 degrees C and at pH 6-9. The major respiratory menaquinone was MK-8. The fatty acid profiles of strains PO-04-20-132T, PO-04-20-144, PO-04-19-125T and ME-04-01-32T were dominated by 16 : 1omega7c, 17 : 0 iso and 15 : 1omega6c, whereas 16 : 1omega7c, 17 : 0 cyclo and 16 : 0 predominated in strain ME-04-04-52T. The DNA G+C contents of strains PO-04-20-132T, PO-04-19-125T, ME-04-01-32T and ME-04-04-52T were 63.2, 63.1, 65.9 and 62.6 mol%, respectively. Strains PO-04-20-132T, PO-04-19-125T, ME-04-01-32T and ME-04-04-52T had gamma radiation D10 (dose required to reduce the bacterial population by 10-fold) values of < or =4 kGy. These four strains showed sensitivity to UV radiation and extended desiccation as compared with Deinococcus radiodurans. On the basis of the phylogenetic analyses, and chemotaxonomic and phenotypic data, it is proposed that strains PO-04-20-132T (=LMG 24019T=NRRL B-41950T; Deinococcus radiomollis sp. nov.), PO-04-19-125T (=LMG 24282T=NRRL B-41949T; Deinococcus claudionis sp. nov.), ME-04-01-32T (=LMG 24022T=NRRL B-41947T; Deinococcus altitudinis sp. nov.) and ME-04-04-52T (=LMG 24283T=NRRL B-41948T; Deinococcus alpinitundrae sp. nov.) represent the type strains of four novel species of the genus Deinococcus.

Physiological and phylogenetic study of an ammonium-oxidizing culture at high nitrite concentrations

Oxidation of high-strength ammonium wastewater can lead to exceptionally high nitrite concentrations; therefore, the effect of high nitrite concentration (> 400 mM) was studied using an ammonium-oxidizing enrichment culture in a batch reactor. Ammonium was fed to the reactor in portions of 40-150 mM until ammonium oxidation rates decreased and finally stopped. Activity was restored by replacing half of the medium, while biomass was retained by a membrane. The ammonium-oxidizing population obtained was able to oxidize ammonium at nitrite concentrations of up to 500 mM. The maximum specific oxidation activity of the culture in batch test was about 0.040 mmol O(2)g(-1)proteinmin(-1) and the K(s) value was 1.5 mM ammonium. In these tests, half of the maximum oxidation activity was still present at a concentration of 600 mM nitrite and approximately 10% residual activity could still be measured at 1200 mM nitrite (pH 7.4), or as a free nitrous acid (FNA) concentration of 6.6 mg l(-1). Additional experiments showed that the inhibition was caused by nitrite and not by the high sodium chloride concentration of the medium. The added ammonium was mainly converted into nitrite and no nitrite oxidation was observed. In addition, gaseous nitrogen compounds were detected and mass balance calculations revealed a nitrogen loss of approximately 20% using this system. Phylogenetic analyses of 16S rRNA and ammonium monooxygenase (amoA) genes of the obtained enrichment culture showed that ammonium-oxidizing bacteria of the Nitrosomonas europaea/Nitrosococcus mobilis cluster dominated the two clone libraries. Approximately 25% of the 16S rRNA clones showed a similarity of 92% to Deinococcus-like organisms. Specific fluorescence in situ hybridization (FISH) probes confirmed that these microbes comprised 10-20% of the microbial community in the enrichment. The Deinococcus-like organisms were located around the Nitrosomonas clusters, but their role in the community is currently unresolved.

Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis.

Deinococcus peraridilitoris sp. nov., isolated from a coastal desert

Three ionizing-radiation-resistant bacterial strains (designated KR-196, KR-198 and KR-200(T)) were isolated from a sample of arid soil collected from a coastal desert in Chile. The soil sample was irradiated before serial dilution plating was performed using one-tenth-strength plate count agar. Phylogenetic analysis of the 16S rRNA gene sequences showed these organisms to represent a novel species of the genus Deinococcus, having sequence similarities of 87.3-90.8 % with respect to recognized Deinococcus species. Strains KR-196, KR-198 and KR-200(T) were aerobic and showed optimum growth at 30 degrees C and pH 6.5-8.0. The major respiratory menaquinone was MK-8. The predominant fatty acids in these strains were 16 : 1 omega 7c, 16 : 0, 15 : 1 omega 6c, 17 : 0 and 18 : 0. The DNA G+C content of strain KR-200(T) was 63.9 mol%. Strains KR-196, KR-198 and KR-200(T) were found to be resistant to >10 kGy gamma radiation. On the basis of the phylogenetic, chemotaxonomic and phenotypic data, strain KR-200(T) represents a novel species of the genus Deinococcus, for which the name Deinococcus peraridilitoris sp. nov. is proposed. The type strain is KR-200(T) (=LMG 22246(T)=CIP 109416(T)).

Deinococcus yunweiensis sp. nov., a gamma- and UV-radiation-resistant bacterium from China

A Gram-negative, non-spore-forming, non-motile, rod-shaped, red-pigmented strain, designated YIM 007T, was found as a contaminant on an agar plate in the laboratory of Yunnan Institute of Microbiology, China. The optimum growth pH and temperature for the isolate were 7.0–7.5 and 30 °C, respectively. The predominant respiratory quinone was MK-8. The polar lipid profile consisted mainly of various unknown phosphoglycolipids and glycolipids. The major cellular fatty acids were C16 : 1 ω7c, C16 : 0, C17 : 0 and C17 : 1 ω8c. l-Ornithine was detected in its peptidoglycan. The DNA G+C content was 64.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 007T showed 16S rRNA gene sequence similarity levels of 86.8–92.1 % to the other described Deinococcus species. Based on the high 16S rRNA gene sequence divergence and phenotypic differences, it is proposed that the unknown strain should be classified as a novel species in the genus Deinococcus with the name Deinococcus yunweiensis sp. nov. The type strain is YIM 007T (=KCTC 3962T=DSM 17005T).