Enterobacter arachidis sp. nov., a plant-growth-promoting diazotrophic bacterium isolated from rhizosphere soil of groundnut

Abstract

A methylotrophic nitrogen-fixing bacterial strain, Ah-143 T , isolated from the rhizosphere soil of field-grown groundnut was analysed by a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis combined with rpoB gene sequence analysis allocated strain Ah-143 T to the family Enterobacteriaceae, with Enterobacter radicincitans and Enterobacter cowanii as the closest relatives. The strain is Gram-stain-negative, non-spore-forming, aerobic and motile, having straight rod-shaped cells with a DNA G+C content of approximately 53.2 mol%. The strain utilizes methanol as a carbon source and the mxaF gene was closely related to the mxaF gene of members of the genus Methylobacterium. The fatty acid profile consisted of C 16 : 0 , C 17 : 0 cyclo, C 18 : 1 v7c, summed feature 2 (iso-C 16 : 1 I and/or C 14 : 0 3-OH) and summed feature 3 (iso-C 15 : 0 2-OH and/or C 16 : 1 v7c) as the major components. DNA-DNA relatedness of strain Ah-143 T with its close relatives was less than 20 %. On the basis of the phylogenetic analyses, DNA-DNA hybridization data, and unique physiological and biochemical characteristics, it is proposed that the strain represents a novel species of the genus Enterobacter and should be named Enterobacter arachidis sp. nov. The type strain is Ah-143 T (5NCIMB 14469 T 5KCTC 22375 T ).The genus Enterobacter is clearly separated from other groups, forming a distinct branch, and at the time of writing included 22 species with validly published names (http://www.bacterio.cict.fr/e/enterobacter.html), Enterobacter cloacae being the type species (Hormaeche & Edwards, 1960). Members of the genus Enterobacter are detected in various environments, such as infant formula (Stephan et al., 2007(Stephan et al., , 2008, clinical specimens (Brenner et al., 1986;Hoffmann et al., 2005) and in association with plants (Egamberdieva et al., 2008; Kämpfer et al., 2005). Several species of the genus Enterobacter are known to interact and exert beneficial effects on plant growth. The plant-growthpromoting effects of beneficial bacteria may occur through direct or indirect mechanisms that include production of phytohormones or enzymes that promote plant growth, increased nutrient uptake, and prevention of deleterious phytopathogens (Glick et al., 1999;Whipps, 2001). The complex mixture of carbohydrates, amino acids, organic acids and other nutrients released from seeds and roots are thought to support the growth of beneficial bacteria such as E. cloacae in the spermosphere and rhizosphere. E. cloacae colonizes the spermospheres and rhizospheres of a number Abbreviation: ACCD, 1-aminocyclopropane-1-carboxylate deaminase.The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, rpoB, nifH and mxaF gene sequences of strain Ah-143 T are EU672801, FJ768683, FJ460712 and EU912491, respectively.Phase-contrast and scanning electron micrographs of cells of strain Ah-143 T , phylogenetic trees based on rpoB and nifH gene sequences, and cellular fatty acid compositions of strain Ah-143 T and related species of the genus...

Budvicia diplopodorum sp. nov. and emended description of the genus Budvicia

“…The component C 17 : 0 was found in three members of the genus Yersinia tested in this study and has been reported for the genus Yersinia and other genera within the family Enterobacteriaceae by other authors (Jantzen & Lassen, 1980;Kämpfer et al, 2005;Whittaker et al, 2005;Madhaiyan et al, 2010;Rameshkumar et al, 2010).…”

Reclassification of Enterobacter oryziphilus and Enterobacter oryzendophyticus as Kosakonia oryziphila comb. nov. and Kosakonia oryzendophytica comb. nov.

“…Although K. sacchari was not included in the study of Hardoim et al (2013), low similarities (90.8 % and 92.0 %; Table S4) between strains LMG 26429 T and LMG 26432 T and K. sacchari LMG 26783 T showed that strains LMG 26429 T and LMG 26432 T represent two different species from K. sacchari. Hardoim et al (2013) reported that the DNA-DNA relatedness values between K. radicincitans LMG 23767 T and K. oryzae LMG 24251 T , between K. radicincitans LMG 23767 T and K. arachidis KCTC 22375 T , and between K. oryzae LMG 24251 T and K. arachidis KCTC 22375 T were 79±6 % (higher than the result reported by Peng et al in 2009), 66±17 % (higher than the result reported by Madhaiyan et al in 2010) and 71±2 %, respectively, suggesting these three species probably had a close relationship. In the present study, four housekeeping gene sequences (rpoB, atpD, gyrB and infB) were available for all these three species, so their taxonomic status was re-examined by multilocus sequence analysis based upon concatenated partial rpoB, atpD, gyrB and infB gene sequences.…”

“…Distinction of K. arachidis and K. radicincitans was also supported by fatty acid profiles (Madhaiyan et al, 2010;Hardoim et al, 2013).…”

“…Table 1. Phenotypic features that differentiate E. oryziphilus and E. oryzendophyticus from all defined species of the genus Kosakonia Species: 1, E. oryziphilus (Hardoim et al, 2013); 2, E. oryzendophyticus (Hardoim et al, 2013); 3, K. oryzae (Peng et al, 2009) (Madhaiyan et al, 2010); 6, K. cowanii (Inoue et al, 2000); 7, K. sacchari (Zhu et al, 2013). +, 80 % or more of strains positive; -, 80 % or more strains of negative; d, 20-80 % of strains positive.…”

Complete genome sequence of Kosakonia oryzae type strain Ola 51T

“… Enterobacter cowanii [1], E. radicincitans [2], E. oryzae [3], E. arachidis [4], E. sacchari [5], E. oryziphilus [6, 7], and E. oryzendophyticus [6, 7] have been transferred into the novel genus Kosakonia of the family “ Enterobacteriaceae ” [8–10]. A novel species “ Kosakonia pseudosacchari” [11] closely related to K. sacchari was recently proposed.…”