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Moya, Gabriela, Yan, Zheng-Fei, Chu, Dong-Hun, Won, KyungHwa, Yang, Jung-Eun, Wang, Qi-Jun, Kook, Moo-Chang, Yi, Tae-Hoo (2018): Deinococcus hibisci sp. nov., isolated from rhizosphere of Hibiscus syriacus L. (mugunghwa flower). International Journal of Systematic and Evolutionary Microbiology 68 (1): 28-34, DOI: 10.1099/ijsem.0.002405, URL: http://dx.doi.org/10.1099/ijsem.0.002405

Kim, Dong-Uk, Kim, Ju-Young, Cha, Chang-Jun, Kim, Wonyong, Kim, Myung Kyum (2018): A report of unrecorded bacterial species of Korea isolated in 2016, belonging to the family Deinococcaceae and Planctomycetaceae. Journal of Species Research 7 (1): 9-12, DOI: 10.12651/JSR.2018.7.1.009

Description of Deinococcus xinjiangensis 6004 Cells are gram-staining-positive, non-flagellated, and cocci-shaped. Colonies are circular, entire, smooth, raised, and pink colored after 2 days of incubation at 30°C on R2A. Positive for urease and gelatinase activities. Negative for nitrate reduction, indole production, glucose fermentation, arginine dihydrolase, esculin hydrolysis, and β -galactosidase activity. Does not utilize L-arabinose, D-mannitol, N-acetyl-glucosamine, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain 6004 (= NIBR BAC000498565) was isolated from a sediment soil sample, Han River, Korea., Published as part of Kim, Dong-Uk, Kim, Ju-Young, Cha, Chang-Jun, Kim, Wonyong & Kim, Myung Kyum, 2018, A report of unrecorded bacterial species of Korea isolated in 2016, belonging to the family Deinococcaceae and Planctomycetaceae, pp. 9-12 in Journal of Species Research 7 (1) on page 11, DOI: 10.12651/JSR.2018.7.1.009, http://zenodo.org/record/8120429

DESCRIPTION OF DEINOCOCCUS HIBISCI SP. NOV. Deinococcus hibisci (hi.bis′ ci. L. gen. n. hibisci of the plant genus Hibiscus). Cells are Gram-positive cocci, 2.7–1.9×1.3–0.9 µm, strictly aerobic and non-motile. Colonies are smooth, bright, flat, circular, pink-coloured and 0.5–0.8 mm in diameter. Catalase and oxidase activities are positive. Flexirubin-type pigments are not produced. Can grow in TSB at 15–38 Ǫ C, optimum growth occurs from 25–30 Ǫ C. Growth occurs on R2A, TSA and NA agar, grows weakly on LA and MacConkey agar but not on MA. Strain THG-AG1.5 T can grow in TSB at pH 6.0–8.5 (optimum 6.5–7.5) and in the presence of additional 0–1.5 % (w/v) NaCl. Cells are able to hydrolyse Tween 80 and CMC but not L- tyrosine, casein, chitin, starch and DNA. Positive for alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, valine arylamidase, cystine arylamidase, trypsin, a- chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, b - galactosidase, a- glucosidase and b- glucosidase; weakly positive for lipase (C14); negative for a- galactosidase, b- glucuronidase, N -acetyl-b- glucosaminidase, a- mannosidase and a- fucosidase. Positive for reduction of nitrate to nitrites, assimilation of PNPG, arginine dihydrolase, D- glucose, L- arabinose, D- mannose, D- mannitol, maltose, and hydrolysis of urea, aesculin and gelatin; weakly positive for trisodium citrate; negative for indole production, glucose acidification, assimilation of N- acetyl-glucosamine, gluconate, caprate, adipate, malate and phenyl-acetate. Positive for utilization of salicin, melibiose, D- sorbitol, L- histidine, 2-ketogluconate, 3- hydroxy-butyrate, L- proline, sucrose, L- alanine and glycogen; weakly positive for valerate, D- ribose, itaconate, sodium malonate, sodium acetate and D,L- lactate; negative for L- fucose, propionate, 4-hydroxy-benzoate, L- rhamnose, inositol, suberate, 5-ketogluconate, 3-hydroxy-benzoate and L- serine. Weakly positive for assimilation of glycerol, D- fructose and trehalose; negative for erythritol, D- arabinose, D- xylose, L- xylose, D- adonitol, methyl b- D- xylopyranoside, D- galactose, L- sorbose, dulcitol, methyl a- D- mannopyranoside, methyl a- D- glucopyranoside, N -acetyl-D- glucosamine, amygdalin, arbutin, cellobiose, lactose, inulin, melezitose, raffinose, xylitol, gentiobiose, D- turanose, D- lyxose, D- tagatose, D- fucose, D- arabitol and L- arabitol. The predominant respiratory quinone is menaquinone-8 (MK-8); and iso-C 15: 0, C 15: 1 Ɯ 6 c, C 16: 0, iso-C 17: 0, C 17: 0, C 18: 0 and summed feature 3 (C 16: 1 Ɯ 7 c and/or C 16: 1 Ɯ 6 c) are the major components of the cellular fatty acids (Ȅ7 %). The major polar lipids are a phosphoglycolipid, six unidentified glycolipids and an unidentified aminophospholipid. The polyamine is spermidine. The novel strain exhibits tolerance to UV irradiation (>1500 J m ‒2) and to gamma radiation (>12 kGy). The G+C content of genomic DNA of strain THG-AG1.5 T is 74.8 mol%. The peptidoglycan amino acids are alanine, valine, glutamic acid, glycine, ornithine, lysine and aspartic acid. The whole-cell-wall sugars are ribose, mannose and glucose. Strain THG-AG1.5 T (=KACC 18850 T =CCTCC AB 2016078 T) was isolated from a rhizosphere soil sample of Hibiscus syriacus L. (Mugunghwa flower), collected in Kyung Hee University, Yongin, Gyeonggi, Republic of Korea.

International audience; Oxygen reducing biocathodes were formed from sludge under constant polarization at − 0.2 and + 0.4 V/SCE. Under chronoamperometry at pH 10.3 ± 0.3, current densities of 0.21 ± 0.03 and 0.12 ± 0.01 A m− 2 were displayed at − 0.2 V/SCE by the biocathodes formed at − 0.2 and 0.4 V/SCE, respectively. Voltammetry revealed similar general characteristics for all biocathodes and higher diffusion-limited current densities (0.84 ± 0.26 A m− 2) than chronoamperometry. Up to 3.7 A m− 2 was reached under air bubbling. A theoretical model was proposed to show the consistency of the chronoamperometric and voltammetric data. The biocathodes formed at − 0.2 V/ECS that gave the highest electrochemical performance showed a homogeneous selection of Deinococcus–Thermus and Gemmatimonadetes, while the biocathodes formed at 0.4 V/SCE were enriched in different bacteria. The biocathode that led to the worst electrochemical characteristics, while formed at − 0.2 V/SCE, showed the largest bacterial diversity. The biocathode performance was consequently related to the enrichment in specific microbial phyla. Moreover, the strong presence of bacteria parented to Deinococci may also have some interest in biotechnology.

Microbiology at the high altitude atmosphere is imp or t ant for asse ssing the chanc e s and limits of microbial transfer from the earth to extraterrestrial bodies. Among the microorganisms isolated from the high- atmospheric samples, spore formers and vegetative Deinococci were highly resistant against harsh environment at high altitude. From limited knowledge available to date, it is suggested that terrestrial microorganisms may have had chances to be ejected and transferred to outer space. Survival of these organisms during their space travel and proliferation on other planets might be also feasible. Directed Panspermia from Earth to extraterrestrial bodies is discussed on the basis of findings reported in literatures. ©2009 Jpn. Soc. Biol. Sci. Space; Article ID: 092303017

International audience; Here we analysed the bacterial diversity of six oxygen reducing biocathodes formed from aerated sludges at different voltages. Pyrosequencing results show unexpectedly high bacterial diversity in cathodic biofilms. Some of the most electroactive bacterial communities are dominated by a new lineage belonging to Deinococci.

Meiothermus silvanus (Tenreiro et al. 1995) Nobre et al. 1996 belongs to a thermophilic genus whose members share relatively low degrees of 16S rRNA gene sequence similarity. Meiothermus constitutes an evolutionary lineage separate from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. M. silvanus is of special interest as it causes colored biofilms in the paper making industry and may thus be of economic importance as a biofouler. This is the second completed genome sequence of a member of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,721,669 bp long genome with its 3,667 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Ther.ma' les. M.L. masc. n. Thermus type genus of the order, -ales ending to denote an order; M.L. fem. pl. n. Thermales the order of Thermus. “Deinococcus-Thermus” / Deinococci / Thermales Keywords: Thermales ord. nov; Thermus; Deinococci class. nov.

Dei.no.coc' ci. M.L. fem. pl. n. Deinococcales type order of the class; dropping the ending to denote a class; M.L. fem. pl. n. Deinococci the class of Deinococcales. “Deinococcus-Thermus” / Deinococci Keywords: Deinococci class. nov.; Deinococcales; Deinococcus-Thermus

Ther.ma' ce.ae. M.L. masc. n. Thermus type genus of the family; −aceae ending to denote a family; M.L. fem. pl. n. Thermaceae the Thermus family. “Deinococcus-Thermus” / Deinococci / Thermales / Thermaceae Keywords: Thermaceae fam. nov.; Thermus; Deinococci class. nov.; Thermales ord. nov

Meiothermus ruber (Loginova et al. 1984) Nobre et al. 1996 is the type species of the genus Meiothermus. This thermophilic genus is of special interest, as its members share relatively low degrees of 16S rRNA gene sequence similarity and constitute a separate evolutionary lineage from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. The temperature related split is in accordance with the chemotaxonomic feature of the polar lipids. M. ruber is a representative of the low-temperature group. This is the first completed genome sequence of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,097,457 bp long genome with its 3,052 protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Thermus aquaticus sp. n. Definition as for genus. The specific epithet was derived from the Latin noun aqua, meaning water. Thus, T. aquaticus is an aquatic thermophile. The type strain is YT-1. It is being deposited in the American Type Culture Collection as ATCC 25104. Also being deposited in this collection are strains Y-VII-51B as ATCC 25105 and Y-IV-69-2 as ATCC 25106. DISCUSSION For many years, microbiologists have enriched for thermophilic bacteria by incubation at 55 C. It is quite clear, however, that thermophilic bacteria do not all grow optimally at 55 C; they represent a continuum of organisms from those with optima near the mesophilic range to those with optima of 70 C or above (2, 4, 5). At 55 C, T. aquaticus grows slowly and hence is probably unable to compete with the sporeforming thermophiles such as B. stearothermophilus. This could explain why it has not been seen in the usual thermophilic enrichments. At 70 to 75 C, Thermus has a selective advantage and can be easily isolated. It is important to emphasize that the media for Thermus enrichments must be fairly dilute in organic constituents, since the organism is inhibited by tryptone and yeast extract at a concentration of approximately 1 %. The high content of organic constituents characteristic of most media used for isolation of thermophiles may also explain why Thermus has not been seen before. The enrichment conditions prescribed here for Thermus are sufficiently selective that the isolation of new strains is extremely easy. We do not imply that all yellow-pigmented organisms isolated by enrichment with our method will be members of a single species. Detailed study of our strains may reveal differences sufficient to warrant creation of other species or genera. For the moment, however, it seems preferable to classify these organisms in a single species. The ecological relationships of Thermus need further work. Yellow- and orange-pigmented filamentous organisms which resemble Thermus morphologically are seen in large numbers in most mildly alkaline hot springs. In the temperature range of 50 to 73 C, these filamentous forms produce extensive gelatinous mats within which the unicellular blue-green alga Synechococcus is embedded (T. D. Brock, Phycologia, in press). We can routinely isolate Thermus from these mats but have not as yet shown that our isolates represent the predominant filamentous organism of the mats, although the physiological and morphological properties of Thermus are in agreement with those of the predominant organisms of the mats. At temperatures above 73 C, where blue-green algae do not grow, masses of filamentous bacteria are frequently seen (2; T. D. Brock, Symp. Soc. Gen. Microbiol. 19th, in press). Spheroplast-like structures similar to those formed by Thermus are often seen in these naturally growing filamentous bacteria (T. D. Brock, Symp. Soc. Gen. Microbiol. 19th, in press). The ease with which Thermus can be isolated from hot tap water and other thermal sources suggests that the organism might be a good indicator of thermal pollution. The determination of the relationship of Thermus to other bacteria must wait further studies. As a yellow-pigmented, nonmotile, gram-negative rod, the organism might be considered related to Flavobacterium, except that this latter genus is itself poorly defined (M. Mandel, personal communication). Also, the formation of long filaments is a property not found in flavobacteria. If the organism could be shown to glide, it might be considered related to the Flexibacterales (16), since this group comprises mostly yellow-pigmented,gram-negativeorganisms,many of which show a rod-filament dimorphism. However, the DNA base composition is considerably higher than that of the flexibacteria (8), and in fact is quite similar to that of the fruiting myxobacteria. In this respect the sensitivity of T. aquaticus to actinomycin D is noteworthy. Martin Dworkin has recently informed us that gliding bacteria are considerably more sensitive to actinomycin D than are other gram-negative bacteria. Since T. aquaticus shows a sensitivity to actinomycin D as great or greater than the gliding bacteria, this is anotherfeature which prompts a further study of the relationship of T. aquaticus to the gliding bacteria. One suggestion is that members of the species T. aquaticus represent forms which have lost the ability to glide, yet retain structural features which are responsible for actinomycin D sensitivity. Filamentous thermophilic bacteria have been described before in hot springs (9, 12, 13) and have usually been given the name Leptothrix or Chlamydothrix (see also 2). Unfortunately, few of these filamentous forms were cultivated or adequately characterized; hence, the relationship of our isolates to these earlier forms is uncertain. Since our isolates do not form either a sheath or motile swarmer cells, it is clear that they bear little relationship to the Leptothrix-Sphaerotilus group (14). We have not seen sheathed organisms of the Leptothrix-Sphaerotilus group in any of our collections of natural material from hot springs. Further understanding of the taxonomic relationships of Thermus to other bacteria will require a better understanding of the taxonomic relationships of the wide variety of filamentous bacteria from nonthermal environments, most of which have been poorly characterized., Published as part of Brock, Thomas D. & Freeze, Hudson, 1969, Thermus aquaticus gen. n. and sp. n., a Nonsporulating Extreme Thermophile, pp. 289-297 in Journal of Bacteriology 98 (1) on pages 295-297, DOI: 10.1128/jb.98.1.289-297.1969, http://zenodo.org/record/5585059, {"references":["2. Brock, T. D. 1967. Life at high temperatures. Science 158: 1012 - 1019.","4. Brock, T. D., and M. L. Brock. 1968. Relationship between environmental temperature and optimum temperature of bacteria along a hot spring thermal gradient. J. Appl. Bacteriol. 31: 54 - 58.","5. Campbell, L. L., and B. Pace. 1968. Physiology of growth at high temperatures. J. Appl. Bacteriol. 31: 24 - 35.","16. Soriano, S., and R. A. Lewin. 1965. Gliding microbes: some taxonomic reconsiderations. Antonie van Leeuwenhoek J. Microbiol. Serol. 31: 66 - 80.","8. Dworkin, M. 1966. Biology of the myxobacteria. Ann. Rev. Microbiol. 20: 75 - 106.","9. Emoto, Y. 1933. Die Mikroorganismen der Thermen. Botan. Mag. (Tokyo) 47: 268 - 295.","12. Miehe, H. 1907. Die Selbsterhitzung des Heus. Gustav Fischer Verlag, Jena.","13. Morrison, L. E., and F. W. Tanner. 1922. Studies on thermophilic bacteria. I. Aerobic thermophilic bacteria from water. J. Bacteriol. 7: 343 - 366.","14. Mulder, E. G., and W. L. vanVeen. 1963. Investigations on the Sphaerotilus-Leptothrix group. Antonie van Leeuwenhoek J. Microbiol. Serol. 29: 121 - 153."]}

Thermus gen. n. Morphology: Rods and filaments, 0.5 to 0.8,um in diameter. Rods 5 to 10 Am in length, filaments of variable length from 20 to greater than 200,um. Rods occurring singly or in aggregates, the latter either side-to-side or end-to-end (rosette-like). Large spheres 10 to 20 Am in diameter usually formed in old cultures. Gram-negative. Flagella and endospores absent. Gliding motility has not been observed. DNA base composition: 65.4 to 67.4% GC. Colony characteristics: Compact slowly spreading colonies. Yellow to bright orange on 0.1% tryptone plus 0.1% yeast extract plus mineral salts-agar. Liquid culture: Yellow surface pellicle often formed in unshaken liquid cultures. Temperature relations: Optimum, 70 to 72 C, maximum 79 C, minimum around 40 C. Nutrition: No growth factor requirements (one strain tested). Nitrogen sources, amino acids and NH4+. Carbon sources, sugars, and organic acids. Grows best in complex media such as 0.1 to 0.3% tryptone plus yeast extract. Relation to oxygen: Obligately aerobic. Relation to pH: Optimum 7.5 to 7.8. No growth below pH 6 or above 9.5. Inhibitor sensitivity: Inhibited by 10 Mg or less of streptomycin, penicillin, novobiocin, actinomycin D, or chloramphenicol per ml. Inhibited by 100 ug or less of cycloserine, tetracycline, and sodium lauryl sulfate per ml. Inhibited by 500 Mug or less of sodium azide per ml. Inhibited by 2% NaCl. Inhibited by 200 ug or less of oxgall per ml. Source: Hot springs, hot tap water. The name given to this organism is derived from the Greek noun, thermos, meaning hot. One species., Published as part of Brock, Thomas D. & Freeze, Hudson, 1969, Thermus aquaticus gen. n. and sp. n., a Nonsporulating Extreme Thermophile, pp. 289-297 in Journal of Bacteriology 98 (1) on page 295, DOI: 10.1128/jb.98.1.289-297.1969, http://zenodo.org/record/5585059