Deinococcus saudiensis sp. nov., isolated from desert

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-resistant bacteria in desiccated soil and their potentiality in applied sciences

A rich diversity of radiation-resistant (Rr) and desiccation-resistant (Dr) bacteria has been found in arid habitats of the world. Evidence from scientific research has linked their origin to reactive oxygen species (ROS) intermediates. Rr and Dr. bacteria of arid regions have the potential to regulate imbalance radicals and evade a higher dose of radiation and oxidation than bacterial species of non-arid regions. Photochemical-activated ROS in Rr bacteria is run through photo-induction of electron transfer. A hypothetical model of the biogeochemical cycle based on solar radiation and desiccation. These selective stresses generate oxidative radicals for a short span with strong reactivity and toxic effects. Desert-inhibiting Rr bacteria efficiently evade ROS toxicity with an evolved antioxidant system and other defensive pathways. The imbalanced radicals in physiological disorders, cancer, and lung diseases could be neutralized by a self-sustaining evolved Rr bacteria antioxidant system. The direct link of evolved antioxidant system with intermediate ROS and indirect influence of radiation and desiccation provide useful insight into richness, ecological diversity, and origin of Rr bacteria capabilities. The distinguishing features of Rr bacteria in deserts present a fertile research area with promising applications in the pharmaceutical industry, genetic engineering, biological therapy, biological transformation, bioremediation, industrial biotechnology, and astrobiology.

Deinococcus arenicola sp. nov., a novel radiation-resistant bacterium isolated from sandy soil in Antarctica

A Gram-stain-positive, aerobic, non-mobile and spherical strain, designated ZS9-10T, belonging to the genus Deinococcus was isolated from soil sampled at the Chinese Zhong Shan Station, Antarctica. Growth was observed in the presence of 0-4 % (w/v) NaCl, at pH 7.0-8.0 and at 4-25 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZS9-10T formed a lineage in the genus Deinococcus. It exhibited highest sequence similarity (97.4 %) to Deinococcus marmoris DSM 12784T. The major phospholipids of ZS9-10T were unidentified phosphoglycolipid, unidentified glycolipids and unidentified lipids. The major fatty acids were summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C16 : 0 and C16 : 1  ω7c. MK-8 was the predominant respiratory quinone. The digital DNA-DNA hybridization and average nucleotide identity values between strain ZS9-10T and its close relative D. marmoris DSM 12784T were 27.4 and 83.9 %, respectively. Based on phenotypic, phylogenetic and genotypic data, a novel species, named Deinococcus arenicola sp. nov., is proposed. The type strain iis ZS9-10T (=CCTCC AB 2019392T=KCTC43192T).

Genome-based reclassification of Deinococcus saudiensis Hussain et al. 2016 as a later heterotypic synonym of Deinococcus soli Cha et al. 2014

Deinococcus saudiensis YIM F302T was compared with Deinococcus soli N5T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of D. saudiensis YIM F302T showed high similarity (99.9 %) to that of D. soli N5T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Deinococcus. A draft genomic comparison between the two strains revealed average nucleotide identity values of 96.8-97.9 % and a digital DNA-DNA hybridization estimate of 80.7±1.9 %, strongly indicating that the two strains represented a single species. Based on the combined phylogenetic, genomic and phenotypic characterization presented here, we propose D. saudiensis as a later heterotypic synonym of D. soli N5T.

Deinococcus aestuarii sp. nov. and Deinococcus aquaedulcis sp. nov., two novel resistant bacteria isolated from pearl river estuary

Two novel species of the genus Deinococcus, designated SYSU M49105^T and SYSU M42101^T, were isolated from freshwater samples of the Pearl River estuary in Guangdong, China. Phylogenetic analysis using 16S rRNA gene sequence indicated that strains SYSU M49105^T and SYSU M42101^T showed the highest sequence similarities to Deinococcus aetherius JCM 11751 ^T (93.6%) and Deinococcus multiflagellatus NBRC 112888 ^T (97.3%), respectively. Cells of both strains were Gram-staining positive, aerobic, coccus-shaped, oxidase-negative and non-motile. The cell wall contained meso-diaminopimelic acid as their diagnostic diamino acid. MK-8 was the predominant respiratory quinone for both strains. The polar lipid profile of SYSU M49105^T contained two unidentified phosphoglycolipids, nine unidentified glycolipids, and five unidentified polar lipids. SYSU M42101^T had one unidentified phosphoglycolipid, nine unidentified glycolipids, one unidentified aminophospholipid and four unidentified polar lipids. The major fatty acids of strains SYSU M49105^T and SYSU M42101^T were summed feature 3 (C_16:1 ω7c and/ or C_16:1 ω6c) and C_16:0. The G + C contents of the novel isolates based on genomic DNAs were 69.6% and 67.4%, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strains SYSU M49105^T and SYSU M42101^T should be considered to represent two novel species in the genus Deinococcus, for which the names Deinococcus aestuarii sp. nov. and Deinococcus aquaedulcis sp. nov. were proposed with the type strains SYSU M49105^T (= KCTC 43258 ^T = CGMCC 1.18609 ^T) and SYSU M42101^T (= KCTC 43257 ^T = CGMCC 1.18614 ^T), respectively.

Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions

In the past ten years, microbiome studies have shown tremendous potentiality for implementation of understanding microbiome structures and functions of various biomes and application of this knowledge for human betterment. Saudi Arabia is full of geographical, ecological, ethnical, and industrial diversities and scientific capacities. Therefore, there is a great potential in Saudi Arabia to conduct and implement microbiome-based research and applications. However, there is no review available on where Saudi Arabia stands with respect to global microbiome research trends. This review highlights the metagenome-assisted microbiome research from Saudi Arabia compared to the global focuses on microbiome research. Further, it also highlights the gaps and areas that should be focused on by Saudi microbiome researchers and the possible initiatives to be taken by Saudi government and universities. This literature review shows that the global trends of microbiome research cover a broad spectrum of human and animal health conditions and diseases, environmental and antimicrobial resistance surveillance, surveillance of food and food processing, production of novel industrial enzymes and bioactive pharmaceutical products, and space applications. However, Saudi microbiome studies are mostly confined to very few aspects of health (human and animal) and environment/ecology in last ten years, without much application. Therefore, Saudi Arabia should focus more on applied microbiome research through government, academic, and industry initiatives and global cooperation to match the global trends.

Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans

Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59^T and D. radiopugnans ATCC 19172^T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensis DY59^T and D. radiopugnans ATCC 19172^T. Interestingly, D. swuensis DY59^T and D. radiopugnans ATCC 19172^T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA-DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59^T and D. radiopugnans ATCC 19172^T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans.

From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes

Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.

Deinococcus terrestris sp. nov., a gamma ray- and ultraviolet-resistant bacterium isolated from soil

Strain SDU3-2^T was isolated from a soil sample collected in Shandong Province, PR China. Cells of SDU3-2^T were spherical, Gram-stain-positive, aerobic and non-motile. Cellular growth of the strain occurred at 25-45 °C, pH 5.5-8.5 and with 0-1.5 % (w/v) of NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SDU3-2^T was closest to the type strain Deinococcus murrayi ALT-1b^T with a similarity of 95.2 %. The draft genome was 3.49 Mbp long with 69.2 mol% G+C content. Strain SDU3-2^T exhibited high resistance to gamma radiation (D₁₀ >12 kGy) and UV (D₁₀ >900 J m^-2). The strain encoded many genes for resistance to radiation and oxidative stress, which were highly conserved with other Deinococcus species, but possessed interspecific properties. The major fatty acids of SDU3-2^T cells were C_15 : 1  ω6c, C_16 : 1  ω7c/C_16 : 1  ω6c, and C_17 : 1  ω8c, the major menaquinone was menaquinone-8, and the major polar lipids were an unidentified phosphoglycolipid, four unidentified glycolipids and an unidentified phospholipid. The average nucleotide identity and DNA-DNA hybridization results further indicated that strain SDU3-2^T represents a new species in the genus Deinococcus, for which the name Deinococcus terrestris sp. nov. is proposed. The type strain is SDU3-2^T (=CGMCC 1.17147^T=KCTC 43098^T).

Draft genome sequence of Deinococcus sp. KR-1, a potential strain for palladium-leaching

Strain KR-1 was isolated from pond water collected in Japan. Because this strain was capable of adsorbing palladium particles in sterilized water, strain KR-1 will be a useful biocatalyst for palladium-leaching from metal waste. Here we present a draft genome sequence of Deinococcus sp. KR-1, which consists of a total of 7 contigs containing 4,556,772 bp with a GC content of 70.0% and comprises 4,450 predicted coding sequences. Based on the 16S rRNA gene sequence analysis, strain KR-1 was identified as Deinococcus sp. KR-1.

Review of microbial resistance to chronic ionizing radiation exposure under environmental conditions

Ionizing radiation (IR) produces multiple types of damage to nucleic acids, proteins and other crucial cellular components. Nevertheless, various microorganisms from phylogenetically distant taxa (bacteria, archaea, fungi) can resist IR levels many orders of magnitude above natural background. This intriguing phenomenon of radioresistance probably arose independently many times throughout evolution as a byproduct of selective pressures from other stresses (e.g. desiccation, UV radiation, chemical oxidants). Most of the literature on microbial radioresistance is based on acute γ-irradiation experiments performed in the laboratory, typically involving pure cultures grown under near-optimal conditions. There is much less information about the upper limits of radioresistance in the field, such as in radioactively-contaminated areas, where several radiation types (e.g. α and β, as well as γ) and other stressors (e.g. non-optimal temperature and nutrient levels, toxic chemicals, interspecific competition) act over multiple generations. Here we discuss several examples of radioresistant microbes isolated from extremely radioactive locations (e.g. Chernobyl and Mayak nuclear plant sites) and estimate the radiation dose rates they were able to tolerate. Some of these organisms (e.g. the fungus Cladosporium cladosporioides, the cyanobacterium Geitlerinema amphibium) are widely-distributed and colonize a variety of habitats. These examples suggest that resistance to chronic IR and chemical contamination is not limited to rare specialized strains from extreme environments, but can occur among common microbial taxa, perhaps due to overlap between mechanisms of resistance to IR and other stressors.

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 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).