Genomic Insights into the Radiation-Resistant Capability of Sphingomonas qomolangmaensis S5-59T and Sphingomonas glaciei S8-45T, Two Novel Bacteria from the North Slope of Mount Everest

Mount Everest provides natural advantages to finding radiation-resistant extremophiles that are functionally mechanistic and possess commercial significance. (1) Background: Two bacterial strains, designated S5-59T and S8-45T, were isolated from moraine samples collected from the north slope of Mount Everest at altitudes of 5700m and 5100m above sea level. (2) Methods: The present study investigated the polyphasic features and genomic characteristics of S5-59^T and S8-45^T. (3) Results: The major fatty acids and the predominant respiratory menaquinone of S5-59^T and S8-45^T were summed as feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA sequences and average nucleotide identity values among these two strains and their reference type strains were below the species demarcation thresholds of 98.65% and 95%. Strains S5-59^T and S8-45^T harbored great radiation resistance. The genomic analyses showed that DNA damage repair genes, such as mutL, mutS, radA, radC, recF, recN, etc., were present in the S5-59^T and S8-45^T strains. Additionally, strain S5-59^T possessed more genes related to DNA protection proteins. The pan-genome analysis and horizontal gene transfers revealed that strains of Sphingomonas had a consistently homologous genetic evolutionary radiation resistance. Moreover, enzymatic antioxidative proteins also served critical roles in converting ROS into harmless molecules that resulted in resistance to radiation. Further, pigments and carotenoids such as zeaxanthin and alkylresorcinols of the non-enzymatic antioxidative system were also predicted to protect them from radiation. (4) Conclusions: Type strains S5-59^T (=JCM 35564T =GDMCC 1.3193T) and S8-45^T (=JCM 34749T =GDMCC 1.2715T) represent two novel species of the genus Sphingomonas with the proposed name Sphingomonas qomolangmaensis sp. nov. and Sphingomonas glaciei sp. nov. The type strains, S5-59^T and S8-45^T, were assessed in a deeply genomic study of their radiation-resistant mechanisms and this thus resulted in a further understanding of their greater potential application for the development of anti-radiation protective drugs.

Community Ecology of Deinococcus in Irradiated Soil

Deinococcus is a genus of soil bacteria known for radiation resistance. However, the effects of radiation exposure on its community structure are unknown. We exposed soil to three levels of gamma radiation, 0.1 kGy/h (low), 1 kGy/h (medium), and 3 kGy/h (high), once a week for 6 weeks and then extracted soil DNA for 16S rRNA amplicon sequencing. We found the following: (1) Increasing radiation dose produced a major increase in relative abundance of Deinococcus, reaching ~ 80% of reads at the highest doses. Differing abundances of the various Deinococcus species in relation to exposure levels indicate distinct "radiation niches." At 3 kGy/h, a single OTU identified as D. ficus overwhelmingly dominated the mesocosms. (2) Corresponding published genome data show that the dominant species at 3 kGy/h, D. ficus, has a larger and more complex genome than other Deinococcus species with a greater proportion of genes related to DNA and nucleotide metabolism, cell wall, membrane, and envelope biogenesis as well as more cell cycle control, cell division, and chromosome partitioning-related genes. Deinococcus ficus also has a higher guanine-cytosine ratio than most other Deinococcus. These features may be linked to genome stability and may explain its greater abundance in this apparently competitive system, under high-radiation exposures. (3) Genomic analysis suggests that Deinococcus, including D. ficus, are capable of utilizing diverse carbon sources derived from both microbial cells killed by the radiation (including C5-C12-containing compounds, like arabinose, lactose, N-acetyl-D-glucosamine) and plant-derived organic matter in the soil (e.g., cellulose and hemicellulose). (4) Overall, based on its metagenome, even the most highly irradiated (3 kGy/h) soil possesses a wide range of the activities necessary for a functional soil system. Future studies may consider the resilience and sustainability of such soils in a high-radiation environment.

Deinococcus psychrotolerans sp. nov., isolated from soil on the South Shetland Islands, Antarctica

A Gram-stain-negative, non-motile, strictly aerobic, coccus-shaped bacterium, designated S14-83^T, was isolated from a soil sample collected from the South Shetland Islands of Antarctica. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain is a novel member of the genus Deinococcus, with Deinococcus alpinitundrae as its closest relative (96.1 % similarity). The DNA G+C content of the strain was 61.1 mol% and the major respiratory quinone was MK-8. Major cellular fatty acids were summed feature 3 (C_16 : 1ω7c/C_16 : 1ω6c) and C_16 : 0. As well as containing glycophospholipid, aminophospholipids and glycolipid as major polar lipids, there were also some unknown polar lipids. The diagnostic diamino acid in the cell-wall peptidoglycan was ornithine, corroborating the assignment of the strain to the genus Deinococcus. Strain S14-83^T was shown to be extremely resistant to gamma radiation (>10 kGy) and UV light (460 Jm^-2). On the basis of phylogenetic, chemotaxonomic and phenotypic data presented here, strain S14-83^T represents a novel species of the genus Deinococcus, for which the name Deinococcus psychrotolerans sp. nov. is proposed. The type strain is S14-83^T (=CCTCC AB 2015449^T= DSM 105285 ^T).

Specific Members of the Gut Microbiota are Reliable Biomarkers of Irradiation Intensity and Lethality in Large Animal Models of Human Health

The development of effective biomarkers for detecting the magnitude of radiation exposure and resiliency of host response is crucial to identifying appropriate treatment strategies after radiation exposure. We hypothesized that the gastrointestinal resident bacteria would demonstrate predictable, dose-dependent changes after radiation exposure across two large animal models of acute radiation syndrome. Here, Göttingen minipigs (GMP) (n = 50) and rhesus macaques (n = 48) were exposed to five dose levels (resulting in mortality rates of 33-100% and 25-68.7%, respectively). Fecal samples taken prior to and after irradiation (day 0 for GMP; day 0, 3 and 14 for macaques) were used for 16S rRNA gene sequence amplicon high-throughput sequencing. Baseline gut microbiota profiles were dissimilar between GMP and macaques, however, radiation appeared to have similar effect at the phylum level, resulting in Bacteroidetes decrease and Firmicutes increase in both models. The abundance of the main Bacteroidetes genus ( Bacteroides for GMP, Prevotella for macaques) was profoundly decreased by irradiation. Intracellular symbionts [Elusimicrobia in GMP, Treponema (Spirochaetes) in macaques] consistently increased after irradiation, suggesting their use as potential biomarkers of intestinal injury, and potential negative effect on health. Prevotella, Lactobacillus, Clostridium XIVa, Oscillibacter and Elusimicrobium/ Treponema abundances were found to be very significantly correlated with radiation intensity. Furthermore, Prevotella, Enterorhabdus and Ruminococcus and Enterorhabdus maintenance was strongly associated with survival in GMP, while Prevotella, Oscillibacter and Treponema were strongly associated with survival and Streptococcus with death in macaques. Overall, we found that a wide range of gut bacterial genera known to be abundant in the human gut microbiota are excellent biomarkers of radiation intensity and resilience in animal models, and that detrimental effects can be monitored, and potentially prevented, by targeting selected genera.

Deinococcus irradiatisoli sp. nov., isolated from gamma ray-irradiated soil

Strain 17bor-2^T, a gamma-resistant, pink-to-red-coloured, aerobic, catalase-positive, oxidase-negative and Gram-stain-negative bacterium, was isolated from gamma ray-irradiated soil. The isolate grew aerobically at 18-37 °C (optimum, 28-30 °C), pH 6.0-8.0 (pH 6.5-7.5) and in the presence of 0-1 % (w/v) NaCl (0 % NaCl). Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain 17bor-2^T belonged to the genus Deinococcus with a highest sequence similarity of 96.4 % to Deinococcus alpinitundrae ME-04-04-52^T. The major fatty acids of the strain were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and cyclo C17 : 0. The only respiratory quinone was MK-8. The major polar lipids of the strain were phosphoglycolipid, aminophospholipid and an unknown glycolipid. The DNA G+C content of strain 17bor-2^T was 62.8 mol%. On the basis of its phenotypic, genotypic and chemotaxonomic characteristics, strain 17bor-2^T should be classified as a novel species in the genus Deinococcus, for which the name Deinococcusirradiatisoli sp. nov. is proposed. The type strain is 17bor-2^T (=KCTC 33907^T=NBRC 113037^T).

Deinococcus lacus sp. nov., a gamma radiation-resistant bacterium isolated from an artificial freshwater pond

A Gram-stain-negative, pink-coloured, non-motile and gamma radiation-resistant bacterium, designated strain IMCC1711^T, was isolated from a freshwater sample collected from an artificial pond (Inkyong Pond). The 16S rRNA gene sequence analysis showed that strain IMCC1711^T was most closely related to Deinococcus piscis 3ax^T (94.2 %) and formed a robust phylogenetic clade with other species of the genus Deinococcus. Optimal growth of strain MCC1711^T was observed at 25 °C and pH 7.0 without NaCl. Strain IMCC1711^T exhibited high resistance to gamma radiation. The DNA G+C content of strain IMCC1711^T was 59.1 mol% and MK-8 was the predominant isoprenoid quinone. Major fatty acid constituents of the strain were C17 : 1ω8c, C16 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C15 : 1ω6c. The major polar lipids constituted phosphatidylethanolamine, one unidentified phosphoglycolipid and two unidentified glycolipids. On the basis of taxonomic data obtained in this study, it was concluded that strain IMCC1711^T represented a novel species of the genus Deinococcus, for which the name Deinococcus lacus sp. nov. is proposed. The type strain of Deinococcus lacus is IMCC1711^T (KCTC 52494^T=KACC 18979^T=NBRC 112440^T).