Draft Genome Sequence of Raoultella terrigena R1Gly, a Diazotrophic Endophyte

Schicklberger, Marcus; Shapiro, Nicole; Loqué, Dominique; Woyke, Tanja; Chakraborty, Romy

doi:10.1128/genomea.00607-15

Cited by 19 publications

(18 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…began to surface. Through the rise of applying WGS for bacterial isolates from environmental samples, detailed genomic information became available for Raoultella ornithinolytica isolated from soil, Raoultella planticola isolated from river water, and the diazotrophic endophyte Raoultella terrigena isolated from Nicotiana tabacum [ 46 – 48 ]. With respect to diazotrophic associations with cereal crops, recent investigation into a diazotrophic strain of R .…”

Section: Discussionmentioning

confidence: 99%

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts

et al. 2020

View full text Add to dashboard Cite

Sierra Mixe maize is a geographically remote landrace variety grown on nitrogen-deficient fields in Oaxaca, Mexico that meets its nutritional requirements without synthetic fertilizer by associating with free-living diazotrophs comprising the microbiota of its aerial root mucilage. We selected nearly 500 diazotrophic (N 2 -fixing) bacteria isolated from Sierra Mixe maize mucilage and sequenced their genomes. Comparative genomic analysis demonstrated that isolates represented diverse genera and composed three major diazotrophic groups based on nitrogen fixation gene content. In addition to nitrogen fixation, we examined deamination of 1-amino-1-cyclopropanecarboxylic acid, biosynthesis of indole-3-acetic acid, and phosphate solubilization as alternative mechanisms of direct plant growth promotion (PGP). Genome mining showed that isolates of all diazotrophic groups possessed marker genes for multiple mechanisms of direct plant growth promotion (PGP). Implementing in vitro assays corroborated isolate genotypes by measuring each isolate’s potential to confer the targeted PGP traits and revealed phenotypic variation among isolates based on diazotrophic group assignment. Investigating the ability of mucilage diazotrophs to confer PGP by direct inoculation of clonally propagated potato plants in planta led to the identification of 16 bio-stimulant candidates. Conducting nitrogen-stress greenhouse experiments demonstrated that potato inoculation with a synthetic community of bio-stimulant candidates, as well as with its individual components, resulted in PGP phenotypes. We further demonstrated that one diazotrophic isolate conferred PGP to a conventional maize variety under nitrogen-stress in the greenhouse. These results indicate that, while many diazotrophic isolates from Sierra Mixe maize possessed genotypes and in vitro phenotypes for targeted PGP traits, a subset of these organisms promoted the growth of potato and conventional maize, potentially through the use of multiple promotion mechanisms.

show abstract

Section: Discussionmentioning

confidence: 99%

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Klebsiella planticola , K. ornithinolytica and K. terrigena were reclassified as Raoultella planticola , R. ornithinolytica and R. terrigena , respectively . N 2 ‐fixing Raoultella has long been found to associate with plants , but its N 2 fixation in association with plants has not been determined.…”

Section: Introductionmentioning

confidence: 99%

“…Klebsiella planticola, K. ornithinolytica and K. terrigena were reclassified as Raoultella planticola, R. ornithinolytica and R. terrigena, respectively [11]. N 2 -fixing Raoultella has long been found to associate with plants [3][4][5][12][13][14][15][16][17][18], but its N 2 fixation in association with plants has not been determined. N 2 -fixing strain L03 was isolated from surfacesterilized roots of a sugarcane cultivar GT28 plant grown in Nanning, Guangxi, China [19].…”

Section: Introductionmentioning

confidence: 99%

Raoultellasp. strain L03 fixes N₂in association with micropropagated sugarcane plants

Luo

Ou-Yang

Yang

et al. 2016

J. Basic Microbiol.

View full text Add to dashboard Cite

N2 -fixing bacteria belonging to the genus Raoultella of the family Enterobacteriaceae are widely associated with plants. Raoultella sp. strain L03 was isolated from surface-sterilized sugarcane roots. In this study, we inoculated the strain L03 to microbe-free micropropagated plantlets of the main sugarcane cultivar ROC22 grown in Guangxi, China and determined N2 -fixation and association between strain L03 and sugarcane plants. Inoculation of strain L03 increased plant biomass, total N, N concentration and chlorophyll, and relieved N-deficiency symptoms of plants under an N-limiting condition. An (15) N isotope dilution assay revealed (15) N isotope dilution in the inoculated sugarcane plants and incorporation of the fixed (14) N from air into chlorophyll. Moreover, a gfp-tagged and antibiotic-resistant L03 strain was reisolated from surface-sterilized sugarcane plants and was detected in plant tissues by fluorescent microscopy. This study for the first time demonstrates that a Raoultella bacterium is able to fix N2 in association with the plant host.

show abstract

“…Accordingly, all of K. pneumoniae isolate genomes are predicted to encode the capacity for nitrogen fixation, consistent with previous results (14, 26). The single Raoultella ornithinolytica isolate characterized here also contains the same 16 nif genes; Raoultella species have previously been isolated from sugarcane (27) and have also been demonstrated to fix nitrogen (28).…”

Section: Resultsmentioning

confidence: 93%

Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

Medina-Cordoba

Chande

Rishishwar

et al. 2019

Preprint

View full text Add to dashboard Cite

23 24 KEYWORDS: biofertilizer, nitrogen fixation, plant growth promoter, genome 25 sequencing, computational phenotyping 26 2ABSTRACT Previous studies have shown that the sugarcane microbiome harbors diverse 27 plant growth promoting (PGP) microorganisms, including nitrogen-fixing bacteria, and the 28 objective of this study was to design a genome-enabled approach to prioritize sugarcane 29 associated nitrogen-fixing bacteria according to their potential as biofertilizers. Using a 30 systematic high throughput approach, 22 pure cultures of nitrogen-fixing bacteria were isolated 31 and tested for diazotrophic potential by PCR amplification of nitrogenase (nifH) genes, common 32 molecular markers for nitrogen fixation capacity. Genome sequencing confirmed the presence 33 of intact nitrogenase nifH genes and operons in the genomes of 18 of the isolates. Isolate 34 genomes also encoded operons for phosphate solubilization, siderophore production operons, 35 and other PGP phenotypes. Klebsiella pneumoniae strains comprised 14 of the 22 nitrogen-36fixing isolates, and four others were members of closely related genera to Klebsiella. A 37 computational phenotyping approach was developed to rapidly screen for strains that have high 38 potential for nitrogen fixation and other PGP phenotypes while showing low risk for virulence 39 and antibiotic resistance. The majority of sugarcane isolates were below a genotypic and 40 phenotypic threshold, showing uniformly low predicted virulence and antibiotic resistance 41 compared to clinical isolates. Six prioritized strains were experimentally evaluated for PGP 42 phenotypes: nitrogen fixation, phosphate solubilization, and the production of siderophores, 43 gibberellic acid and indole acetic acid. Results from the biochemical assays were consistent 44 with the computational phenotype predictions for these isolates. Our results indicate that 45 computational phenotyping is a promising tool for the assessment of benefits and risks 46 associated with bacteria commonly detected in agricultural ecosystems. IMPORTANCE A genome-enabled approach was developed for the prioritization of 48 native bacterial isolates with the potential to serve as biofertilizers for sugarcane fields 49 in Colombia's Cauca Valley. The approach is based on computational phenotyping, 50 which entails predictions related to traits of interest based on bioinformatic analysis of 51 whole genome sequences. Bioinformatic predictions of the presence of plant growth 52 promoting traits were validated with experimental assays and more extensive genome 53 comparisons, thereby demonstrating the utility of computational phenotyping for 54 assessing the benefits and risks posed by bacterial isolates that can be used as 55 biofertilizers. The quantitative approach to computational phenotyping developed here 56 for the discovery of biofertilizers has the potential for use with a broad range of 57 applications in environmental and industrial microbiology, food safety, water quality, and 58 antibiotic resistance studies. 6...

show abstract

Draft Genome Sequence of Raoultella terrigena R1Gly, a Diazotrophic Endophyte

Cited by 19 publications

References 16 publications

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts

Raoultellasp. strain L03 fixes N₂in association with micropropagated sugarcane plants

Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

Contact Info

Product

Resources

About

Draft Genome Sequence of Raoultella terrigena R1Gly, a Diazotrophic Endophyte

Cited by 19 publications

References 16 publications

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts

Raoultellasp. strain L03 fixes N2in association with micropropagated sugarcane plants

Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

Contact Info

Product

Resources

About

Raoultellasp. strain L03 fixes N₂in association with micropropagated sugarcane plants