Arthrobacter dokdonellae sp. nov., isolated from a plant of the genus Campanula.

A Gram-stain-positive, oxidase- and catalase-positive motile, aerobic, and rod-shaped bacterial strain, designated as DCT-5T, was isolated from a native plant belonging to the genus Campanula at Dokdo island, Republic of Korea. Growth of the strain DCT-5T was observed at 15-37°C (optimum 30°C) on R2A broth, pH 6.0-8.0 (optimum 7.0), and 0-5% (w/v) NaCl concentration (optimum 0%). The 16S rRNA gene sequence analysis revealed that strain DCT-5T was most closely related to Arthrobacter silviterrae KIS14-16T, Arthrobacter livingstonensis LI2T, Arthrobacter stackebrandtii CCM 2783T, Arthrobacter cryoconiti Cr6-08T, Arthrobacter ramosus CCM 1646T, and Arthrobacter psychrochitiniphilus GP3T with pairwise sequence similarities of 98.76%, 97.47%, 97.25%, 97.11%, 97.11%, and 97.00%, respectively. The DNA G+C content of strain DCT-5T was 64.7 mol%, and its DNA-DNA relatedness values with A. silviterrae KIS14-16T, A. livingstonensis LI2T, A. stackebrandtii CCM 2783T, A. psychrochitiniphilus GP3T, A. ramosus CCM 1646T, and A. cryoconiti Cr6-08T were 32.57 ± 2.02%, 28.75 ± 0.88%, 31.93 ± 1.15%, 34.73 ± 1.86%, 29.12 ± 1.56%, and 27.23 ± 0.88%, respectively. The major quinone was MK-9(H2) and major fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C15:0, and iso-C16:0. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), unidentified glycolipid (GL), two unidentified aminophospholipids (APLs), and three unidentified lipids (Ls). The peptidoglycan type was A3α. On the basis of phenotypic, phylogenetic, genotypic, and chemotaxonomic characteristics, strain DCT-5T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter dokdonellae sp. nov. is proposed. The type strain is DCT-5T (= KCTC 49189T = LMG 31284T).

Pusillimonas thiosulfatoxidans sp. nov., a thiosulfate oxidizer isolated from activated sludge.

A Gram-stain-negative, motile bacterium, designated strain YE3T, was isolated from activated sludge obtained from a municipal wastewater treatment plant in Daejeon Metropolitan City, Republic of Korea. The cells were oxidase- and catalase-positive, and grew under aerobic conditions at 10-40 °C (optimum, 30 °C), with 1.0-8.0 % (w/v) NaCl (1.0 %) and at pH 5.5-9.0 (pH 7.0). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YE3T was most closely related to Pusillimonasharenae KACC 14927T (98.2 % sequence similarity) and Pusillimonasginsengisoli KCTC 22046T (98.0 %). DNA-DNA relatedness values for strain YE3T and P. harenae KACC 14927T, P. ginsengisoli KCTC 22046T and P. soli KCTC 22455T were 28.7±2.27 %, 21.3±1.16 %, and 14.0±0.67 %, respectively. The genomic G+C content of the type strain YE3T was 59.3 mol%, as determined by whole-genome sequencing. The dominant fatty acids were C16 : 0 (39.2 %) and C17 : 0cyclo (37.5 %). The major polar lipids of strain YE3T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Two aminophospholipids and four unidentified lipids were also detected. Furthermore, strain YE3T was able to oxidize thiosulfate under heterotrophic conditions. Based on the phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, strain YE3T represents a novel species of the genus Pusillimonas, for which the name Pusillimonas thiosulfatoxidans sp. nov. is proposed. The type strain is YE3T (=KCTC 62737T=NBRC 113113T).

Physiological and genomic insights into the lifestyle of arsenite-oxidizing Herminiimonas arsenitoxidans.

Arsenic, a representative toxic metalloid, is responsible for serious global health problems. Most organisms possess arsenic resistance strategies to mitigate this toxicity. Here, we reported a microorganism, strain AS8, from heavy metal/metalloid-contaminated soil that is able to oxidize arsenite, and investigated its physiological and genomic traits. Its cells were rod-shaped and Gram-negative, and formed small beige-pigmented colonies. 16S rRNA-based phylogenetic analysis indicated that the strain belongs to the genus Herminiimonas and is closely related to Herminiimonas glaciei UMB49T (98.7% of 16S rRNA gene sequence similarity), Herminiimonas arsenicoxydans ULPAs1T (98.4%), and Herminiimonas saxobsidens NS11T (98.4%). Under chemolithoheterotrophic conditions, the strain utilized some organic acids and amino acids as carbon and/or nitrogen sources but not electron sources. Further, the strain grew as a sulfur oxidizer in a complex medium (trypticase soy agar). Unexpectedly, most carbohydrates failed to support its growth as sole carbon sources. Genome sequencing supported these observations, and very few ABC transporters capable of oligo/monosaccharide uptake were identified in the AS8 genome. The genome harbored genes required for the colonization, flagella biosynthesis, urea degradation, and heavy metal and antibiotic resistance. Based on these polyphasic and genomic analyses, we propose that the strain AS8 be named Herminiimonas arsenitoxidans.

Haloplanus salinarum sp. nov., an extremely halophilic archaeon isolated from a solar saltern.

An extremely halophilic archaeal strain SP28T was isolated from the Gomso solar saltern, Republic of Korea. Cells of the new strain SP28T were pleomorphic and Gram stain negative, and produced red-pigmented colonies. These grew in medium with 2.5-4.5 M NaCl (optimum 3.1 M) and 0.05-0.5 M MgCl2 (optimum 0.1 M), at 25-50 °C (optimum 37 °C) and at a pH of 6.5-8.5 (optimum pH 8.0). Mg2+ was required for growth. A concentration of at least 2 M NaCl was required to prevent cell lysis. Polar lipids included phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and one glycolipid chromatographically identical to sulfated mannosyl glucosyl diether. 16S rRNA and rpoB' gene sequence analyses showed that strain SP28T is closely related to Haloplanus ruber R35T (97.3 and 94.1 %, 16S rRNA and rpoB' gene sequence similarity, respectively), Haloplanus litoreus GX21T (97.0 and 92.1 %), Haloplanus salinus YGH66T (96.0 and 91.9 %), Haloplanus vescus RO5-8T (95.9 and 90.9 %), Haloplanus aerogenes TBN37T (95.6 and 90.3 %) and Haloplanus natans RE-101T (95.3 and 89.8 %). The DNA G+C content of the novel strain SP28T was 66.2 mol%, which is slightly higher than that of Hpn.litoreus GX21T (65.8 mol%) and Hpn.ruber R35T (66.0 mol%). DNA-DNA hybridization values betweenHpn.ruber R35T and strain SP28T and between Hpn.litoreus GX21T and strain SP28T were about 24.8 and 20.7 %, respectively. We conclude that strain SP28T represents a novel species of the genus Haloplanus and propose the name Haloplanus salinarum sp. nov. The type strain is SP28T (=JCM 31424T=KCCM 43210T).

Marinobacter salinus sp. nov., a moderately halophilic bacterium isolated from a tidal flat environment.

Two Gram-stain-negative, aerobic, motile, halophilic, rod-shaped bacteria, designated Hb8T and Hb20, were isolated from a tidal flat environment located on the South-West Korean peninsula. The isolates grew at 10-37 °C, at pH 5.0-9.0 and in NaCl concentrations of 0.5-15 % (w/v; optimum, 3.0-6.0 %). Sequence analysis of the 16S rRNA indicated that the isolates belong to the genus Marinobacter and are most closely related to Marinobacter sediminumR65T (98.3 %), followed by Marinobacter lipolyticus SM19T, Marinobacter salsuginis SD-14BT and Marinobacter similis A3d10T. The overall 16S rRNA gene sequence similarity with these species was 97.9 %, but Hb8T and Hb20 showed 100 % sequence similarity with each other. DNA-DNA relatedness values of H8T and Hb20 suggested that these isolates represent a single species, while DNA-DNA relatedness values of the two novel isolates with M. sediminum DSM 27079T and M. similis DSM 15400T were only 21.3 and 22.9 %, respectively. The major fatty acids present in strain Hb8T were identified as C16 : 0, C16 : 1ω9c, C18 : 1ω9c, C18 : 0 3-OH and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). Ubiquinone-9 was the main respiratory quinone in both the novel strains. The polar lipids found to be present included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified phospholipids and five unidentified lipids. The genomic DNA G+C content of Hb8T and Hb20 was 54.5 mol%. Polyphasic analysis indicated that the two isolates are representatives of a novel species of the genus Marinobacte, for which the name Marinobacter salinus sp. nov. is proposed. The type strain is Hb8T (=KCTC 52255T=JCM 31416T).

Detection and Diversity of the Nitrite Oxidoreductase Alpha Subunit (nxrA) Gene of Nitrospina in Marine Sediments.

Nitrite-oxidizing bacteria (NOB) are chemolithoautotrophs that catalyze the oxidation of nitrite to nitrate, which is the second step of aerobic nitrification. In marine ecosystems, Nitrospina is assumed to be a major contributor to nitrification. To date, two strains of Nitrospina have been isolated from marine environments. Despite their ecological relevance, their ecophysiology and environmental distribution are understudied owing to fastidious cultivation techniques and the lack of a sufficient functional gene marker. To estimate the abundance, diversity, and distribution of Nitrospina in various marine sediments, we used nxrA, which encodes the alpha subunit of nitrite oxidoreductase, as a functional and phylogenetic marker. We observed that Nitrospina diversity in polar sediments was significantly lower than that of non-polar samples. Moreover, nxrA-like sequences revealed an unexpected diversity of Nitrospina, with approximately 41,000 different sequences based on a 95% similarity cutoff from six marine sediments. We detected nxrA gene copy numbers of up to 3.57 × 104 per gram of marine sediment sample. The results of this study provide insight into the distribution and diversity of Nitrospina, which is fundamentally important for understanding their contribution to the nitrogen cycle in marine sediments.

Microbial Community Composition in the Marine Sediments of Jeju Island: Next-Generation Sequencing Surveys.

Marine sediments are a microbial biosphere with an unknown physiology, and the sediments harbor numerous distinct phylogenetic lineages of Bacteria and Archaea that are at present uncultured. In this study, the structure of the archaeal and bacterial communities was investigated in the surface and subsurface sediments of Jeju Island using a next-generation sequencing method. The microbial communities in the surface sediments were distinct from those in the subsurface sediments; the relative abundance of sequences for Thaumarchaeota, Actinobacteria, Bacteroides, Alphaproteobacteria, and Gammaproteobacteria were higher in the surface than subsurface sediments, whereas the sequences for Euryarchaeota, Acidobacteria, Firmicutes, and Deltaproteobacteria were relatively more abundant in the subsurface than surface sediments. This study presents detailed characterization of the spatial distribution of benthic microbial communities of Jeju Island and provides fundamental information on the potential interactions mediated by microorganisms with the different biogeochemical cycles in coastal sediments.

Rhodanobacter aciditrophus sp. nov., an acidophilic bacterium isolated from mine wastewater.

A novel strain (designated sjH1T), characterized as aerobic, Gram-stain-negative, oxidase-positive, catalase-negative, motile and rod-shaped, was isolated from mine wastewater. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain sjH1T belonged to the genus Rhodanobacter. Strain sjH1T was closely related to Rhodanobacter thiooxydans LCS2T (98.0% 16S rRNA gene sequence similarity), Rhodanobacter denitrificans 2APBS1T (97.7%), Rhodanobacter soli DCY45T (97.2%) and Rhodanobacter caeni MJ01T (97.0%). The DNA G+C content of strain sjH1T was 69.2 mol%. DNA-DNA relatedness ( < 60%) indicated that strain sjH1T represents a distinct species that is separate from R. thiooxydans, R. denitrificans, R. soli and R. caeni. The major ubiquinone was Q-8, and major fatty acids were summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. Based on data from this polyphasic study, it is proposed that sjH1T ( = KCTC 42660T = JCM 30774T) is the type strain of a novel species, Rhodanobacter aciditrophus sp. nov.

Changes in the Swine Gut Microbiota in Response to Porcine Epidemic Diarrhea Infection.

The gastrointestinal tract of mammals is a complex ecosystem with distinct environments and comprises hundreds of different types of bacterial cells. The gut microbiota may play a critical role in the gut health of the host. We herein attempted to identify a microbiota shift that may be affected by porcine epidemic diarrhea (PED). We observed significant differences in microbiota between the control and PED virus (PEDV)-infected groups at both the phylum and genus level. Most commensal bacteria (i.e. Psychrobacter, Prevotella, and Faecalibacterium) in the healthy gastrointestinal tract were decreased due to dysbiosis induced by PEDV infection.

Halolamina sediminis sp. nov., an extremely halophilic archaeon isolated from solar salt.

An extremely halophilic archaeal strain, halo-7T, was isolated from brine sediment of the Gomso solar saltern, Republic of Korea. Cells of strain halo-7T were pleomorphic, stained Gram-negative, lysed in distilled water and formed red-pigmented colonies. Strain halo-7T grew in the range of 25-45°C (optimum 37-40°C), pH 6.5-9.5 (optimum pH 7.0-8.0), 15-30% (w/v) NaCl (optimum, 20-25%), and 0.05-0.5 M MgCl2 (optimum 0.1-0.3 M). The minimal NaCl concentration to prevent cell lysis of strain halo-7T was 10% (w/v). The major polar lipids of the isolate were phosphatidylglycerol, phosphatidylglycerolphosphate methyl ester, an unidentified phospholipid, an unidentified lipid, and two unidentified glycolipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain halo-7T is closely related to the members of the genus Halolamina, Halolamina salina WSY15-H3T (98.7% 16S rRNA gene sequence similarity), Halolamina pelagica TBN21T (98.2%) and Halolamina rubra CBA1107T (97.4%). The genomic DNA G+C content determined for strain halo-7T (68.0 mol%) was slightly higher than those of H. salina JCM 18549T and H. rubra CBA1107T. DNA-DNA hybridization values between strain halo-7T and reference strains were < 25%. Based on phenotypic, chemotaxonomic and phylogenetic properties, we describe a novel species of the genus Halolamina, represented by strain halo-7T, for which we propose the name Halolamina sediminis sp. nov. The type strain is halo-7T ( = JCM 30187T = CECT 8739T).