Spirosoma jeollabukense sp. nov., isolated from soil

Isolation of Spirosoma foliorum sp. nov. from the fallen leaf of Acer palmatum by a novel cultivation technique

In the effort of isolating novel microbial species, the strain PL0132T was isolated from a fallen leaf under fresh water at a stream, which glided when grown on a tap water medium (without nutrients). The strain was determined to be Gram-negative, strictly aerobic, and rod-shaped, which grew optimally at 25 °C, pH 6-7, and the strain tolerates 1% (w/v) NaCl concentration. The complete genome of strain PL0132T comprises one contig with a sequencing depth of 76×, consisting of 8,853,064 base pairs and the genomic DNA G + C content was 46.7% (genome). 16S rRNA gene sequence analysis revealed that strain PL0132T represents a member of the phylum Bacteroidetes and is affiliated with the genus Spirosoma. Based on genomic, phenotypic, and chemotaxonomic characteristics, the strain PL0132T represents a novel species of the genus Spirosoma, for which the name Spirosoma foliorum sp. nov. is proposed (= KCTC 72228 T = InaCC B1447T).

Spirosoma rhododendri sp. nov., isolated from a flower of royal azalea (Rhododendron schlippenbachii)

A Gram-negative, non-motile, strictly aerobic and rod- or filamentous-shaped strain, CJU-R4T, was isolated from a flower of royal azalea (Rhododendron schlippenbachii) collected in the Republic of Korea. Strain CJU-R4T was catalase-positive and oxidase-negative, and grew at 15–33 °C (optimum, 28–20 °C), at pH 5.0–8.0 (optimum, pH 7.0–8.0), and in the presence of 0–1 % NaCl (w/v; optimum, 0 %). Strain CJU-R4T had the highest 16S rRNA gene sequence similarity to Spirosoma oryzae RHs22T (96.6 %), revealing less than 93 % sequence similarity to other type strains. Phylogenetic and phylogenomic analysis also revealed strain CJU-R4T formed a robust cluster with S. oryzae RHs22T. The major fatty acids were summed feature 3 (comprising C16 : 1  ω7c and/or C16 : 1  ω6c; 33.0 %), C16 : 1  ω5c (22.1 %), iso-C15 : 0 (12.6 %) and C16 : 0 (10.7 %). The polar lipids were composed of phosphatidylethanolamine, three unidentified aminophospholipids, one unidentified phospholipid and four unidentified lipids. Menaquinone-7 was detected as the sole respiratory quinone. The genomic DNA G+C content was 55.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain CJU-R4T and Spirosoma oryzae DSM 28354T were 81.5 and 23.9 %, respectively. Based on the results of the phenotypic and genotypic analyses, strain CJU-R4T is considered to represent a novel species of the genus Spirosoma , for which the name Spirosoma rhododendri sp. nov. is proposed. The type strain is CJU-R4T (=KACC 21264T=NBRC 114513T).

Adhaeribacter terrigena sp. nov., Isolated from Korean Soil

A bacterial strain, designated BT258^T, was isolated from a soil sample collected from Uijeongbu-si, Gyeong-do Province, Republic of Korea. Cells were Gram stain negative, aerobic, rod shaped, motile by gliding, and formed light pink-pigmented colonies on agar plates. Growth of the isolate was observed at 10-37 °C and pH 6-7. A 16S rRNA gene sequence analysis revealed that strain BT258^T is a member of the genus Adhaeribacter in the family Hymenobacteraceae and had the highest sequence similarity with 'Adhaeribacter soli' MA2^T (97.1%), Adhaeribacter terreus DNG6^T (96.6%), and Adhaeribacter terrae HY02^T (96.5%). The predominant respiratory quinone of the isolate was MK-7, the main polar lipid was phosphatidylethanolamine, and the major fatty acids were C_15:0 iso (37.7%), summed feature 4 (C_17:1 anteiso B/iso-C_17:1 I; 16.8%), and C_16:0 (10.3%). The draft genome of strain BT258^T had a whole length of 4,974,022 bp and DNA G + C content of 46.0 mol%. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the novel isolate and 'Adhaeribacter soli' and seven other Adhaeribacter species ranged from 17.9 to 22.7% and 69.7 to 77.9%, respectively. On the basis of its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain BT258^T represents a novel species in the genus Adhaeribacter, for which the name Adhaeribacter terrigena sp. nov. is proposed. The type strain is BT258^T (= KCTC 72409 ^T = JCM 34303 ^T).

Flavobacterium agrisoli sp. nov., a novel bacterium isolated from soil

A Gram-stain negative, rod shaped, motile by gliding, yellow-pigmented, aerobic bacterium, designated SE-1-e^T, was isolated from a soil sample collected on Dokdo Island, South Korea. The isolate was characterized taxonomically using a polyphasic approach based on the phenotypic and genomic analyses. The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SE-1-e^T belonged to the genus Flavobacterium in the family Flavobacteriaceae and had the highest sequence similarity with Flavobacterium cheongpyeongense IMCC34759^T (97.5%), Flavobacterium arsenitoxidans S2-3H^T (97.4%), Flavobacterium resistens BD-b365^T (97.4%), and Flavobacterium chungangense CJ7^T (97.4%). The predominant respiratory quinone of the isolate was found to be MK-6; the main polar lipid was phosphatidylethanolamine; and the major fatty acids were identified as summed feature 3 (C_16:1 ω7c/C_16:1 ω6c), C_15:0 iso, and C_16:0. The draft genome of strain SE-1-e^T had a length of 3,715,609 bp and a DNA G + C content of 34.8 mol%. The nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the novel isolate and F. cheongpyeongense IMCC34759^T, F. resistens BD-b365^T, and Flavobacterium chungangense CJ7^T ranged from 74.9 to 75.3% and from 20.2 to 20.9%, respectively. On the basis of its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain SE-1-e^T represents a novel species in the genus Flavobacterium, for which the name Flavobacterium agrisoli sp. nov. is proposed. The type strain is SE-1-e^T (= KCTC 82352 ^T = JCM 34302 ^T).

Spirosoma profusum sp. nov., and Spirosoma validum sp. nov., radiation-resistant bacteria isolated from soil in South Korea

Two novel Gram-negative, rod-shaped bacterial strains BT702^T and BT704^T were isolated from soil collected in Jeongseon (37° 22' 45″ N, 128° 39' 53″ E), Gangwon province, South Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains BT702^T and BT704^T belong to distinct lineage within the genus Spirosoma (family Cytophagaceae, order Cytophagales, class Cytophagia and phylum Bacteroidetes). The strain BT702^T was closely related to Spirosoma flavus 15J11-2^T (96.7% 16S rRNA gene similarity) and Spirosoma metallilatum TX0405^T (93.3%). The strain BT704^T was closely related to Spirosoma koreense 15J8-5^T (94.6%), Spirosoma endophyticum DSM 26130^T (93.8%) and Spirosoma humi S7-4-1^T (93.8%). The genome sizes of type strains BT702^T and BT704^T are 8,731,341 bp and 8,221,062 bp, respectively. The major cellular fatty acids of strains BT702^T and BT704^T were C_16:1 ω5c and summed feature 3 (C_16:1 ω6c/C_16:1 ω7c). The strains were found to have the same quinone system, with MK-7 as the major respiratory quinone. The major polar lipids of strain BT702^T was identified to be phosphatidylethanolamine (PE), aminophospholipid (APL) and aminolipid (AL), while that of strain BT704^T consisted of phosphatidylethanolamine (PE) and aminophospholipid (APL). Based on the polyphasic analysis (phylogenetic, chemotaxonomic and biochemical), strains BT702^T and BT704^T can be suggested as two new bacterial species within the genus Spirosoma and the proposed names are Spirosoma profusum and Spirosoma validum, respectively. The type strain of Spirosoma profusum is BT702^T (= KCTC 82115^T = NBRC 114859^T) and type strain of Spirosoma validum is BT704^T (= KCTC 82114^T = NBRC 114966^T).

Mucilaginibacter segetis sp. nov., Isolated from Soil

A bacterial strain, SD-g^T, was isolated from a soil sample collected on Dokdo Island, South Korea. Cells were observed to be Gram stain negative and short rod shaped, and colonies to be pink in color. Growth of the isolate was observed at 4-30 °C, pH 6-8, and in the presence of 0-2.0% NaCl. Analysis of 16S rRNA gene sequences identified strain SD-g^T as a member of the genus Mucilaginibacter in the family Sphingobacteriaceae, with high levels of sequence similarity with Mucilaginibacter terrenus ZH6^T (96.9%), Mucilaginibacter lutimaris BR-3^T (96.8%), Mucilaginibacter carri PR0008K^T (96.8%), Mucilaginibacter gilvus F01003^T (96.7%), Mucilaginibacter litoreus BR-18^T (96.6%), and Mucilaginibacter terrigena 17JY9-4^T (96.5%). The genomic DNA G+C content of strain SD-g^T was calculated to be 40.6 mol%. The predominant respiratory quinone of the isolate was found to be MK-7; the main polar lipid was phosphatidylethanolamine; and the major fatty acids were identified as summed feature 3 (C_16:1 ω7c/C_16:1 ω6c; 29.0%), C_15:0 iso (19.1%), C_15:0 iso (28.1%), C_16:0 (14.9%), and C_17:0 iso 3-OH (7.4%). The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SD-g^T and M. terrenus ZH6^T, M. gilvus F01003^T, and M. terrigena ranged from 17.7 to 18.4% and 72.1 to 74.0%, respectively. On the basis of its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain SD-g^T represents a novel species in the genus Mucilaginibacter, for which the name Mucilaginibacter segetis sp. nov. is proposed. The type strain is SD-g^T (= KCTC 82353^T = JCM 34284^T).

Spirosoma utsteinense sp. nov. isolated from Antarctic ice-free soils from the Utsteinen region, East Antarctica

Between 2014 and 2016, 16 Gram-stain-negative, aerobic, rod-shaped and yellow-orange pigmented bacteria were isolated from exposed soils from the Utsteinen region, Sør Rondane Mountains, East Antarctica. Analysis of their 16S rRNA gene sequences revealed that the strains form a separate cluster in the genus Spirosoma, with Spirosoma rigui KCTC 12531^T as its closest neighbour (97.8 % sequence similarity). Comparative genome analysis of two representative strains (i.e. R-68523^T and R-68079) of the new group with the type strains of Spirosoma rigui (its closest neighbour) and Spirosoma linguale (type species of the genus), yielded average nucleotide identity values of 73.9-78.7 %. Digital DNA-DNA reassociation values of the two strains and these type strains ranged from 20.3 to 22.0 %. The predominant cellular fatty acids of the two novel strains were summed feature 3 (i.e. C_16 : 1  ω7c and/or iso-C₁₅ 2-OH), C_16 : 1  ω5c, C_16 : 0 and iso-C_15 : 0. The new Spirosoma strains grew with 0-0.5 % (w/v) NaCl, at pH 6.5-8.0 and displayed optimum growth between 15 and 25 °C. Based on the results of phenotypic, genomic, phylogenetic and chemotaxonomic analyses, the new strains represent a novel species of the genus Spirosoma for which the name Spirosoma utsteinense sp. nov. is proposed. The type strain is R-68523^T (=LMG 31447^T=CECT 9925^T).

Spirosoma endbachense sp. nov., isolated from a natural salt meadow

A Gram-stain-negative bacterium, designated I-24^T, was isolated from soil of a natural salt meadow. Strain I-24^T was aerobic, non-motile, rod-shaped, catalase-positive, oxidase-positive and grew optimally at pH 7 and 25 °C. Comparative 16S rRNA gene analysis indicated that strain I-24^T has closest similarities to Spirosoma agri KCTC 52727^T (95.9 %) and Spirosoma terrae KCTC 52035^T (95.5 %). Strain I-24^T contained summed feature 3 (C_16 : 1  ω7c/C_16 : 1  ω6c) and C_16 : 1  ω5c as the major fatty acids, the predominant respiratory quinone was menaquinone MK-7, and the major polar lipids were phosphatidylethanolamine as well as an unidentified phosphoaminolipid. The draft genome of strain I-24^T consists of 10 326 072 base pairs with 9153 predicted coding sequences and a G+C content of 47.7 mol%. Clear distinctions between strain I-24^T and S. agri KCTC 52727^T or S. terrae KCTC 52035^T were shown in the pairwise average nucleotide identity results with values of 76.71 and 74.01 %, respectively. Moreover, the digital DNA-DNA relatedness values to these strains were 20.8 and 19.0 %. Based on its phenotypic, genotypic and chemotaxonomic characteristics, strain I-24^T represents a novel species of the genus Spirosoma, for which the name Spirosoma endbachense sp. nov. is proposed. The type strain is I-24^T (DSM 111055^T=KCTC 72613^T).

Draft Genome Sequences of Spirosoma agri KCTC 52727 and Spirosoma terrae KCTC 52035

Spirosoma agri S7-3-3 (KCTC 52727) and Spirosoma terrae 15J9-4 (KCTC 52035) are type strains isolated from an apple orchard and beach soil in South Korea, respectively; their draft genome sequences were assembled and annotated. The draft genome sequences of S7-3-3^T (7,239,915 bp; G+C content, 50.6%) and 15J9-4^T (7,551,610 bp; G+C content, 47.3%) are reported.

Spirosoma agri S7-3-3 (KCTC 52727) and Spirosoma terrae 15J9-4 (KCTC 52035) are type strains isolated from an apple orchard and beach soil in South Korea, respectively; their draft genome sequences were assembled and annotated. The draft genome sequences of S7-3-3^T (7,239,915 bp; G+C content, 50.6%) and 15J9-4^T (7,551,610 bp; G+C content, 47.3%) are reported.

Preferential flow paths shape the structure of bacterial communities in a clayey till depth profile

Preferential flow paths in subsurface soils serve as transport routes for water, dissolved organic matter and oxygen. Little is known about bacterial communities in flow paths or in subsoils below ∼4 m. We compared communities from preferential flow paths (biopores, fractures and sand lenses) with those in adjacent matrix sediments of clayey till from the plough layer to a depth of 6 m. 16S rRNA gene-targeted community analysis showed bacterial communities of greater abundance and diversity in flow paths than in matrix sediments at all depths. Deep fracture communities contained a higher relative abundance of aerobes and plant material decomposers like Nitrospirae, Acidobacteria and Planctomycetes than adjacent matrix sediments. Similarly, analyses of the relative abundances of archaeal amoA, nirK and dsrB genes indicated transition from aerobic to anaerobic nitrogen and sulphur cycling at greater depth in preferential flow paths than in matrix sediments. Preferential flow paths in the top 260 cm contained more indicator operational taxonomic units from the plough layer community than the matrix sediments. This study indicates that the availability of oxygen and organic matter and downward transport of bacteria shape bacterial communities in preferential flow paths, and suggests that their lifestyles differ from those of bacteria in matrix communities.