Comparative Genomics Reveal a Flagellar System, a Type VI Secretion System and Plant Growth-Promoting Gene Clusters Unique to the Endophytic Bacterium Kosakonia radicincitans

Abstract

The recent worldwide discovery of plant growth-promoting (PGP) Kosakonia radicincitans in a large variety of crop plants suggests that this species confers significant influence on plants, both in terms of yield increase and product quality improvement. We provide a comparative genome analysis which helps to unravel the genetic basis for K. radicincitans' motility, competitiveness and plant growth-promoting capacities. We discovered that K. radicincitans carries multiple copies of complex gene clusters, among them two flagellar systems and three type VI secretion systems (T6SSs). We speculate that host invasion may be facilitated by different flagella, and bacterial competitor suppression by effector proteins ejected via T6SSs. We found a large plasmid in K. radicincitans DSM 16656T, the species type strain, that confers the potential to exploit plant-derived carbon sources. We propose that multiple copies of complex gene clusters in K. radicincitans are metabolically expensive but provide competitive advantage over other bacterial strains in nutrient-rich environments. The comparison of the DSM 16656T genome to genomes of other genera of enteric plant growth-promoting bacteria (PGPB) exhibits traits unique to DSM 16656T and K. radicincitans, respectively, and traits shared between genera. We used the output of the in silico analysis for predicting the purpose of genomic features unique to K. radicincitans and performed microarray, PhyloChip, and microscopical analyses to gain deeper insight into the interaction of DSM 16656T, plants and associated microbiota. The comparative genome analysis will facilitate the future search for promising candidates of PGPB for sustainable crop production.

Phage tail-like particles are versatile bacterial nanomachines – A mini-review

“…Kosakonia radicincitans is a bacterium of the Gram-negative family Enterobacteriaceae with plant growth-promoting properties [37]. The species has been found to be a native endophyte of a large variety of crop plants around the world [38]. Type strain DSM 16656 was repeatedly inoculated into diverse plant species and proved capable of establishing biofilms on roots [39].…”

“…Type strain DSM 16656 was repeatedly inoculated into diverse plant species and proved capable of establishing biofilms on roots [39]. Comparison of the genome of DSM 16656 to other fully sequenced genomes of K. radicincitans and closely related bacterial taxa revealed that all to date known members of K. radicincitans exhibit genomic features that are absent from other closely related bacterial species, such as a duplicated flagellar system and an additional type VI secretion system [38].…”

First Report of Kosakonia radicincitans Bacteraemia from Europe (Austria) - Identification and Whole-Genome Sequencing of Strain DSM 107547

“…The first case of a human bloodstream infection with K. radicincitans was reported in a 61-year-old man with cholangiocarcinoma in Houston, TX, USA, in Dec. 2016 4 . Unfortunately, the authors of this report considered some common features of enteric bacteria to be virulence factors, and confused type IV secretion systems with type IV pili that are involved in several phenomena, not only pathogenicity 12 . Comparison of the cases from Austria and the USA showed that both patients had problems in the bile duct system.…”

Whole-Genome Sequence of a Plant Growth-Promoting Strain, Serratia marcescens BTL07, Isolated from the Rhizoplane of Capsicum annuum L

“…Genome analyses divulged a number of orthologs to innate plant growthpromoting genes for facilitating sustained production, such as those encoding stimulation of seedling germination (amyAS) and growth promotion (nasD, glnA, and nirD; phoABPR, acpho, phnCDEFGHJKLMNP, pqqCDEF, and gcd; and kdpABCDE and trkADGH) by inducing NPK uptake (10)(11)(12)(13)(14), heat shock proteins (dnaJK, groEL, and clpP), cold shock proteins (cspACDE and csh), and trehalose biosynthesis (otsAB), involved in abiotic stress tolerance (10). Furthermore, some genes involved in biocontrol functions, for instance, production of hydrogen cyanide (hcnABC), cell wall-degrading enzyme (chiDE), and acetoin (alsS and gdh) (10,11,15,16), and heavy metal efflux-mediated proteins (arsB, czcD, and nikAB) for arsenic, cadmium, cobalt, zinc, and nickel were incorporated in the genome of BTL07. Functional annotation also detected genes related to IAA phytohormones (dhaS, bioA, patB, and aldA), a siderophore (entABCDES), and antioxidant enzymes (katEG, sodABC, and bsaA) in this genome; these genes are likely to be linked with plant growth promotion by both direct and indirect pathways (10,11).…”

“…Furthermore, some genes involved in biocontrol functions, for instance, production of hydrogen cyanide (hcnABC), cell wall-degrading enzyme (chiDE), and acetoin (alsS and gdh) (10,11,15,16), and heavy metal efflux-mediated proteins (arsB, czcD, and nikAB) for arsenic, cadmium, cobalt, zinc, and nickel were incorporated in the genome of BTL07. Functional annotation also detected genes related to IAA phytohormones (dhaS, bioA, patB, and aldA), a siderophore (entABCDES), and antioxidant enzymes (katEG, sodABC, and bsaA) in this genome; these genes are likely to be linked with plant growth promotion by both direct and indirect pathways (10,11).…”