Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil

Abstract

Three novel bacterial strains, designated Vu-144 T , Vu-7 and Vu-35, were isolated on minimal medium from rhizosphere soil of field-grown cowpea and subjected to a taxonomic study using a polyphasic approach. Cells of the strains were Gram-stain-negative, non-motile, non-sporeforming, coccoid rods, and formed non-pigmented colonies. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Vu-144 T was affiliated with an uncultivated lineage of the phylum Bacteroidetes. Its closest phylogenetic neighbour was the recently described species Niastella populi, a member of the family Chitinophagaceae, with just 90.7 % sequence similarity to the type strain. The only isoprenoid quinone detected was menaquinone 7 (MK-7). The fatty acid profiles showed large amounts of iso-C 15 : 0 , iso-C 17 : 0 3-OH and iso-C 15 : 1 G and minor amounts of summed feature 3 (C 16 : 1 v7c and/or iso-C 15 : 0 2-OH), C 16 : 0 and other fatty acids, allowing the differentiation of the strains from other genera. The G+C content of the genomic DNA of the three strains ranged from 43.1 to 44.3 mol%. In addition to phosphatidylethanolamine, the major polar lipids were three unidentified aminophospholipids (APL1-APL3), two unidentified phospholipids (PL1, PL2) and three unidentified lipids (UL1-UL3). Biochemical test patterns also differed from those of Niastella populi and members of other genera. All three isolates showed plant-growth-promoting properties, e.g. the ability to produce indole-3-acetic acid and NH 3 and to solubilize phosphate, utilized 1-aminocyclopropane 1-carboxylate (ACC) as a sole source of nitrogen and possessed the ACC deaminase enzyme. The novel isolates readily colonized roots and stimulated growth of tomato and cowpea under glasshouse conditions. Inoculated plants showed a 45-60 % increase in dry matter weight with respect to uninoculated controls. On the basis of the evidence from our polyphasic study, isolate Vu-144 T represents a novel genus and species in the family Chitinophagaceae, for which the name Arachidicoccus rhizosphaerae gen. nov., sp. nov. is proposed. The type strain of Arachidicoccus rhizosphaerae is Vu-144 T (5KCTC 22378 T 5NCIMB 14473 T). Abbreviations: ACC, 1-aminocyclopropane 1-carboxylate; IAA, indole-3acetic acid. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains Vu-144 T , Vu-35 and Vu-7 are EU672808, EU672809 and EU672810, respectively. Two supplementary tables and five supplementary figures are available with the online Supplementary Material.

Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil

“…Similarly, some affiliates of this family show diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE) as the major polar lipids. At the time of writing, the family Chitinophagaceae contained 31 genera including the following recently described genera with validly published names: Hydrobacter (Eder et al, 2015), Parasediminibacterium (Kang et al, 2016), Flaviaesturariibacter (Kang et al, 2015), Arachidicoccus (Madhaiyan et al, 2015), Thermoflavifilum (Anders et al, 2014), Vibrionimonas (Albert et al, 2014) and Cnuella (Zhao et al, 2014). Based on 16S rRNA gene sequence similarity, the family Chitinophagaceae possesses not only a large number of genera but also shows wide phylogenetic extent between species (minimum 90 %) in the family (Hanada et al, 2014).…”

Microbial Toluene Removal in Hypoxic Model Constructed Wetlands Occurs Predominantly via the Ring Monooxygenation Pathway

“…Toluene degraders such as Comamonas testosteroni R5, Methylibium petroleiphilum, Ralstonia pickettii PKO1, and Burkholderia vietnamensis G4 are prominent members of these families (47)(48)(49)(50). Bacteria belonging to the less represented families (Յ3%) Sphingobacteriaceae, Chitinophagaceae, Rhodocyclaceae, and Bradyrhizobiaceae have been detected in diverse environments, including soil, rhizosphere, and as endophytes (51)(52)(53), and some of them have been also associated with aromatic compound degradation (54,55). Although the bacterial compositions of the two PFRs were globally similar, one remarkable difference was the higher representation (6%) of the family Rhodospirillaceae in PFR-2.…”

Compostibacter hankyongensis gen. nov.,  sp. nov., isolated from compost

“…Some affiliates of the family Chitinophagaceae which have been described recently show phosphatidylethanolamine as the major polar lipid (Siddiqi & Im, 2016a, b;Eder et al, 2015;Albert et al, 2014;Lee et al, 2013;Leandro et al, 2013). Members of this family are widespread microorganisms commonly isolated from various sources, including purified water (Eder et al, 2015), wetland (Kang et al, 2016), estuarine water , rhizosphere soil (Madhaiyan et al, 2015), hot springs (Anders et al, 2014), lake water (Albert et al, 2014) and Takakia lepidozioides (Zhao et al, 2014).…”