Aeromicrobium terrae sp. nov., isolated from a maize field

Description of Flavobacterium agricola sp. nov., an auxin producing bacterium isolated from paddy field

An auxin-producing bacterial strain, CC-SYL302T, was isolated from paddy soil in Taiwan and identified using a polyphasic taxonomic approach. The cells were observed to be aerobic, non-motile, non-spore-forming rods, and tested positive for catalase and oxidase. Produced carotenoid but flexirubin-type pigments were absent. Optimal growth of strain CC-SYL302T was observed at 25 °C, pH 7.0, and with 2% (w/v) NaCl present. Based on analysis of 16S rRNA gene sequences, it was determined that strain CC-SYL302T belongs to the genus Flavobacterium of the Flavobacteriaceae family. The closest known relatives of this strain are F. tangerinum YIM 102701-2 T (with 93.3% similarity) and F. cucumis R2A45-3 T (with 93.1% similarity). Digital DNA-DNA hybridization (dDDH) values were calculated to assess the genetic distance between strain CC-SYL302T and its closest relatives, with mean values of 21.3% for F. tangerinum and 20.4% for F. cucumis. Strain CC-SYL302T exhibited the highest orthologous average nucleotide identity (OrthoANI) values with members of the Flavobacterium genus, ranging from 67.2 to 72.1% (n = 22). The dominating cellular fatty acids (> 5%) included iso-C14:0, iso-C15:0, iso-C16:0, iso-C15:0 3-OH, iso-C17:0 3-OH, C16:1 ω6c/C16:1 ω7c and C16:0 10-methyl/iso-C17:1 ω9c. The polar lipid profile consisted of phosphatidylethanolamine, an unidentified aminolipid, an unidentified aminophospholipid, and nine unidentified polar lipids. The genome (2.7 Mb) contained 33.6% GC content, and the major polyamines were putrescine and sym-homospermidine. Strain CC-SYL302T exhibits distinct phylogenetic, phenotypic, and chemotaxonomic characteristics, as well as unique results in comparative analysis of 16S rRNA gene sequence, OrthoANI, dDDH, and phylogenomic placement. Therefore, it is proposed that this strain represents a new species of the Flavobacterium genus, for which the name Flavobacterium agricola sp. nov. is proposed. The type strain is CC-SYL302T (= BCRC 81320 T = JCM 34764 T).

Aeromicrobium stalagmiti sp. nov., isolated from a lava cave

A Gram-reaction-positive, strictly aerobic, non-sporulating, non-motile, rod-shaped bacterium, designated YC3-14T, was isolated from pieces of stalagmite collected in a lava cave in Jeju, Republic of Korea. Cells showed growth at 15–35 °C, pH 6.0–9.0 and with 0–3 % (w/v) NaCl. Colonies of the cells were circular, smooth, convex and cream in colour. A 16S rRNA gene-based neighbour-joining tree indicated that the organism belonged to the genus Aeromicrobium and formed a sublineage between an Aeromicrobium endophyticum–Aeromicrobium fastidiosum cluster and an Aeromicrobium yanjiei–Aeromicrobium chenweiae cluster. The highest 16S rRNA gene similarity values of strain YC3-14T were with the type strains of A. yanjiei (99.2 %), A. endophyticum (99.1 %), A. fastidiosum (98.8 %), A. ginsengisoli (98.8 %) and A . chenweiae (98.7 %). The cell-wall peptidoglycan contained ll-diaminopimelic acid as the diagnostic diamino acid. The major menaquinone was MK-9(H4). The predominant fatty acids were C18 : 0.10-methyl, C18 : 1  ω9c and C16 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and two unidentified lipids. The G+C content of the genome DNA was 69.9 mol%. These chemotaxonomic features of the isolate were typical for the genus Aeromicrobium . The genome-based phylogeny showed the same tree topology as the 16S rRNA gene phylogeny. The average nucleotide identity (≤84.5 %) and digital DNA–DNA hybridization (≤27.5 %) values supported that the isolate belongs to a novel species of the genus Aeromicrobium . On the basis of data obtained by a polyphasic approach, strain YC3-14T (=KCTC 49469T=NBRC 114653T) represents a novel species of the genus Aeromicrobium , for which the name Aeromicrobium stalagmiti sp. nov. is proposed.

Zeimonas arvi gen. nov., sp. nov., of the family Burkholderiaceae, harboring biphenyl- and phenolic acid-metabolizing genes, isolated from a long-term ecological research field

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT501^T, harboring xenobiotic- and allelochemical-metabolizing genes, isolated from a long-term ecological research field in Taiwan. Cells of strain CC-CFT501^T were catalase- and oxidase-positive, non-motile and short rods. Optimal growth occurred at 30 °C, pH 8 and 1% NaCl. Strain CC-CFT501^T was found to share high 16S rRNA gene sequence similarity with the members of genera Quisquiliibacterium (94.3%, n = 1), Pandoraea (93.4-94.0%, n = 23) and Paraburkholderia (93.3-94.0%, n = 9), affiliated to the family Burkholderiaceae. Strain CC-CFT501^T shared 76.4% orthologous average nucleotide identity (OrthoANI) and 20.9% digital DNA-DNA hybridization (dDDH) values with Quisquiliibacterium transsilvanicum DSM 29781^T. Draft genome sequence (3.83 Mb) of strain CC-CFT501^T revealed several genes encoding the proteins involved in biphenyl and phenolic acid metabolism. Fatty acid profile contained C_16:0, C_18:0, C_10:0 3-OH, C_16:1 ω7c/C_16:1 ω6c and C_18:1 ω7c/C_18:1 ω6c in predominant amounts. The polar lipid profile consisted of phosphatidylethanolamine, thirteen unidentified amino lipids, two unidentified phospholipids and two unidentified glycolipids. The major polyamine was spermidine and ubiquinone Q-8 was the sole respiratory quinone. The DNA G + C content was 70.0 mol%. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-CFT501^T is considered to represent a novel genus and species of the family Burkholderiaceae, for which the name Zeimonas arvi gen. nov., sp. nov. is proposed. The type strain of the type species is CC-CFT501^T (= BCRC 81218^T = JCM 33506^T).