Sphingomonas flavescens sp. nov., isolated from soil.

An aerobic bacterium, designated as PT-12T, was isolated from soil collected from agriculture field, and its taxonomic position was validated through a comprehensive polyphasic methodology. The strain was identified as Gram-stain-negative, non-motile, rod-shaped, and catalase- and oxidase-positive. The yellow-colored colonies showed growth ability at temperature range of 18-37 °C, NaCl content of 0-1.0% (w/v), and at a pH of 6.0-8.0. The 16S rRNA gene and phylogenetic analysis showed that strain PT-12T affiliated with the genus Sphingomonas in the family Sphingomonadaceae, and displayed the highest 16S rRNA nucleotide sequence similarity with Sphingomonas limnosediminicola 03SUJ6T (98.4%). The genome size of strain PT-12T was 2,656,862 bp and the DNA G + C content estimated from genome was 63.5%. The highest values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were observed between strain PT-12T and Sphingomonas segetis YJ09T, accounting to 76.2% and 20.2%, respectively. In addition, both ANI and dDDH values between strain PT-12T and other phylogenetically related neighbors ranged between 69.6% and 76.2% and 18.4% and 20.2%, respectively. Chemotaxonomic features exhibited Q-10 as the only ubiquinone; homospermidine as the major polyamine; summed feature 8 (C18:1ω7c and/or C18:1ω6c), C16:0, and 10-methyl C18:0 as the notable fatty acids; and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, and sphingoglycolipid as dominating polar lipids. Overall, the comprehensive polyphasic data supported that strain PT-12T represents a novel bacterial species within the genus Sphingomonas. Accordingly, we propose the name Sphingomonas flavescens sp. nov. The type strain is PT-12T (= KCTC 92114T = NBRC 115717T).

Enterovirga aerilata sp. nov. and Knoellia koreensis sp. nov., isolated from an automobile air conditioning system.

Two strictly aerobic and rod-shaped bacteria, labelled as DB1703T and DB2414ST, were obtained from an automobile air conditioning system. Strain DB1703T was Gram-stain-negative, while strain DB2414ST was Gram-stain-positive. Both strains were catalase-positive and oxidase-negative. Strains DB1703T and DB2414ST were able to grow at 18-42 °C. Strain DB1703T grew within a NaCl range of 0-3 % and a pH range of 6.0-8.0; while strain DB2414ST grew at 0-1 % and pH 6.5-8.5. The phylogenetic and 16S rRNA gene sequence analysis indicated that strains DB1703T and DB2414ST belonged to the genera Enterovirga and Knoellia, respectively. Strain DB1703T showed the closest phylogenetic similarity to Enterovirga rhinocerotis YIM 100770T (94.8 %), whereas strain DB2414ST was most closely related to Knoellia remsis ATCC BAA-1496T (97.7 %). The genome sizes of strains DB1703T and DB2414ST were 4 652 148 and 4 282 418 bp, respectively, with DNA G+C contents of 68.8 and 70.5 mol%, respectively. Chemotaxonomic data showed Q-10 as the sole ubiquinone in DB1703T and ML-8 (H4) in DB2414ST. The predominant cellular fatty acid in DB1703T was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), whereas iso-C16 : 0, C17 : 1 ω8c, and iso-C15 : 0 were dominant in DB2414ST. Overall, the polyphasic taxonomic comparisons showed that strains DB1703T and DB2414ST were distinct from their closest taxa and represent novel species within the genera Enterovirga and Knoellia, respectively. Accordingly, we propose the names Enterovirga aerilata sp. nov., with the type strain DB1703T (=KCTC 72724T=NBRC 114759T), and Knoellia koreensis sp. nov., with the type strain DB2414ST (=KCTC 49355T=NBRC 114620T).

Microbacterium humicola sp. nov., Microbacterium terrisoli sp. nov., Paenibacillus pedocola sp. nov., Paenibacillus silviterrae sp. nov., Flavobacterium terrisoli sp. nov., and Aquabacterium humicola sp. nov., isolated from soil.

Four Gram-stain-positive and two Gram-stain-negative bacterial strains, designated as W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T, were isolated from soil samples collected from the Republic of Korea. The 16S rRNA gene sequence analysis showed that strains W4T and FW7T belonged to the genus Microbacterium, strains TW48T and UW52T were affiliated to the genus Paenibacillus, strain PT-3T was related to the genus Flavobacterium, and strain RJY3T was associated with the genus Aquabacterium. The closest phylogenetic taxa to W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T were Microbacterium bovistercoris NEAU-LLET (97.7 %), Microbacterium protaetiae DFW100M-13T (97.9 %), Paenibacillus auburnensis JJ-7T (99.6 %), Paenibacillus allorhizosphaerae JJ-447T (95.7 %), Flavobacterium buctense T7T (97.1 %), and Aquabacterium terrae S2T (99.5 %), respectively. Average nucleotide identity and digital DNA-DNA hybridization values between the novel strains and related reference type strains were <95.0 % and <70.0 %, respectively. The major cellular fatty acid in strains W4T, FW7T TW48T, and UW52T was antiso-C15 : 0. Similarly, strain PT-3T revealed iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, and iso-C15 : 0 3-OH as its principal fatty acids. On the other hand, RJY3T exhibited summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), and C12 : 0 as its predominant fatty acids. Overall, the polyphasic taxonomic data indicated that strains W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T represent novel species within the genera Microbacterium, Paenibacillus, Flavobacterium, and Aquabacterium. Accordingly, we propose the names Microbacterium humicola sp. nov., with the type strain W4T (=KCTC 49888T=NBRC 116001T), Microbacterium terrisoli sp. nov., with the type strain FW7T (=KCTC 49859T=NBRC 116000T), Paenibacillus pedocola sp. nov., with the type strain TW48T (=KCTC 43470T=NBRC 116017T), Paenibacillus silviterrae sp. nov., with the type strain UW52T (=KCTC 43477T=NBRC 116018T), Flavobacterium terrisoli sp. nov., with the type strain PT-3T (=KCTC 92106T=NBRC 116012T), and Aquabacterium humicola sp. nov., with the type strain RJY3T (=KCTC 92105T=NBRC 115831T).

Paenibacillus agricola sp. nov., isolated from agricultural soil.

A white-coloured, rod-shaped, motile, aerobic, and Gram-stain-positive bacterial strain S3N08T was isolated from agricultural soil. The strain grew at temperature 10-40 °C, at 0-1.0% (w/v) NaCl concentration, and at pH 6.5-8.0. Catalase was negative and oxidase was positive. The phylogenetic analysis inferred that the strain S3N08T belonged to the genus Paenibacillus, with the closest relative being Paenibacillus periandrae PM10T (95.6% 16S rRNA gene sequence similarity). The only menaquinone was MK-7 and the major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylglycerol, and phosphatidylethanolamine. The predominant fatty acids were antiso-C15:0, C16:0, and iso-C15:0. The DNA G + C content was 45.1%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain S3N08T and with closest members were < 72.0% and < 19.0%, respectively. Altogether, the phylogenetic, genomics, phenotypic, and chemotaxonomic evidence illustrated in this study suggested that strain S3N08T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus agricola sp. nov. is proposed. The type strain is S3N08T (= KACC 19666 T = NBRC 113430 T).

Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov., isolated from forest soil.

During the study of microbial ecology of forest soil, two circular, white-colored bacterial colonies were isolated and labeled as strains TW38T and TW40T. Both strains were catalase positive and oxidase negative. Strains TW38T and TW40T demonstrated growth within a temperature range of 10-37 °C and 18-37 °C, respectively, and thrived within a pH range of 5.5-9.0 and 6.0-8.0, respectively. Both strains grew at 0-2.0% (w/v) NaCl concentrations. The phylogenetic analysis indicated that strains TW38T and TW40T affiliated to the genus Paenibacillus, with the closest neighbors being Paenibacillus montanisoli RA17T (98.6%) and Paenibacillus arachidis E3T (95.4%), respectively. In both strains, the sole respiratory quinone was MK-7, the signature fatty acid was antiso-C15:0, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The digital DNA-DNA hybridization and the average nucleotide identity values between TW38T, TW40T, and closest reference strains were < 29.0% and < 85.0%, respectively. The DNA G+C content of TW38T and TW40T was 54.5% and 57.1%, respectively. In general, the phylogenetic, genomics, chemotaxonomic, and phenotypic data support the differentiation of TW38T and TW40T from other closest members of the genus Paenibacillus. Thus, we conclude both strains TW38T and TW40T represent novel species of the genus Paenibacillus, for which the name Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov. are proposed, respectively. The type strain of Paenibacillus silvisoli is TW38T (= KCTC 43468T = NBRC 116015T) and type strain of Paenibacillus humicola is TW40T (= KCTC 43469T = NBRC 116016T).

Paenibacillus caseinilyticus sp. nov., isolated forest soil.

A milky-white-coloured, aerobic, Gram-stain-positive, rod-shaped and motile bacterial strain (GW78T) was isolated from forest soil. GW78T was catalase-positive and oxidase-negative. The strain was able to grow optimally at 37 °C and at pH 7.0 in Reasoner's 2A media. The phylogenetic and 16S rRNA gene sequence analysis of GW78T showed its affiliation with the genus Paenibacillus. The 16S rRNA gene sequence of GW78T revealed 98.3 % similarity to its nearest neighbour Paenibacillus mucilaginosus VKPM B-7519T. Its chemotaxonomic properties included MK-7 as the sole menaquinone, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidylethanolamine as major polar lipids, and anteiso-C15 : 0, C16 : 1 ω11c and anteiso-C17 : 0 as predominant fatty acids. Digital DNA-DNA hybridization and average nucleotide identity results with its closest relatives were <74.0 % and <14.0 %, respectively. Overall, 16S rRNA gene sequence comparisons, phylogenetic and genomic evidence, and phenotypic and chemotaxonomic data allow the differentiation of GW78T from other members of the genus Paenibacillus. Thus, we propose that strain GW78T represents a novel species of the genus Paenibacillus, with the name Paenibacillus caseinilyticus sp. nov. The type strain is GW78T (=KCTC 43430T=NBRC 116023T).

Kaistella soli sp. nov., isolated from oil-contaminated experimental soil.

A light yellow-coloured, non-motile, aerobic, Gram-stain-negative, and rod-shaped bacterial strain DKR-2T was isolated from oil-contaminated experimental soil. The strain was catalase and oxidase positive, and grew at 0-1.5% (w/v) NaCl concentration, at temperature 10-35 °C, and at pH 6.0-9.5. The phylogenetic analysis suggested that the strain DKR-2T was affiliated to the genus Kaistella, with the closest species being Kaistella haifensis DSM 19056T (97.6% 16S rRNA gene sequence similarity). The principle fatty acids were iso-C15:0, summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl), and antiso-C15:0. The sole menaquinone was MK-6 and major polar lipid was phosphatidylethanolamin. The DNA G+C content was 39.5%. The dDDH (in silico DNA-DNA hybridization) and ANI (average nucleotide identity) values between strain DKR-2T and K. haifensis DSM 19056T were 22.4% and 79.3%, respectively. In addition, both dDDH and ANI values between strain DKR-2T and other phylogenetically related neighbours were < 25.0% and < 77.0%, respectively. In overall, the polyphasic taxonomic data presented in this study clearly indicated that strain DKR-2T represents a novel species in the genus Kaistella, for which the name Kaistella soli sp. nov. is proposed. The type strain is DKR-2T (=KACC 22070T=NBRC 114725T).

Cellulomonas fulva sp. nov., isolated from oil-contaminated soil.

A yellow-coloured, Gram-stain-positive, motile, aerobic and rod-shaped bacteria, designated DKR-3T, was isolated from oil-contaminated experimental soil. Strain DKR-3T could grow at pH 5.0-10.5 (optimum, pH 7.0-8.5), at 10-40 °C (optimum, 25-32 °C) and tolerated 3.5 % of NaCl. Phylogenetic analyses based on its 16S rRNA gene sequence indicated that strain DKR-3T formed a lineage within the family Cellulomonadaceae and was clustered with members of the genus Cellulomonas. Strain DKR-3T had highest 16S rRNA gene sequence similarities to Cellulomonas gelida DSM 20111T (98.3 %), Cellulomonas persica JCM 18111T (98.2 %) and Cellulomonas uda DSM 20107T (97.8 %). The predominant respiratory quinone was tetrahydrogenated menaquinone with nine isoprene units [MK-9(H4)]. The principal cellular fatty acids were anteiso-C15 : 0, C16 : 0 and anteiso-C17 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The cell-wall diamino acid was l-ornithine whereas rhamnose and glucose were the cell-wall sugars. The DNA G+C content was 74.2mol %. The genome of strain DKR-3T was 3.74 Mb and contained three putative biosynthetic gene clusters. The average nucleotide identity and digital DNA-DNA hybridization relatedness values between strain DKR-3T and its phylogenetically related members were below the species threshold values. Based on a polyphasic study, strain DKR-3T represents a novel species belonging to the genus Cellulomonas, for which the name Cellulomonas fulva sp. nov. is proposed. The type strain is DKR-3T (=KACC 22071T=NBRC 114730T).

Seasonal trends of mercury bioaccumulation and assessment of toxic effects in Asian clams and microbial community from field study of estuarine sediment.

This study investigated seasonal trends in bioaccumulation potential and toxic effects of mercury (Hg) in Asian clams (Corbicula fluminea) and microbial community. For this, a clam-exposure experiment was performed during summer, fall, and winter seasons in four different sites (HS1: control/clean site; HS2, HS3, and HS4: contaminated sites) of Hyeongsan River estuary, South Korea. Total mercury (THg) and methylmercury (MeHg) in whole sediments were highest at HS4 site during fall, sustained similar levels during winter, but decreased during summer. Unlike whole sediment, pore water reported higher levels in summer, and gradually declined during fall and winter. Asian clams from HS4 site collected during summer presented highest bioaccumulations of THg (521.52 µg/kg, dry weight) and MeHg (161.04 µg/kg, dry weight), which also correlated with the higher levels of Hg present in pore water in the same season. Moreover, biota-sediment-pore water accumulation factor (BSpAF) were comparatively greater in clams collected from HS2∼HS4 compared to HS1 sites, suggesting that porewater was a better indicator of accumulation of Hg. Upregulation of biomarker genes responsible for detoxifying process (gsts1), scavenging oxidative stress (cat), and protein reparation (hsp70 and hsp90) were observed in clams collected from HS2∼HS4. The overexpression of these biomarkers implied that Asian clams can be considered as promising warning tools for Hg-contamination. Both bacterial and metabolic diversities were negatively affected by higher levels of THg and MeHg. Phylum Proteobacteria was enriched in HS2∼HS4 compared to HS1. In contrast, phylum Bacteroidetes showed a reverse trend. The metabolic profile was highest in HS1 and lowest in HS4, revealing higher stress of Hg in HS4 site. Overall, the outcomes of this field study broaden the information on seasonal trends of bioaccumulation of Hg and its toxic effects. These findings may be helpful in Hg monitoring and management programs in other river systems.

Genome mining revealed polyhydroxybutyrate biosynthesis by Ramlibacter agri sp. nov., isolated from agriculture soil in Korea.

A white-colony-forming, facultative anaerobic, motile and Gram-stain-negative bacterium, designated G-1-2-2 T was isolated from soil of agriculture field near Kyonggi University, Republic of Korea. Strain G-1-2-2 T synthesized the polyhydroxybutyrate and could grow at 10-35 °C. The phylogenetic analysis based on 16S rRNA gene sequence showed that, strain G-1-2-2 T formed a lineage within the family Comamonadaceae and clustered as a member of the genus Ramlibacter. The 16S rRNA gene sequence of strain G-1-2-2 T showed high sequence similarities with Ramlibacter ginsenosidimutans BXN5-27 T (97.9%), Ramlibacter monticola G-3-2 T (97.9%) and Ramlibacter alkalitolerans CJ661T (97.5%). The sole respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and an unidentified phospholipid. The principal cellular fatty acids were C16:0, cyclo-C17:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and summed feature 8 (C18:1ω7c and/or C18:1ω6c). The genome of strain G-1-2-2 T was 7,200,642 bp long with 13 contigs, 6,647 protein-coding genes, and DNA G + C content of 68.9%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain G-1-2-2 T and close members were ≤ 81.2 and 24.1%, respectively. The genome of strain G-1-2-2 T showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Genome mining revealed the presence of atoB, atoB2, phaS, phbB, phbC, and bhbD genes in the genome which are responsible for polyhydroxybutyrate biosynthesis. Based on these data, strain G-1-2-2 T represents a novel species in the genus Ramlibacter, for which the name Ramlibacter agri sp. nov. is proposed. The type strain is G-1-2-2 T (= KACC 21616 T = NBRC 114389 T).