Whole genome analysis of halotolerant and alkalotolerant plant growth-promoting rhizobacterium Klebsiella sp. D5A

Abstract

This research undertook the systematic analysis of the Klebsiella sp. D5A genome and identification of genes that contribute to plant growth-promoting (PGP) traits, especially genes related to salt tolerance and wide pH adaptability. The genome sequence of isolate D5A was obtained using an Illumina HiSeq 2000 sequencing system with average coverages of 174.7× and 200.1× using the paired-end and mate-pair sequencing, respectively. Predicted and annotated gene sequences were analyzed for similarity with the Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme database followed by assignment of each gene into the KEGG pathway charts. The results show that the Klebsiella sp. D5A genome has a total of 5,540,009 bp with 57.15% G + C content. PGP conferring genes such as indole-3-acetic acid (IAA) biosynthesis, phosphate solubilization, siderophore production, acetoin and 2,3-butanediol synthesis, and N2 fixation were determined. Moreover, genes putatively responsible for resistance to high salinity including glycine-betaine synthesis, trehalose synthesis and a number of osmoregulation receptors and transport systems were also observed in the D5A genome together with numerous genes that contribute to pH homeostasis. These genes reveal the genetic adaptation of D5A to versatile environmental conditions and the effectiveness of the isolate to serve as a plant growth stimulator.

Novel consortium ofKlebsiella variicolaandLactobacillusspecies enhances the functional potential of fermented dairy products by increasing the availability of branched-chain amino acids and the amount of distinctive volatiles

“…On the other hand, K. variicola has been reported to grow at pH values between 4 and 10, surviving acidic pH through phosphate uptake and the expression of amino acid decarboxylases (Liu et al . ). These facts could contribute to its survival in the consortium.…”

“…The antagonistic activity of Lactobacillus species is mainly due to the production of organic acids and the consequent reduction in pH (Zhang et al 2011;Belicov a et al 2013). On the other hand, K. variicola has been reported to grow at pH values between 4 and 10, surviving acidic pH through phosphate uptake and the expression of amino acid decarboxylases (Liu et al 2016). These facts could contribute to its survival in the consortium.…”

“…The production of these volatiles is the result of the metabolic contribution of K. variicola 35H. This strain possesses the metabolic pathways for the production of acetoin and 2,3-butanediol from pyruvate, which is related to the fermentative capacity of citrate and fermentable sugars (Bandell et al 1998;Liu et al 2016). Enterobacteriaceae capable of degrading citrate can produce ethanol, acetoin, diacetyl and 2,3-butanediol during the fermentation of milk, while within LAB, acetoin production is limited to some strains of Lc.…”

Genome Insights of the Plant-Growth Promoting Bacterium Cronobacter muytjensii JZ38 With Volatile-Mediated Antagonistic Activity Against Phytophthora infestans

“…JZ38 contains genes encoding polyamine transporters (potABCD, potFGHI, potE, puuP), for synthesis of putrescine from L-arginine (speAB) and L-orthinine (two copies of speC), its conversion to spermidine (speE) and N-acetyl spermidine (speG), synthesis of spermidine from S-adenosyl-L-methionine (speD), and synthesis of cadaverine from L-lysine (cadA) (Furuchi et al, 1991;Pistocchi et al, 1993;Kashiwagi et al, 1997;Kurihara et al, 2005) ( Supplementary Table S8). In the case of pH, a number of genes found in JZ38 were previously shown to be involved in acid resistance, including antiporters (nhaA, nhaB, nhaP2, chaA, yrbG), molecular chaperones (groEL, dnaK), starvation inducible proteins (two copies of phoH, dps), ATPases (atpABCDEFGHI), sigma factors and regulators (rpoS, ariR, nhaR) transcriptional repressor LexA (lexA) and proteases (clpXP) (Kuhnert et al, 2004;Guazzaroni et al, 2013;Liu et al, 2016) ( Supplementary Table S8). JZ38 also possesses genes encoding for resistance to heavy metals such as copper (copA, copC, copD, cueO, cueR, bhsA) and zinc/cadmium/cobalt (zntA, zntR), arsenate (arsC1) and chromate (chrR) ( Supplementary Table S9).…”

Sodium-resistant plant growth-promoting rhizobacteria isolated from a halophyte, Salsola grandis, in saline-alkaline soils of Turkey

“…To date, some bacteria such as Klebsiella sp. D5A showed the high plant growth promoting activity on the glycophytic crop in saline-alkaline soils (Liu et al, 2014;Liu et al, 2016). Likewise, many studies have been published on beneficial effects of bacterial application on growth of wheat under salt stress (Ashraf et al, 2004;Sadeghi et al, 2012;Upadhyay et al, 2012;Chakraborty et al, 2013;Paul and Lade, 2014).…”