Comparative survival analysis of 12 histidine kinase mutants of Deinococcus radiodurans after exposure to DNA-damaging agents

Pontibacter rufus sp. nov., Pontibacter humidus sp. nov. and Pontibacter coccineus sp. nov. isolated from UV-irradiated soil in Korea

Three novel bacterial strains, 172403-2T, BT310T and BT731T, were isolated from UV-irradiated soil samples collected in South Korea. All strains are Gram-negative, aerobic, non-motile and grow at 20-35 °C, optimally at 30 °C and pH 7.0. The optimal NaCl concentration for strains 172403-2T and BT310T is 1.5%, while strain BT731T grows optimally in the absence of NaCl (0.0%). Phylogenetic analysis based on 16S rRNA gene sequences positioned these strains within the genus Pontibacter, with strain 172403-2T closest to Pontibacter chitinilyticus (95.96%), BT310T to Pontibacter pudoricolor (97.87%) and BT731T to Pontibacter virosus (98.06%). Cellular fatty acid profiles identified C15:0 iso and Summed Feature 4 as predominant fatty acids. All strains contained ubiquinone MK-7 and phosphatidylethanolamine as major respiratory quinone and primary polar lipids, respectively. Genome sizes were 5.08 Mb for 172403-2T, 4.29 Mb for BT310T and 4.66 Mb for BT731T, with average nucleotide identity and digital DNA-DNA hybridization values with other Pontibacter species ranging between 70.41%-88.56% and 11.55%-24.66%, respectively. These biochemical, chemotaxonomic and phylogenetic analyses confirm that strains 172403-2T, BT310T and BT731T represent three novel species of Pontibacter, proposed as Pontibacter rufus sp. nov. (172403-2T = KCTC 62072 T=NBRC 114967T), Pontibacter humidus sp. nov. (BT310T = KCTC 72363T = NBRC 114846T) and Pontibacter coccineus sp. nov. (BT731T = KCTC 92910T = NBRC 116069T).

Insights into the radiation and oxidative stress mechanisms in genus Deinococcus

Deinococcus species, noted for their exceptional resistance to DNA-damaging environmental stresses, have piqued scientists' interest for decades. This study dives into the complex mechanisms underpinning radiation resistance in the Deinococcus genus. We have examined the genomes of 82 Deinococcus species and classified radiation-resistance proteins manually into five unique curated categories: DNA repair, oxidative stress defense, Ddr and Ppr proteins, regulatory proteins, and miscellaneous resistance components. This classification reveals important information about the various molecular mechanisms used by these extremophiles which have been less explored so far. We also investigated the presence or lack of these proteins in the context of phylogenetic relationships, core, and pan-genomes, which offered light on the evolutionary dynamics of radiation resistance. This comprehensive study provides a deeper understanding of the genetic underpinnings of radiation resistance in the Deinococcus genus, with potential implications for understanding similar mechanisms in other organisms using an interactomics approach. Finally, this study reveals the complexities of radiation resistance mechanisms, providing a comprehensive understanding of the genetic components that allow Deinococcus species to flourish under harsh environments. The findings add to our understanding of the larger spectrum of stress adaption techniques in bacteria and may have applications in sectors ranging from biotechnology to environmental research.

Radiation-Tolerant Fibrivirga spp. from Rhizosphere Soil: Genome Insights and Potential in Agriculture

The rhizosphere of plants contains a wide range of microorganisms that can be cultivated and used for the benefit of agricultural practices. From garden soil near the rhizosphere region, Strain ES10-3-2-2 was isolated, and the cells were Gram-negative, aerobic, non-spore-forming rods that were 0.3-0.8 µm in diameter and 1.5-2.5 µm in length. The neighbor-joining method on 16S rDNA similarity revealed that the strain exhibited the highest sequence similarities with "Fibrivirga algicola JA-25" (99.2%) and Fibrella forsythia HMF5405T (97.3%). To further explore its biotechnological potentialities, we sequenced the complete genome of this strain employing the PacBio RSII sequencing platform. The genome of Strain ES10-3-2-2 comprises a 6,408,035 bp circular chromosome with a 52.8% GC content, including 5038 protein-coding genes and 52 RNA genes. The sequencing also identified three plasmids measuring 212,574 bp, 175,683 bp, and 81,564 bp. Intriguingly, annotations derived from the NCBI-PGAP, eggnog, and KEGG databases indicated the presence of genes affiliated with radiation-resistance pathway genes and plant-growth promotor key/biofertilization-related genes regarding Fe acquisition, K and P assimilation, CO2 fixation, and Fe solubilization, with essential roles in agroecosystems, as well as genes related to siderophore regulation. Additionally, T1SS, T6SS, and T9SS secretion systems are present in this species, like plant-associated bacteria. The inoculation of Strain ES10-3-2-2 to Arabidopsis significantly increases the fresh shoot and root biomass, thereby maintaining the plant quality compared to uninoculated controls. This work represents a link between radiation tolerance and the plant-growth mechanism of Strain ES10-3-2-2 based on in vitro experiments and bioinformatic approaches. Overall, the radiation-tolerant bacteria might enable the development of microbiological preparations that are extremely effective at increasing plant biomass and soil fertility, both of which are crucial for sustainable agriculture.

Comparative genomics of Deinococcus radiodurans: unveiling genetic discrepancies between ATCC 13939K and BAA-816 strains

The Deinococcus genus is renowned for its remarkable resilience against environmental stresses, including ionizing radiation, desiccation, and oxidative damage. This resilience is attributed to its sophisticated DNA repair mechanisms and robust defense systems, enabling it to recover from extensive damage and thrive under extreme conditions. Central to Deinococcus research, the D. radiodurans strains ATCC BAA-816 and ATCC 13939 facilitate extensive studies into this remarkably resilient genus. This study focused on delineating genetic discrepancies between these strains by sequencing our laboratory's ATCC 13939 specimen (ATCC 13939K) and juxtaposing it with ATCC BAA-816. We uncovered 436 DNA sequence differences within ATCC 13939K, including 100 single nucleotide variations, 278 insertions, and 58 deletions, which could induce frameshifts altering protein-coding genes. Gene annotation revisions accounting for gene fusions and the reconciliation of gene lengths uncovered novel protein-coding genes and refined the functional categorizations of established ones. Additionally, the analysis pointed out genome structural variations due to insertion sequence (IS) elements, underscoring the D. radiodurans genome's plasticity. Notably, ATCC 13939K exhibited a loss of six ISDra2 elements relative to BAA-816, restoring genes fragmented by ISDra2, such as those encoding for α/β hydrolase and serine protease, and revealing new open reading frames, including genes imperative for acetoin decomposition. This comparative genomic study offers vital insights into the metabolic capabilities and resilience strategies of D. radiodurans.

Development and Regulation of the Extreme Biofilm Formation of Deinococcus radiodurans R1 under Extreme Environmental Conditions

To grow in various harsh environments, extremophiles have developed extraordinary strategies such as biofilm formation, which is an extremely complex and progressive process. However, the genetic elements and exact mechanisms underlying extreme biofilm formation remain enigmatic. Here, we characterized the biofilm-forming ability of Deinococcus radiodurans in vitro under extreme environmental conditions and found that extremely high concentrations of NaCl or sorbitol could induce biofilm formation. Meantime, the survival ability of biofilm cells was superior to that of planktonic cells in different extreme conditions, such as hydrogen peroxide stress, sorbitol stress, and high UV radiation. Transcriptome profiles of D. radiodurans in four different biofilm development stages further revealed that only 13 matched genes, which are involved in environmental information processing, carbohydrate metabolism, or stress responses, share sequence homology with genes related to the biofilm formation of Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. Overall, 64% of the differentially expressed genes are functionally unknown, indicating the specificity of the regulatory network of D. radiodurans. The mutation of the drRRA gene encoding a response regulator strongly impaired biofilm formation ability, implying that DrRRA is an essential component of the biofilm formation of D. radiodurans. Furthermore, transcripts from both the wild type and the drRRA mutant were compared, showing that the expression of drBON1 (Deinococcus radioduransBON domain-containing protein 1) significantly decreased in the drRRA mutant during biofilm development. Further analysis revealed that the drBON1 mutant lacked the ability to form biofilm and DrRRA, and as a facilitator of biofilm formation, could directly stimulate the transcription of the biofilm-related gene drBON1. Overall, our work highlights a molecular mechanism mediated by the response regulator DrRRA for controlling extreme biofilm formation and thus provides guidance for future studies to investigate novel mechanisms that are used by D. radiodurans to adapt to extreme environments.

Characterization of radiation-resistance mechanism in Spirosoma montaniterrae DY10T in terms of transcriptional regulatory system

To respond to the external environmental changes for survival, bacteria regulates expression of a number of genes including transcription factors (TFs). To characterize complex biological phenomena, a biological system-level approach is necessary. Here we utilized six computational biology methods to infer regulatory network and to characterize underlying biologically mechanisms relevant to radiation-resistance. In particular, we inferred gene regulatory network (GRN) and operons of radiation-resistance bacterium Spirosoma montaniterrae DY10[Formula: see text] and identified the major regulators for radiation-resistance. Our results showed that DNA repair and reactive oxygen species (ROS) scavenging mechanisms are key processes and Crp/Fnr family transcriptional regulator works as a master regulatory TF in early response to radiation.

Hymenobacter puniceus sp. nov., radiation resistant bacteria isolated from soil in South Korea

Two novel Gram-negative bacterial strains BT190^T and BT191 were isolated from soil collected in Uijeongbu city (37°44'55″N, 127°02'20″E), Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains BT190^T and BT191 belong to a distinct lineage within the genus Hymenobacter (family Hymenobacteraceae, order Cytophagales, class Cytophagia). The level of 16S rRNA gene sequence similarity between the strains BT190^T and BT190 was 99.5%. The strains BT190^T and BT191 were closely related to Hymenobacter swuensis DY53^T (97.0% 16S rRNA gene similarity), Hymenobacter metallilatus 9PBR-2 ^T (96.8%), Hymenobacter tibetensis XTM003^T (96.8%) and Hymenobacter yonginensis HMD1010^T (96.6%). The genome size of strain BT190^T was 4,859,864 bp. The DNA G+C content of strain BT190^T was 55.3 mol%. Bacterial growth was observed at 4-30 °C (optimum 25 °C) and pH 6.0-9.0 (optimum, pH 6.0-7.0) on R2A agar. Colonies of strains BT190^T and BT191 were raised, smooth, circular and red-pink colored. The sole respiratory quinone of strain BT190^T was MK-7 and the predominant cellular fatty acids were iso-C_15:0, C_16:1 ω5c, summed feature 3 (C_16:1 ω6c / C_16:1 ω7c) and summed feature 4 (iso-C_17:1 I / anteiso-C_17:1 B). The major polar lipids of strain BT190^T were aminophospholipid (APL) and phosphatidylethanolamine (PE). Based on the chemotaxonomic, biochemical, and phylogenetic analysis, strains BT190^T and BT191 can be suggested as a novel bacterial species within the genus Hymenobacter, for which the name Hymenobacter puniceus sp. nov is proposed. The type strain of Hymenobacter puniceus is BT190^T (= KCTC 72342 ^T = NBRC 114860 ^T).

Lack of the Bacterial Phytochrome Protein Decreases Deinococcus radiodurans Resistance to Mitomycin C

Deinococcus radiodurans known for its extraordinary resistance to ionizing radiation contains bacterial phytochrome (BphP), a member of the family of red/far-red light-sensing proteins. In this study, we constructed a bphP mutant strain (ΔbphP) to investigate the role of D. radiodurans BphP (DrBphP) in the DNA damage response. When cells were incubated under light and dark conditions following exposure to DNA damaging agents, such as γ- and UV-radiation and mitomycin C (MMC), no significant difference in cell survival was observed between the wild-type D. radiodurans strain (WT) and ΔbphP. However, when continuously exposed to MMC under light conditions, the WT strain notably exhibited increased survival compared to cells grown in the dark. The increased survival was not observed in the ΔbphP strain. These results are indicative of the protective role of light-activated DrBphP in the presence of MMC. Site-directed mutagenesis revealed that the conserved amino acids Cys-24 and His-532 involved in chromophore binding and signal transduction, respectively, were essential for the protective function of DrBphP. Inactivation of the cognate response regulator (RR; DrBphR) of DrBphP increased MMC resistance in the dark. In trans complementation of the bphP bphR double mutant strain (ΔbphPR) with DrBphR decreased MMC resistance. Considering that DrBphP acts as a light-activated phosphatase that dephosphorylates DrBphR, it appears that phosphorylated DrBphR exerts a negative effect on cell survival in the presence of MMC. DrBphP overexpression resulted in an increase in MMC resistance of ΔbphPR, implying that other RRs might be involved in the DrBphP-mediated signaling pathway. A mutant lacking the dr_0781 gene (Δdr_0781) demonstrated the same MMC phenotype as ΔbphR. Survival was further increased in the bphR dr_0781 double mutant strain compared to each single mutant ΔbphR or Δdr_0781, suggesting that DR_0781 is also involved in the DrBphP-dependent MMC sensitivity. This study uncovered a previously unknown phenomenon of red/far-red light-dependent DNA damage survival mediated by BphP by identifying the conditions under which DrBphP exhibits a fitness advantage.

Spirosoma aureum sp. nov., and Hymenobacter russus sp. nov., radiation-resistant bacteria in Cytophagales order isolated from soil

A Gram-stain-negative, aerobic, nonmotile, yellow-colored strain BT328^T and Gram-stain-negative, aerobic, non-motile, red-colored strain BT18^T were isolated from the soil collected in Korea. Phylogenetic analyses based on 16S rRNA gene sequence revealed that strain BT328^T formed a distinct lineage within the family Spirosomaceae (order Cytophagales, class Cytophagia) and was most closely related to a member of the genus Spirosoma, Spirosoma terrae 15J9-4^T (95.9% 16S rRNA gene sequence similarity). Optimal growth occurred at 25 °C, pH 7.0 and in the absence of NaCl. The predominant cellular fatty acids were summed feature 3 (C_16:1 ω6c/C_16:1 ω7c) and C_16:1 ω5c. The major respiratory quinone was MK-7. The major polar lipid was phosphatidylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BT18^T formed a distinct lineage within the family Hymenobacteraceae (order Cytophagales, class Cytophagia, phylum Bacteroidetes) and was most closely related to members of the genus Hymenobacter, Hymenobacter knuensis 16F7C-2^T (97.0% 16S rRNA gene sequence similarity). Optimal growth occurred at 25 °C and pH 7.0 without NaCl. The major fatty acids were iso-C_15:0 and anteiso-C_15:0. The major menaquinone was MK-7. The major polar lipid was phosphatidylethanolamine. Biochemical, chemotaxonomic and phylogenetic analyses indicated that strains BT328^T and BT18^T represents a novel bacterial species within the genus Spirosoma and Hymenobacter, respectively. For which the name Spirosoma aureum and Hymenobacter russus is proposed. The type strain of S. aureum is BT328^T (=KCTC 72365^T = NBRC 114506^T) and the type strain of H. russus is BT18^T (=KCTC 62610^T = NBRC 114380^T).

Rhodocytophaga rosea sp. nov. and Nibribacter ruber sp. nov., two radiation-resistant bacteria isolated from soil

Two bacterial strains, 172606-1^T and BT10^T, were isolated from soil, Korea. Both strains were Gram-stain-negative and rod-shaped bacteria. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 172606-1^T formed a distinct lineage within the family Cytophagaceae (order Cytophagales, class Cytophagia, phylum Bacteroidetes). Strain 172606-1^T was most closely related to a member of the genus Rhodocytophaga (93.8% 16S rRNA gene sequence similarity to Rhodocytophaga aerolata 5416T-29^T). The complete genome sequence of strain 172606-1^T is 8,983,451 bp size. Optimal growth occurred at 25 °C and pH 7.0 without NaCl. The major cellular fatty acids were identified as iso-C_15:0 and C_16:1 ω5c. The major respiratory quinone was MK-7. The major polar lipid was phosphatidylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BT10^T belongs to the genus Nibribacter and is closely related to Nibribacter koreensis GSR 3061^T (96.5%), Rufibacter glacialis MDT1-10-3^T (95.7%), Rufibacter sediminis H-1^T (95.1%) and Rufibacter quisquiliarum CAI-18b^T (94.9%). The complete genome sequence of strain BT10^T is 4,374,810 bp size. The predominant (> 10%) cellular fatty acids of strain BT10^T were iso-C_15:0 and summed feature 4 (anteiso-C_17:1 B/iso-C_17:1 I) and a predominant quinone was MK-7. In addition, strain BT10^T has phosphatidylethanolamine (PE) as the major polar lipid. On the basis of biochemical, chemotaxonomic and phylogenetic analyses, strain 172606-1^T represents a novel bacterial species of the genus Rhodocytophaga, for which the name Rhodocytophaga rosea is proposed and strain BT10^T represents a novel species of the genus Nibribacter, for which the name Nibribacter ruber is proposed. The type strains of Rhodocytophaga rosea and Nibribacter ruber are 172606-1^T (= KCTC 62096^T = NBRC 114410^T) and BT10^T (= KCTC 62607^T = NBRC 114383^T), respectively.

Pontibacter pudoricolor sp. nov., and Pontibacter russatus sp. nov. radiation-resistant bacteria isolated from soil

Gram-stain-negative, aerobic, non-flagellated, red-colored strains BT214^T and BT326^T were isolated from soil collected in Uijeongbu city, Korea. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains BT214^T and BT326^T formed a distinct lineage within the family Hymenobacteraceae (order Chitinophagales, class Chitinophagia) and were most closely related to members of the genus Pontibacter, Pontibacter populi HLY7-15^T (96.9% 16S rRNA gene sequence similarity) and Pontibacter amylolyticus 9-2^T (96.1%), respectively. Optimal growth of two strains occurred at 25 °C, pH 7.0 and in the absence of NaCl. The predominant cellular fatty acids were summed feature 4 (iso-C_17:1 I/anteiso-C_17:1 B) and iso-C_15:0. The major respiratory quinone of two strains was MK-7. The major polar lipid of two strains was phosphatidylethanolamine. Biochemical, chemotaxonomic and phylogenetic analyses indicated that strains BT214^T and BT326^T represent novel bacterial species within the genus Pontibacter, for which the names Pontibacter pudoricolor and Pontibacter russatus are proposed. The type strains of Pontibacter pudoricolor and Pontibacter russatus are BT214^T and BT326^T, respectively.

Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima

Chernobyl and Fukushima were subjected to radionuclide (RN) contamination that has led to environmental problems. In order to explore the ability of microorganisms to survive in these environments, we used a combined 16S rRNA and metagenomic approach to describe the prokaryotic community structure and metabolic potential over a gradient of RN concentrations (137Cs 1680–0.4 and 90Sr 209.1–1.9 kBq kg−1) in soil samples. The taxonomic results showed that samples with low 137Cs content (37.8–0.4 kBq kg−1) from Fukushima and Chernobyl clustered together. In order to determine the effect of soil chemical parameters such as organic carbon (OC), Cesium-137 (137Cs) and Strontium-90 (90Sr) on the functional potential of microbial communities, multiple predictor model analysis using piecewiseSEM was carried out on Chernobyl soil metagenomes. The model identified 46 genes that were correlated to these parameters of which most have previously been described as mechanisms used by microorganisms under stress conditions. This study provides a baseline taxonomic and metagenomic dataset for Fukushima and Chernobyl, respectively, including physical and chemical characteristics. Our results pave the way for evaluating the possible RN selective pressure that might contribute to shaping microbial community structure and their functions in contaminated soils.

Proteomic and Metabolomic Profiling of Deinococcus radiodurans Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions

The polyextremophile, gram-positive bacterium Deinococcus radiodurans can withstand harsh conditions of real and simulated outer space environment, e.g., UV and ionizing radiation. A long-term space exposure of D. radiodurans has been performed in Low Earth Orbit (LEO) in frames of the Tanpopo orbital mission aiming to investigate the possibility of interplanetary life transfer. Space vacuum (10^-4–10^-7 Pa) is a harmful factor, which induces dehydration and affects microbial integrity, severely damaging cellular components: lipids, carbohydrates, proteins, and nucleic acids. However, the molecular strategies by which microorganisms protect their integrity on molecular and cellular levels against vacuum damage are not yet understood. In a simulation experiment, we exposed dried D. radiodurans cells to vacuum (10^-4–10^-7 Pa), which resembles vacuum pressure present outside the International Space Station in LEO. After 90 days of high vacuum exposure, survival of D. radiodurans cells was 2.5-fold lower compared to control cells. To trigger molecular repair mechanisms, vacuum exposed cells of D. radiodurans were recovered in complex medium for 3 and 6 h. The combined approach of analyzing primary metabolites and proteins revealed important molecular activities during early recovery after vacuum exposure. In total, 1939 proteins covering 63% of D. radiodurans annotated protein sequences were detected. Proteases, tRNA ligases, reactive oxygen species (ROS) scavenging proteins, nucleic acid repair proteins, TCA cycle proteins, and S-layer proteins are highly abundant after vacuum exposure. The overall abundance of amino acids and TCA cycle intermediates is reduced during the recovery phase of D. radiodurans as they are needed as carbon source. Furthermore, vacuum exposure induces an upregulation of Type III histidine kinases, which trigger the expression of S-layer related proteins. Along with the highly abundant transcriptional regulator of FNR/CRP family, specific histidine kinases might be involved in the regulation of vacuum stress response. After repair processes are finished, D. radiodurans switches off the connected repair machinery and focuses on proliferation. Combined comparative analysis of alterations in the proteome and metabolome helps to identify molecular key players in the stress response of D. radiodurans, thus elucidating the mechanisms behind its extraordinary regenerative abilities and enabling this microorganism to withstand vacuum stress.

Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species

Deinococcus bacteria are famous for their extreme resistance to ionising radiation and other DNA damage- and oxidative stress-generating agents. More than a hundred genes have been reported to contribute to resistance to radiation, desiccation and/or oxidative stress in Deinococcus radiodurans. These encode proteins involved in DNA repair, oxidative stress defence, regulation and proteins of yet unknown function or with an extracytoplasmic location. Here, we analysed the conservation of radiation resistance-associated proteins in other radiation-resistant Deinococcus species. Strikingly, homologues of dozens of these proteins are absent in one or more Deinococcus species. For example, only a few Deinococcus-specific proteins and radiation resistance-associated regulatory proteins are present in each Deinococcus, notably the metallopeptidase/repressor pair IrrE/DdrO that controls the radiation/desiccation response regulon. Inversely, some Deinococcus species possess proteins that D. radiodurans lacks, including DNA repair proteins consisting of novel domain combinations, translesion polymerases, additional metalloregulators, redox-sensitive regulator SoxR and manganese-containing catalase. Moreover, the comparisons improved the characterisation of several proteins regarding important conserved residues, cellular location and possible protein–protein interactions. This comprehensive analysis indicates not only conservation but also large diversity in the molecular mechanisms involved in radiation resistance even within the Deinococcus genus.

Deinococcus koreensis sp. nov., a gamma radiation-resistant bacterium isolated from river water

A gamma radiation-resistant, Gram-stain-negative, rod-shaped bacterial strain, designated SJW1-2^T, was isolated from freshwater samples collected from the Seomjin River, Republic of Korea. The 16S rRNA gene sequence analyses showed that strain SJW1-2^T was most closely related to Deinococcus metalli 1PNM-19^T (94.3 % sequence similarity) and formed a robust phylogenetic clade with other species of the genus Deinococcus. The optimum growth pH and temperature for the isolate were pH 7.0-7.5 and 25 °C, respectively. Strain SJW1-2^T exhibited high resistance to gamma radiation. The predominant respiratory quinone was MK-8. The polar lipid profile consisted of different unidentified glycolipids, two unidentified lipids, two unidentified phospholipids and an unidentified phosphoglycolipid. The major peptidoglycan amino acids were alanine, d-glutamic acid, glycine and l-ornithine. The predominant fatty acids (>10 %) were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (25.2 %) and C16 : 0 (21.2 %), and the DNA G+C content was 69.5 mol%. On the basis of phenotypic, genotypic and phylogenetic analyses, strain SJW1-2^T (=KACC 19332^T=NBRC 112908^T) represents a novel species of the genus Deinococcus, for which the name Deinococcus koreensis sp. nov. is proposed.

Spirosoma swuense sp. nov., isolated from wet soil

Strain JBM2-3T, a pale-yellow-coloured, aerobic, catalase-negative, oxidase-positive and Gram-stain-negative bacterium, was isolated from wet soil. The isolate grew aerobically at 25-30 °C (optimum 25 °C), pH 6.0-8.0 (optimum pH 7.0) and in the presence of 0-0.5 % (w/v) NaCl (optimum 0 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain JBM2-3T belonged to the genus Spirosoma, with a sequence similarity of 96.2 % with Spirosoma panaciterrae Gsoil 1519T. The strain showed the typical chemotaxonomic characteristics of the genus Spirosoma, with the presence of menaquinone 7 as the respiratory quinone; the major fatty acids were summed feature 3 (composed of C16: 1ω6c/ω7c), C16: 1ω5c and iso-C15: 0. The DNA G+C content of strain JBM2-3T was 47.4 mol%. The polar lipid profile contained major amounts of phosphatidylethanolamine and aminophospholipids. On the basis of its phenotypic and genotypic properties, and phylogenetic distinctiveness, strain JBM2-3T should be classified as a representative of a novel species in the genus Spirosoma, for which the name Spirosoma swuense sp. nov. is proposed. The type strain is JBM2-3T (=KCTC 52176T=JCM 31298T).

Deinococcus rubellus sp. nov., bacteria isolated from the muscle of antarctic fish

Two new bacterial strains designated as Ant6^T and Ant18 were isolated from the muscle of a fish which had been caught in the Antarctic Ocean. Both strains are Gram-stain-positive, catalase positive, oxidase negative, aerobic, and coccoid bacteria. Phylogenetic analysis based on the 16S rRNA gene sequences of strains Ant6^T and Ant18 revealed that the strains Ant6^T and Ant18 belong to the genus Deinococcus in the family Deinococcaceae in the class Deinococci. The highest degrees of sequence similarities of strains Ant6^T and Ant18 were found with Deinococcus alpinitundrae LMG 24283^T by 96.4% and 96.8%, respectively. Strain Ant6^T exhibited a high level of DNA- DNA hybridization values with strain Ant18 (82 ± 0.6%). Chemotaxonomic data revealed that the predominant fatty acids were C_{17: 0} cyclo, 16:0, and feature 3 (C_16:1 ω6c/ω7c) for both strains. A complex polar lipid profile consisted of major amounts of unknown phosphoglycolipids (PGL) and unknown aminophospholipid (APL). Based on the phylogenetic, phenotypic, and chemotaxonomic data, strains Ant6^T (=KEMB 9004-169^T =JCM 31434^T) and Ant18 (=KEMB 9004-170) should be classified as a new species, for which the name Deinococcus rubellus sp. nov. is proposed.

Mechanisms of Stress Resistance and Gene Regulation in the Radioresistant Bacterium Deinococcus radiodurans

The bacterium Deinococcus radiodurans reveals extraordinary resistance to ionizing radiation, oxidative stress, desiccation, and other damaging conditions. In this review, we consider the main molecular mechanisms underlying such resistance, including the action of specific DNA repair and antioxidation systems, and transcription regulation during the anti-stress response.

Deinococcus seoulensis sp. nov., a bacterium isolated from sediment at Han River in Seoul, Republic of Korea

Strain 16F1E(T) was isolated from a 3-kGy-irradiated sediment sample collected at Han River in Seoul, Republic of Korea. Cells of this strain were observed to be Gram-positive, pililike structure, and short rod shape, and colonies were red in color. The strain showed the highest degree of 16S rRNA gene sequence similarity to Deinococcus aquaticus PB314(T) (98.8%), Deinococcus depolymerans TDMA-24(T) (98.1%), Deinococcus caeni Ho-08(T) (98.0%), and Deinococcus grandis DSM 3963(T) (97.0%). 16S rRNA gene sequence analysis identified this strain as a member of the genus Deinococcus (Family: Deinococcaceae). The genomic DNA G+C content of strain 16F1ET was 66.9 mol%. The low levels of DNA-DNA hybridization (< 56.2%) with the species mentioned above identified strain 16F1E(T) as a novel Deinococcus species. Its oxidase and catalase activities as well as the production of acid from glucose were positive. Growth of the strain was observed at 10-37°C (optimum: 20-30°C) and pH 4-10 (optimum: pH 7-8). The cells tolerated less than 5% NaCl and had low resistance to gamma radiation (D10 < 4 kGy). Strain 16F1ET possessed the following chemotaxonomic characteristics: C16:0, C15:1 ω6c, and C16:1 ω7c as the major fatty acids; phosphoglycolipid as the predominant polar lipid; and menaquinone-8 as the predominant respiratory isoprenoid quinone. Based on the polyphasic evidence, as well as the phylogenetic, genotypic, phenotypic, and chemotaxonomic characterization results, strain 16F1E(T) (=KCTC 33793(T) =JCM 31404(T)) is proposed to represent the type strain of a novel species, Deinococcus seoulensis sp. nov.

Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil

A Gram-negative, yellow-pigmented, long-rod shaped bacterial strain designated DY10(T) was isolated from a soil sample collected at Mt. Deogyusan, Jeonbuk province, South Korea. Optimum growth observed at 30°C and pH 7. No growth was observed above 1% (w/v) NaCl. Comparative 16S rRNA gene sequence analysis showed that strain DY10(T) belonged to the genus Spirosoma and was distantly related to Spirosoma arcticum R2-35(T) (91.0%), Spirosoma lingual DSM 74(T) (90.8%), Spirosoma endophyticum EX36(T) (90.7%), Spirosoma panaciterrae DSM 21099(T) (90.5%), Spirosoma rigui WPCB118(T) (90.2%), Spirosoma spitsbergense DSM 19989(T) (89.8%), Spirosoma luteum DSM 19990(T) (89.6%), Spirosoma oryzae RHs22(T) (89.6%), and Spirosoma radiotolerans DG5A(T) (89.1%). Strain DY10(T) showed resistance to gamma and ultraviolet radiation. The chemotaxonomic characteristics of strain DY10(T) were consistent with those of the genus Spirosoma, with the quinone system with MK-7 as the predominant menaquinone, iso-C15:0, C16:1 ω5c, and summed feature3 (C16:1 ω7c/C16:1 ω6c), and phosphatidylethanolamine as the major polar lipid. The G+C content of the genomic DNA was 53.0 mol%. Differential phenotypic properties with the closely related type strains clearly distinguished strain DY10(T) from previously described members of the genus Spirosoma and represents a novel species in this genus, for which the name Spirosoma montaniterrae sp. nov. is proposed. The type strain is DY10(T) (=KCTC 23999(T) =KEMB 9004-162(T) =JCM 18492(T)).

DNA repair in hyperthermophilic and hyperradioresistant microorganisms

The genome of a living cell is continuously under attack by exogenous and endogenous genotoxins. Especially, life at high temperature inflicts additional stress on genomic DNA, and very high rates of potentially mutagenic DNA lesions, including deamination, depurination, and oxidation, are expected. However, the spontaneous mutation rates in hyperthermophiles are similar to that in Escherichia coli, and it is interesting to determine how the hyperthermophiles preserve their genomes under such grueling environmental conditions. In addition, organisms with extremely radioresistant phenotypes are targets for investigating special DNA repair mechanisms in extreme environments. Multiple DNA repair mechanisms have evolved in all organisms to ensure genomic stability, by preventing impediments that result in genome destabilizing lesions.

Expression and mutational analysis of DinB-like protein DR0053 in Deinococcus radiodurans

In order to understand the mechanism governing radiation resistance in Deinococcus radiodurans, current efforts are aimed at identifying potential candidates from a large repertoire of unique Deinococcal genes and protein families. DR0053 belongs to the DinB/YfiT protein family, which is an over-represented protein family in D. radiodurans. We observed that dr0053 transcript levels were highly induced in response to gamma radiation (γ-radiation) and mitomycin C (MMC) exposure depending on PprI, RecA and the DrtR/S two-component signal transduction system. Protein profiles demonstrated that DR0053 is a highly induced protein in cultures exposed to 10 kGy γ-radiation. We were able to determine the transcriptional start site of dr0053, which was induced upon irradiation, and to assign the 133-bp promoter region of dr0053 as essential for radiation responsiveness through primer extension and promoter deletion analyses. A dr0053 mutant strain displayed sensitivity to γ-radiation and MMC exposure, but not hydrogen peroxide, suggesting that DR0053 helps cells recover from DNA damage. Bioinformatic analyses revealed that DR0053 is similar to the Bacillus subtilis protein YjoA, which is a substrate of bacterial protein-tyrosine kinases. Taken together, the DNA damage-inducible (din) gene dr0053 may be regulated at the transcriptional and post-translational levels.

Spirosoma radiotolerans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil

A Gram-negative, short-rod-shaped bacterial strain with gliding motility, designated as DG5A(T), was isolated from a rice field soil in South Korea. Phylogenic analysis using 16S rRNA gene sequence of the new isolate showed that strain DG5A(T) belong to the genus Spirosoma in the family Spirosomaceae, and the highest sequence similarities were 95.5 % with Spirosoma linguale DSM 74(T), 93.4 % with Spirosoma rigui WPCB118(T), 92.8 % with Spirosoma luteum SPM-10(T), 92.7 % with Spirosoma spitsbergense SPM-9(T), and 91.9 % with Spirosoma panaciterrae Gsoil 1519(T). Strain DG5A(T) revealed resistance to gamma and UV radiation. Chemotaxonomic data showed that the most abundant fatty acids were summed feature C(16:1) ω7c/C(16:1) ω6c (36.90 %), C(16:1) ω5c (29.55 %), and iso-C(15:0) (14.78 %), and the major polar lipid was phosphatidylethanolamine (PE). The DNA G+C content of strain DG5A(T) was 49.1 mol%. Together, the phenotypic, phylogenetic, and chemotaxonomic data supported that strain DG5A(T) presents a novel species of the genus Spirosoma, for which the name Spirosoma radiotolerans sp. nov., is proposed. The type strain is DG5A(T) (=KCTC 32455(T) = JCM19447(T)).