Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost

Abstract

BackgroundPlant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range of environments, including soil.ResultsHere we describe the genome sequencing and assessment of plant growth-promoting abilities of S. marcescens UENF-22GI, a strain isolated from mature cattle manure vermicompost. In vitro, S. marcescens UENF-22GI is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with this strain remarkably increased seedling growth and biomass under greenhouse conditions. The S. marcescens UENF-22GI genome has 5 Mb, assembled in 17 scaffolds comprising 4662 genes (4528 are protein-coding). No plasmids were identified. S. marcescens UENF-22GI is phylogenetically placed within a clade comprised almost exclusively of non-clinical strains. We identified genes and operons that are likely responsible for the interesting plant-growth promoting features that were experimentally described. The S. marcescens UENF-22GI genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to its competitiveness against other bacteria.ConclusionsCollectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for agriculture.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5130-y) contains supplementary material, which is available to authorized users.

Pseudomonas PS01 Isolated from Maize Rhizosphere Alters Root System Architecture and Promotes Plant Growth

“…Therefore, it is highly desirable to use phylogenomic data for exact taxonomy classification. In this context, high-throughput sequencing technologies and genome annotation have provided whole-genome sequencing as an efficient tool for not only bacteria classification but also provide insight into the molecular mechanisms and functional capabilities of PGPR [24,25]. Recently, whole genome sequencing has been applied to study the genome of some Pseudomonas species, such as, Pseudomonas sp.…”

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence of blaCTX-M-55, blaNDM-5 and blaIMI-1, along with sophisticated iron acquisition strategies

“…The sequencing procedures and basic data processing were performed as previously described [53]. In summary, paired-end libraries were prepared with the TruSeq Nano DNA LT Library Prep (Illumina) and sequenced on a HiSeq 2500 instrument at the Life Sciences Core Facility (LaCTAD; UNICAMP, Campinas, Brazil).…”

Mutualistic interaction with Trichoderma longibrachiatum UENF-F476 boosted plant growth-promotion of Serratia marcescens UENF-22GI

“…Genome sequencing and plant growth-promotion traits of Serratia marcescens strain UENF-22GI were detailed reported at Matteoli and colleagues (27).…”

“…The physical colony-colony compatibility between Sm-22GI and Tl-F476 was demonstrated. Curiously, the same strain was effective in countering two phytopathogenic fungi (27,28). The previous results were confirmed by evaluating the same strains over ten days (10-d) incubation time, according (27).…”

“…Overall ecological advantages suggest that certain saprotrophic fungi may be selected to enhance the ecological fitness and beneficial properties of PGPB that give rise to several potential technological applications on bacterial-fungal interactions. In the present study, a well-characterized plant growth-promoting bacterium Serratia marcescens (Sm-22GI) strain UENF-22GI (27) and the saprotrophic fungi Trichoderma longibrachiatum (Tl-F476) UENF-F476 were combined to test potential enhancement of the bacteria ecological fitness and plant growth-promoting properties in-vitro and exvitro. The taxonomic position of the fungi at species level was defined herein, and the compatible colony-colony physical interaction between Sm-22GI and Tl-F476 was previously demonstrated (28).…”