Nesterenkonia haasae sp. nov., an alkaliphilic actinobacterium isolated from a degraded pasture in Songnen Plain.

An alkaliphilic actinobacterial strain, designated Hz 6-5T, was isolated from saline-alkaline soil from Songnen Plain in north-eastern China. The isolate formed light yellow-colored colonies and its cells were Gram-staining positive, non-motile, and non-spore-forming short rods. The strain was aerobic with optimal growth at 33 °C, pH 9.0, and in the presence of 0.5% (w/v) NaCl or 3% (w/v) KCl. It was catalase-positive and oxidase-negative. The isolate had highest 16S rRNA gene sequence similarities to the type strains of the species Nesternkonia natronophila M8T (98.2%), N. salmonea GY074T (98.1%), and N. sphaerica GY239T (97.4%), and the isolate formed a subclade with the type strains of these species in the neighbor-joining tree based on the 16S rRNA gene sequences. The phylogenetic tree based on the phylogenomic analysis also showed the same results. The DNA‒DNA relatedness (DDH) values of isolate Hz 6-5T with N. natronophila M8T, N. halophila DSM 16378T, and N. halobia CGMCC 1.2323T were 21.2%, 36.5%, and 32.0%, respectively. The characteristic diamino acid of strain Hz 6-5T was found to be lysine. The respiratory quinones were MK-9, MK-8, MK-7(H4), MK-7(H2) and MK-7 and the major cellular fatty acids (> 10%) were anteiso-C15:0, anteiso-C17:0 and iso-C16:0. The polar lipids detected for strain Hz 6-5T were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid, and two unidentified phospholipids. The DNA G + C content of isolate Hz 6-5T was 60.8%. Based on the results of phylogenetic analysis supported by morphological, physiological, chemotaxonomic, and other differentiating phenotypic evidence, strain Hz 6-5T is considered to represent a novel species of the genus Nesterenkonia, for which the name Nesterenkonia haasae sp. nov. is proposed. The type strain is Hz 6-5T (=CPCC 205100T=NBRC 113521T).

Zafaria cholistanensis gen. nov. sp. nov., a moderately thermotolerant and halotolerant actinobacterium isolated from Cholistan desert soil of Pakistan.

A Gram-staining positive, non-spore forming, non-pigmented and non-motile bacterium, designated strain NCCP-1664T, was isolated from Cholistan desert, Pakistan. Cells of strain NCCP-1664T were strictly aerobic, catalase positive and oxidase negative with a rod to coccus growth cycle and can grow at pH 6.0-9.0 (optimum pH 7-8) at 28-45 °C (optimum 37 °C) and could tolerate 0-16% NaCl (optimum 2%). Phylogenetic analyses based on 16S rRNA gene sequence revealed that strain NCCP-1664T belongs to the family Micrococcaceae and was related to members of the genus Arthrobacter having highest sequence similarities with Arthrobacter ginkgonis (98.9%), A. halodurans (97.7%) and A. oryzae (97.1%) and less than 97% with other related taxa. DNA-DNA relatedness values of strain NCCP-1664T with above mentioned type strains were found to be less than 54%, whereas digital DDH and average nucleotide identity (ANI) values with A. oryzae were 20.9 and of 74.3%, respectively. DNA G + C content of strain NCCP-1664T was 70.0 mol%. Chemotaxonomic data of strain NCCP-1664T showed the peptidoglycan type as A3α L-Lys-L -Ala; menaquinones as MK-9(H2) (67%), MK-8(H2) (32%) and MK-7(H2) (1%), major fatty acids as anteiso -C15:0 (51.2%), anteiso-C17:0 (9.6%) and C18:1ω9c (6.9%) and polar lipids profile comprising of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, digalactosyldiacylglycerol, small amounts of monogalactosyldiacylglycerol, trimannosyldiacylglycerol and three unidentified lipids. The phylogenomic analyses along with chemotaxonomic data, physiological, biochemical characteristics allowed to describe it as representative of a novel genus, for which the name Zafaria cholistanensis gen. nov. sp. nov. is proposed with the type strain NCCP-1664T (= DSM 29936T = KCTC 39549T).

Catabolic enzyme activities during biodegradation of three-ring PAHs by novel DTU-1Y and DTU-7P strains isolated from petroleum-contaminated soil.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants having health hazards. PAH-utilizing bacterial strains were isolated from petroleum-contaminated soil from siding area, Bijwasan supply location of BPCL, Delhi, India. Bacterial strains with different morphology were isolated and acclimatized to a mixture of low molecular weight PAH compounds in the concentration range of 50-10,000 mg/L. Two bacterial strains surviving at 10,000 mg/L PAH concentration were identified as Kocuria flava and Rhodococcus pyridinivorans, based on 16S rRNA gene sequencing and phylogenetic analysis over MEGA X, are reported for the first time for PAH degradation. The strain K. flava could degrade phenanthrene, anthracene, and fluorene with efficiency of 55.13%, 59.01%, and 63.46%, whereas R. pyridinivorans exhibited 62.03%, 64.99%, and 66.79% degradation for respective PAHs at initial PAH concentration of 10 mg/L. Slightly lower degradation of phenanthrene could be attributed to its more stable chemical structure. The consortium of both the strains degraded 61.32%, 64.72%, and 66.64%, of 10 mg/L of phenanthrene, anthracene, and fluorene, respectively, in 15 days of incubation period indicating no synergistic or antagonistic effect towards degradation. Catechol 2,3-dioxygenase (C23O), dehydrogenase and peroxidase enzyme activities during PAH degradation coincided with degradation of PAHs, thus highlighting the role of these enzymes in catabolising three-ring PAHs. This is the first investigation confirming the participation of C23O, dehydrogenase and peroxidases enzyme profiles throughout the period of degradation. The study concludes that these strains can play significant role in microbial remediation of PAH-contaminated environment.

Enhanced growth and yield of oyster mushroom by growth-promoting bacteria Glutamicibacter arilaitensis MRC119.

Promotion of mushroom growth by means of biological agents replacing chemicals is an emerging and highly demanded issue in the sector of mushroom cropping. The present study was aimed to search for a novel bacterium potentially able to enhance mushroom growth and yield. A total of 2165 bacterial isolates purified from different samples were scrutinized through various growth-promoting attributes. As a consequence of rigorous screening, 26 isolates found exhibiting positive traits of mushroom growth promotion. Thereafter, in response to the cocultivation (fungus and bacteria), a potent bacterial strain was isolated capable to improve significantly the mycelial growth. In cocultivation the highest radial and linear growth rate was 7.6 and 8.1 mm/day on 10th and 11th days, respectively. The fruitbody yields and biological efficiency (BE) of the inoculated sets were 28% and 58% higher than the uninoculated control sets. The bacterium was molecularly identified based on 16S ribosomal RNA sequencing and confirmed as Glutamicibacter arilaitensis MRC119. Therefore, the bioinoculant of the current bacterium can be potentially useful as an ecofriendly substitute stimulating the production of mushroom fruit bodies with improved BE.

Glutamicibacter mishrai sp. nov., isolated from the coral Favia veroni from Andaman Sea.

A novel aerobic marine actinobacterium (strain S5-52T) belonging to the genus Glutamicibacter was isolated from the coral Favia veroni sampled from the Andaman Sea, India. Cells are Gram stain positive and rod shaped. The DNA G+C content was 58.7 mol%. The major quinones were MK-8 and MK-9. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid, trimannosyldiacylglycerol, phospholipid and dimannosylglyceride. The peptidoglycan type was A4α. Strain S5-52T showed a maximum 16S rRNA similarity of 99.36% with Glutamicibacter halophytocola DSM 101718T. The genome of strain S5-52T was 3.57 Mb that contains 3274 protein coding sequences (CDS). DNA-DNA similarity and ANI values between S5-52T and the reference strains were below 70% and 95-96%, respectively. Analysis of genomic reduction events in the evolutionary path from the LUCA (last universal common ancestor) to G. mishrai LMG 29155T and G. halophytocola DSM 101718T exhibit a number of genes involved in amino acid metabolism, cell wall biogenesis and replication, recombination and repair mechanism that reduced in both the species. Based on phenotypic, chemotaxonomic properties and comparative genomic studies, the strain S5-52T is considered a novel species of the genus Glutamicibacter, for which the name Glutamicibacter mishrai sp. nov. is proposed. The type strain is S5-52T (= KCTC 39846T = LMG 29155T).

Pseudarthrobacter psychrotolerans sp. nov., a cold-adapted bacterium isolated from Antarctic soil.

A novel cold-tolerant bacterium, designated strain YJ56T, was isolated from Antarctic soil collected from the Cape Burk area. Phylogenetic analysis through 16S rRNA gene sequence similarity revealed that strain YJ56T was most closely related to the genus Pseudarthrobacter, including Pseudarthrobacter oxydans DSM 20119T (99.06 % similarity), Pseudarthrobacter polychromogenes DSM 20136T (98.98 %) and Pseudarthrobacter sulfonivorans ALLT (98.76 %). The genome size (5.2 Mbp) of strain YJ56T was the largest among all the published genomes of Pseudarthrobacter type strains (4.2-5.0 Mbp). The genomic G+C content of strain YJ56T (64.7 mol%) was found to be consistent with those of other Pseudarthrobacter strains (62.0-71.0 mol%). The average nucleotide identity and average amino acid identity values between strain YJ56T and P. sulfonivorans ALLT were estimated at 84.1 and 84.2 %, respectively. The digital DNA-DNA hybridization value between the two strains was calculated to be 28.0 %. This rod-shaped and obligate aerobic strain exhibited no swimming or swarming motility. It had catalase activity but no oxidase activity. Cells grew at 4-28 °C (optimum, 13 °C) and pH 5.0-11.0 (optimum, pH 7.0) and with 0-6.0 % (w/v) NaCl (optimum, 0%) in Reasoner's 2A medium. MK-9 (H2) was the sole menaquinone. Two-dimensional TLC results revealed that the primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two glycolipids and phosphatidylinositol. Fatty acid methyl ester analysis showed that anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0 were the major cellular fatty acids in strain YJ56T. Based on phenotypic and genotypic characteristics, strain YJ56T represents a novel species of the genus Pseudarthrobacter, and thus the name Pseudarthrobacter psychrotolerans sp. nov is proposed. The type strain is YJ56T (=JCM 33881T=KACC 21510T).

Emendation of the Genus Auritidibacter Yassin et al. 2011 and Auritidibacter ignavus Yassin et al. 2011 based on features observed from Canadian and Swiss clinical isolates and whole-genome sequencing analysis.

Auritidibacter ignavus is a Gram-stain-positive bacillus derived from otorrhea. Four strains derived from ear discharges in Canada and Switzerland, with features consistent with but distinguishable from Auritidibacter ignavus IMMIB L-1656T (accession number FN554542) by 16S rRNA gene sequencing (97.5 % similarity), were thought to represent a novel species of the genus Auritidibacter. Auritidibacter ignavus DSM 45359T (=IMMIB L-1656T) was acquired to compare with Canadian and Swiss strains by whole-genome sequencing (WGS). Unexpectedly, those isolates were observed to be consistent with A. ignavus DSM 45359T by WGS (ANIb scores >98 %), MALDI-TOF (Bruker), cellular fatty acid analysis and biochemically (some differences were observed). A nearly full 16S rRNA gene sequence could not be readily prepared from A. ignavus DSM 45359T, even after multiple attempts. A 16S rRNA gene chimeric consensus sequence created from the genome assembly of A. ignavus DSM 45359T had only 97.5 % similarity to that of A. ignavus IMMIB L-1656T, implying that 16S rRNA sequence accession number FN554542 could not be replicated. We concluded that our isolates of members of the genus Auritidibacter were consistent with A. ignavus DSM 45359T, did not represent a novel species, and that the sequence corresponding to FN554542 was not reproducible. By WGS, A. ignavus DSM 45359T had genome of 2.53×106 bp with a DNA G+C content of 59.34%, while genomes of Canadian and Swiss isolates ranged from 2.47 to 2.59×106 bp with DNA G+C contents of 59.3-59.52 %. A. ignavus NML 100628 (=NCTC 14178=LMG 30897) did not demonstrate a rodcoccus cycle. Emendation of Auritidibacter ignavus was proposed based on these results.

Kocuria coralli sp. nov., a novel actinobacterium isolated from coral reef seawater.

An actinobacterial strain, SCSIO 13007T, was isolated from seawater collected from the Luhuitou fringing reef at a depth of 4.2 m. Phylogenetic and phenotypic properties of the organism supported the hypothesis that it represented a member of the genus Kocuria. Phylogenetic analysis indicated that the levels of 16S rRNA gene sequence similarity between SCSIO 13007T and type strains of other recognized members of the genus Kocuria were lower than 96.99 %. Growth in the presence of up to 15 % (w/v) NaCl was a distinctive characteristic of SCSIO 13007T. Other biochemical and physiological properties and the major fatty acids also differentiated the isolate from its phylogenetically closest relative Kocuria subflava YIM 13062T. The menaquinone types were MK-7(H2) and MK-8(H2). Major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unidentified lipid and an unidentified aminolipid. The DNA G+C content was 73.7 mol%. The combined genotypic and phenotypic data indicated that strain SCSIO 13007T represents a novel species of the genus Kocuria, for which the name Kocuria coralli sp. nov. is proposed; the type strain is SCSIO 13007T (=DSM 27811T=NBRC 109942T).

Nesterenkonia salmonea sp. nov. and Nesterenkonia sphaerica sp. nov., isolated from the Southern Atlantic Ocean.

Two Gram-positive, aerobic, non-motile and non-spore-forming actinobacteria, strains GY074T and GY239T, were isolated from deep-sea sediment of the Southern Atlantic Ocean. The results of phylogenetic analysis of 16S rRNA gene sequences placed both isolates within the genus Nesterenkonia, and showed a sequence similarity of 98.3 % between the two strains and similarites of 94.3-97.2 % with respect to Nesterenkonia species with validly published names. Based on whole-genome sequences, the values of in silico DNA-DNA hybridization and the average nucleotide identity between strains GY074T and GY239T were 21.2 and 78.1 %, respectively, less than the proposed cut-off level for species delineation, i.e. 70 and 95 %. For both strains, the major cellular fatty acids were anteiso-C17 : 0 and anteiso-C15 : 0, and the major menaquinones were MK-7, MK-8 and MK-9. The major polar lipid contents of the two strains were similar with phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The genomic DNA G+C contents of strains GY074T and GY239T were 61.1 and 64.2 mol%, respectively. On the basis of the phylogenetic analysis and physiological and chemotaxonomic data, the isolates represent two novel species of the genus Nesterenkonia, for which the names Nesterenkonia salmonea sp. nov. (type strain GY074T=KCTC 39639T=MCCC 1A11256T) and Nesterenkonia sphaerica sp. nov. (type strain GY239T=KCTC 39640T=MCCC 1A10688T) are proposed.

Nesterenkonia muleiensis sp. nov., a novel actinobacterium isolated from sap of Populus euphratica.

A novel, Gram-stain-positive, aerobic, non-endospore-forming, non-motile and rod-shaped bacterium designated RB2T was isolated from sap of Populus euphratica collected in Mulei county, Xinjiang province, PR China. RB2T was able to grow at 10-45 °C (optimum 35 °C), pH 6.0-12.0 (optimum 8.0) and with 0-12 % (w/v) NaCl (optimum 1 %). The genomic DNA G+C content was 63.5 % (from the genome sequence). The results of the chemotaxonomic analysis indicated that the predominant isoprenoid quinones were MK-8 and MK-9. The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The major polar lipids of RB2T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two glycolipids. The peptidoglycan type of RB2T was A4α, l-Lys-Gly-l-Glu. The results of the phylogenetic analysis, along with the phenotypic and chemotaxonomic characteristics, indicate that strain RB2T represents a novel species of the genus Nesterenkonia, for which the name Nesterenkonia muleiensis sp. nov. is proposed. The type strain is RB2T (=MCCC 1K03528T=KCTC 49017T).

Descriptions of Clavibacter insidiosus sp. nov. and Clavibacter tessellarius sp. nov.

To complete the valid publication of the new species names resulting from reclassification of the genus Clavibacter, we here provide descriptions of Clavibacter insidiosus sp. nov. and Clavibacter tessellarius sp. nov.

Reclassification of Arthrobacter enclensis as Pseudarthrobacter enclensis comb. nov., and emended descriptions of the genus Pseudarthrobacter, and the species Pseudarthrobacter phenanthrenivorans and Pseudarthrobacter scleromae.

Arthrobacterenclensis was reported to cluster with species of the genus Pseudarthrobacter but the peptidoglycan containing lysine, alanine and glutamic acid and the presence of minor amounts of menaquinone MK-8(H4) were not in line with the description of the genus. Re-analysis of these traits revealed a peptidoglycan with l-Lys-l-Ser-l-Thr-l-Ala and no MK-8(H4), but major amounts of MK-9(H2) in the quinone system of A. enclensis DSM 25279T. These data demonstrate that A. enclensis shares the characteristics of the genus Pseudarthrobacter. Since the reported quinone systems of Pseudarthrobacterphenanthrenivorans [MK-8 and MK-9(H2)] and Pseudarthrobacterscleromae [MK-8(H2] were clearly different from those of other species of the genus, the quinone systems of the two species were re-analyzed. Since the polar lipid profile of P. phenanthrenivorans was reported to contain phosphatidylethanolamine, which is unusual for a member of the Micrococcaceae, and the polar lipid profile of P. scleromae was unknown, the polar lipids of these two species were also analysed. The quinone system of P. phenanthrenivorans DSM 18606T was composed of the major menaquinones MK-9(H2), MK-8(H2) and MK-10(H2) and that of P. scleromae DSM 17756T was composed of the major menaquinones MK-9(H2) and MK-8(H2) and MK-9. In the polar lipid profile of P. phenanthrenivorans DSM 18606T no phosphatidylethanolamine could be detected. Based on these results we here propose the reclassification of A. enclensis as Pseudarthrobacterenclensis comb. nov. and emend the descriptions of the genus Pseudarthrobacter and the two species P. phenanthrenivorans and P. scleromae.

Reclassification of Arthrobacter endophyticus (Wang et al. 2015) as Glutamicibacter endophyticus comb. nov.

The species Arthrobacterendophyticus is phylogenetically placed within the Glutamicibacter clade and shares 97.3-98.4 % 16S rRNA gene sequence similarities with the species of this genus. The quinone system with the major menaquinone MK-9 and the peptidoglycan amino acids alanine, glutamic acid and lysine are consistent with the characteristics of the members of the genus Glutamicibacter but the polar lipid profile with phosphatidylinositol distinguishes A. endophyticus from species of the genus Glutamicibacter. Re-analysis of both peptidoglycan structure and polar lipid profile revealed peptidoglycan type l-Lys-l-Ala-l-Glu (A11.35) and a polar lipid profile lacking phosphatidylinositol. These traits are consistent with those of representatives of the genus Glutamicibacter and distinguish A. endophyticus from members of the genus Arthrobacter sensu stricto. Due to its phylogenetic position and congruence with the key characteristics of members of the genus Glutamicibacter we here propose the reclassification of Arthrobacter endophyticus as a species of the genus Glutamicibacter, Glutamicibacter endophyticus comb. nov. (EGI 6500322T=DSM 28750T=KCTC 29490T=JCM 30091T).

Kocuria soli sp. nov., an actinobacterium isolated from soil.

A Gram-stain-positive, aerobic, coccoid-shaped, non-spore-forming actinobacterial strain, designated M5W7-7T, was isolated from a hot spring soil sample collected from Anshan, Liaoning province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain M5W7-7T clustered closely with species of the genus Kocuria, and showed the highest sequence similarity of 97.1 % to Kocuria subflava YIM 13062T. Strain M5W7-7T grew at 10-37 °C (optimum, 37 °C), pH6.0-11.0 (pH 6.0-7.0) and in the presence of 0-7 % (w/v) NaCl (0 %). Substrate mycelia and aerial mycelia were not formed, and diffusible pigments were not observed on any media tested. Strain M5W7-7T contained MK-6(H2) and MK-7(H2) as the dominant menaquinones. The polar lipid profile of strain M5W7-7T contained diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, an unidentified phospholipid and an unidentified lipid. The predominant whole-cell sugars were galactose and glucose. The predominant fatty acid was anteiso-C15 : 0. The DNA G+C content of strain M5W7-7T was 67.0 mol%. On the basis of phylogenetic relationships, phenotypic characterization and chemotaxonomic analyses, strain M5W7-7T represents a novel species of the genus Kocuria, for which the name Kocuriasoli sp. nov. is proposed. The type strain is M5W7-7T (=KCTC 49195T =CGMCC 1.13744T).

Nesterenkonia natronophila sp. nov., an alkaliphilic actinobacterium isolated from a soda lake, and emended description of the genus Nesterenkonia.

A Gram-stain-positive, alkaliphilic, moderately halophilic, cocci-shaped actinobacterium (strain M8T) was isolated from a sample of soda lake sediment (Lake Magadi, Tanzania). The isolate was heterotrophic, strictly aerobic, catalase-positive, oxidase-negative and formed orange-pigmented colonies in solid media. It utilized various sugars and organic acids as sole carbon sources. The organism grew at 10-38 °C, at pH 7.5-12.0 and in the presence of 1-12 % (w/v) NaCl, with optimal growth occurring at 30 °C, at pH 10 and in the presence of 5 % (w/v) NaCl. Comparative 16S rRNA gene sequence analysis showed that strain M8T belonged to the genus Nesterenkonia, sharing the closest similarities to Nesterenkoniahalobia DSM 20541T, Nesterenkoniahalophila YIM 70179T and Nesterenkoniaaethiopica DSM 17733T (97.5, 97.5 and 97.1 %, respectively). The characteristic diamino acid of strain M8T was found to be lysine and the polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified glycolipids and two unidentified phospholipids. The DNA G+C content was 61.8 mol% (genome). The strain contained MK-7, MK-9 and MK-10 as the respiratory quinones, and the major fatty acids (>10 %) comprised anteiso-C17 : 0 and anteiso-C15 : 0. On the basis of phylogenetic analyses and phenotypic data, strain M8T is considered to represent a novel species, for which the name Nesterenkonianatronophila sp. nov. is proposed. The type strain is M8T (=JCM 32100T=CGMCC 1.16706T=MCC 3367T).

Kocuria tytonis sp. nov., isolated from the uropygial gland of an American barn owl (Tyto furcata).

Avian uropygial glands have received increasing attention in recent years, but little is known about micro-organisms in uropygial glands. In this study, we isolated a strain of Gram-stain-positive, non-motile, non-spore-forming cocci, designated 442T, from the uropygial gland of an American barn owl (Tyto furcata) and characterized it using a polyphasic approach. 16S rRNA gene sequence analysis placed the isolate in the genus Kocuria. The G+C content was 70.8 mol%, the major menaquinone was MK-7(H2) and the predominant cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. Phylogenetic analyses based on the 16S rRNA gene identified Kocuria rhizophila DSM 11926T (99.6 % similarity), Kocuria salsicia DSM 24776T (98.7 %), Kocuria varians DSM 20033T (98.3 %) and Kocuria marina DSM 16420T (98.3 %) as the most closely related species. However, average nucleotide identity values below 86 % indicated that the isolate differed from all species hitherto described. Chemotaxonomic analyses and whole-cell protein profiles corroborated these findings. Accordingly, the isolate is considered to be a member of a novel species, for which the name Kocuria tytonis sp. nov. is proposed. The type strain is 442T (=DSM 104130T=LMG 29944T).

Specibacter cremeus gen. nov., sp. nov., a new member of the family Micrococcaceae isolated from a natural cave.

A Gram-reaction-positive, non-spore-forming, rod-shaped bacterium, strain C1-50T, was isolated from a natural cave in Jeju, Republic of Korea by using the serial dilution plating method. Results of phylogenetic analysis using 16S rRNA gene sequences showed that strain C1-50T belonged to the family Micrococcaceae but had the highest sequence similarity to Arthrobacter halodurans JSM 078085T (96.18 %) and Arthrobacter globiformis DSM 20124T (96.04 %). The 16S rRNA gene sequence similarities between strain C1-50T and other members of the family were lower than 96.0 %. The cell-wall peptidoglycan type was A3α with an l-Lys-l-Ala2. Whole-cell sugars consisted largely of glucose and galactose. The predominant menaquinone was MK-9(H2) with smaller components of MK-7(H2) and MK-8(H2). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The cellular fatty acids consisted of saturated, unsaturated, anteiso-branched and iso-branched components. The G+C content of genomic DNA was 68.8 mol% (draft genome sequence). On the basis of morphological and chemotaxonomic differences and distinct phylogenetic clustering, it was concluded that the organism represents a novel species of a new genus in the family Micrococcaceae, for which the name Specibacter cremeus gen. nov., sp. nov. is proposed. The type strain is C1-50T (=KCTC 39557T=DSM 100066T).

Galactobacter caseinivorans gen. nov., sp. nov. and Galactobacter valiniphilus sp. nov., two novel species of the family Micrococcaceae, isolated from high bacterial count raw cow's milk.

Four Gram-stain positive, rod-shaped bacterial isolates, strains JZ R-183T, JZ RK-117, DI-46 and JZ R-35T, were recovered from bulk tank raw cow's milk from three different dairy farms in Germany. Analysis of their 16S rRNA gene sequences indicated that these isolates belonged to the family Micrococcaceae, closely related to the genera Arthrobacter, Neomicrococcus,Glutamicibacter and Citricoccus. The 16S rRNA gene sequence similarity between the isolates and the next related type strains was below 97.3 %. Phylogenetic analysis of 16S rRNA, recA and gyrB genes revealed that these isolates formed two different groups in an independent cluster within the family Micrococcaceae. Chemotaxonomic analyses determined anteiso-C15 : 0 as predominant fatty acid, but also large amounts of iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 were detected. The menaquinones MK-9(H2) and MK-7(H2) were present in all of the isolates and the polar lipid pattern contained the phospholipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol and a glycolipid. The peptidoglycan type of the isolates was A4α, with alanine, lysine and glutamate as dominating cell wall amino acids. The fatty acid and menaquinone profile differentiated the strains from the genera Arthrobacter, Neomicrococcus,Citricoccus and Glutamicibacter. The results of phylogenetic, phenotypic and chemotaxonomic analyses indicated that the isolates belonged to two novel species of a novel genus, for which the names Galactobacter caseinivorans gen. nov., sp. nov. and Galactobacter valiniphilus sp. nov. are proposed. The type strains are JZ R-183T (=DSM 107700T=LMG 30902T) and JZ R-35T (=DSM 107699T=LMG 30901T).

Development of a loop-mediated isothermal amplification assay for specific detection of all known subspecies of Clavibacter michiganensis.

AIMS: Clavibacter michiganensis is an important bacterial plant pathogen that causes vast destruction to agriculturally important crops worldwide. Early detection is critical to evaluate disease progression and to implement efficient control measures to avoid serious epidemics. In this study, we developed a sensitive, specific and robust loop-mediated isothermal amplification (LAMP) assay for detection of all known subspecies of C. michiganensis. METHODS AND RESULTS: Whole genome comparative genomics approach was taken to identify a unique and conserved region within all known subspecies of C. michiganensis. Primer specificity was evaluated in silico and with 64 bacterial strains included in inclusivity and exclusivity panels; no false positives or false negatives were detected. Both the sensitivity and spiked assay of the developed LAMP assay was 1 fg of the pathogen DNA per reaction. A 100% accuracy was observed when tested with infected plant samples. CONCLUSIONS: The developed LAMP assay is simple, sensitive, robust and easy to perform using different detection platforms and chemistries. SIGNIFICANCE AND IMPACT OF THE STUDY: The developed LAMP assay can detect all known subspecies of C. michiganensis. The LAMP process can be performed isothermally at 65°C and results can be visually assessed, which makes this technology a promising tool for monitoring the disease progression and for accurate pathogen detection at point-of-care.

Ornithinimicrobium panacihumi sp. nov., Antagonistic Bacteria Against Root Rot Fungal Pathogens, Isolated from Cultivated Ginseng Soil.

A Gram-positive bacterium (DCY118T) was isolated from ginseng-cultivated soil in Gochang-gun, Republic of Korea. This isolate was assigned to the genus Ornithinimicrobium and is closely related to Ornithinimicrobium kibberense K22-20T (98.8%), O. pekingense DSM 21552T (98.5%), O. algicola JC311T (98.2%), and O. humiphilum DSM 12362T (97.9%) based on 16S rRNA gene sequence analysis. However, strain DCY118T showed < 55% DNA-DNA homology with closely related reference strains. Cells were non-motile, non-sporulating, catalase- and oxidase-positive, aerobic, short rods, and cocci, and produced light-yellow, circular, and smooth colonies on TSA medium. MK-8(H4) was the predominant menaquinone. The major cellular fatty acids were iso-C15:0, anteiso-C15:0, and C16:0. The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), an unknown phospholipid (PL1), an unknown amino lipid (AL1), and unidentified polar lipids (L1-5). The genomic DNA G+C content was 71.1 mol%. The peptidoglycan contained L-ornithine as the diagnostic diamino acid. Whole-cell sugars were composed of glucose, arabinose, and xylose. Overall, data collected from phenotypic and genotypic tests during this study indicated that strain DCY118T could not be assigned to a recognized species. Strain DCY118T showed antagonistic activity against the fungal pathogens causing root rot in ginseng, i.e., Fusarium solani (KACC 44891T) and Cylindrocarpon destructans (KACC 44660T). The results from this study confirm the DCY118T strain as a new species within the genus Ornithinimicrobium, for which the name Ornithinimicrobium panacihumi is proposed. The type strain is DCY118T (=KCTC 39962T=JCM 32156T).