Reclassification of Enterobacter sp. FY-07 as Kosakonia oryzendophytica FY-07 and Its Potential to Promote Plant Growth

Shaojing Wang,Guoqiang Li,Nusratgul Anwar,Ting Ma,Yu Chen,Shaofang Niu,Shuai Chen,Ge Gao,Yan Zhang

doi:10.3390/microorganisms10030575

Abstract

Precise classification of bacteria facilitates prediction of their ecological niche. The genus Enterobacter includes pathogens of plants and animals but also beneficial bacteria that may require reclassification. Here, we propose reclassification of Enterobacter FY-07 (FY-07), a strain that has many plant-growth-promoting traits and produces bacterial cellulose (BC), to the Kosakonia genera. To re-examine the taxonomic position of FY-07, a polyphasic approach including 16S rRNA gene sequence analysis, ATP synthase β subunit (atpD) gene sequence analysis, DNA gyrase (gyrB) gene sequence analysis, initiation translation factor 2 (infB) gene sequence analysis, RNA polymerase β subunit (rpoB) gene sequence analysis, determination of DNA G + C content, average nucleotide identity based on BLAST, in silico DNA–DNA hybridization and analysis of phenotypic features was applied. This polyphasic analysis suggested that Enterobacter sp. FY-07 should be reclassified as Kosakonia oryzendophytica FY-07. In addition, the potential of FY-07 to promote plant growth was also investigated by detecting related traits and the colonization of FY-07 in rice roots.

Highlights

With Kosakonia oryzendophytica LMG 16432T (Figure 1). These results indicated that FY-07 was closely related to the genus Kosakonia
R4-368 should probably be reclassified to the genus Kosakonia, and it is indicated that there may be many bacteria in the genus Enterobacter that have not been correctly classified
These results confirmed the reliability of the multilocus sequence analysis (MLSA) method for identifying the taxonomic status of Enterobacteriaceae, and strongly supported that the strain FY-07 should be transferred to the genus Kosakonia

Summary

Introduction

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Many studies have shown that due to the low phylogenetic resolution of 16S rRNA gene, it is difficult to classify a species into the genus Enterobacter only by analyzing the 16S rRNA gene sequence [2]. Enterobacter into several genera including Kosakonia through multilocus sequence analysis (MLSA) [3]. Most Kosakonia strains are isolated from commercial crops including maize, rice, sugarcane, cotton, wheat, and have been found to promote the growth of host plants [8,9]. The effect of these strains on promoting plant growth is attributed to the strain’s ability to biologically fix atmospheric nitrogen, dissolve rock phosphates and secrete plant growth hormones [10]. Its potential to promote plant growth was investigated by measuring its ability of IAA (Indoleacetic acid) production, siderophore production, ammonia production, solubilization for insoluble phosphate and potassium, nitrogen fixation, 1aminocyclopropane-1-carboxylic acid (ACC) deaminase production

Materials

Sequences Acquisition and Phylogenetic Analysis

Comparative Genomics Analysis

IAA Production

Siderophore Production

Phosphate Solubilization

Nitrogen Fixation

Ammonia Production

ACC Deaminase Production

Colonization of Rice Roots

Phylogenetic Analysis

Biochemical Characteristics of FY-07