<i>Raoultella</i>sp. strain L03 fixes N<sub>2</sub>in association with micropropagated sugarcane plants

Luo, Ting; Ou-Yang, Xue-Qing; Yang, Li‐Tao; Li, Yang–Rui; Song, Xiu–Peng; GeMin, Zhang; Gao, Yi-jing; WeiXing, Duan; An, Qianli

doi:10.1002/jobm.201500738

Cited by 16 publications

(9 citation statements)

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“…Our discovery of diazotrophs in the DSP group classified as Gammaproteobacteria suggested that bacteria of this taxonomic class from the mucilage environment are likely to contribute to the BNF phenotype of Sierra Mixe maize. This is supported by previous studies describing species from enterobacterial genera classified among genomes in the DSP group (Enterobacter, Klebsiella, Kosakonia, Rahnella, and Raoultella) as diazotrophic endophytes associated with cereal crops such as sugarcane, rice, and maize [56][57][58][59][60]. Recent reports demonstrated the successful engineering of a Pseudomonas strain capable of associating with wheat and maize as a diazotrophic endophyte [61], as well as successful growth promotion of maize using a diazotrophic strain of Pseudomonas isolated from the rhizosphere of rice [62].…”

Section: Diazotrophs Formed Three Distinct Nitrogen Fixation Groups Bsupporting

confidence: 83%

Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage

et al. 2020

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A geographically isolated maize landrace cultivated on nitrogen-depleted fields without synthetic fertilizer in the Sierra Mixe region of Oaxaca, Mexico utilizes nitrogen derived from the atmosphere and develops an extensive network of mucilage-secreting aerial roots that harbors a diazotrophic (N 2-fixing) microbiota. Targeting these diazotrophs, we selected nearly 600 microbes of a collection obtained from mucilage and confirmed their ability to incorporate heavy nitrogen (15 N 2) metabolites in vitro. Sequencing their genomes and conducting comparative bioinformatic analyses showed that these genomes had substantial phylogenetic diversity. We examined each diazotroph genome for the presence of nif genes essential to nitrogen fixation (nifHDKENB) and carbohydrate utilization genes relevant to the mucilage polysaccharide digestion. These analyses identified diazotrophs that possessed the canonical nif gene operons, as well as many other operon configurations with concomitant fixation and release of >700 different 15 N labeled metabolites. We further demonstrated that many diazotrophs possessed alternative nif gene operons and confirmed their genomic potential to derive chemical energy from mucilage polysaccharide to fuel nitrogen fixation. These results confirm that some diazotrophic bacteria associated with Sierra Mixe maize were capable of incorporating atmospheric nitrogen into their small molecule extracellular metabolites through multiple nif gene configurations while others were able to fix nitrogen without the canonical (nifHDKENB) genes.

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Section: Diazotrophs Formed Three Distinct Nitrogen Fixation Groups Bsupporting

confidence: 83%

Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage

et al. 2020

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“…With respect to diazotrophic associations with cereal crops, recent investigation into a diazotrophic strain of R . planticola demonstrated that it was capable of conferring BNF-mediated PGP to sugar cane through endophytic colonization [ 49 ]. While reference genomes for these species exist in GenBank [ 50 ] and the Genome Taxonomy Database (GTDB) [ 51 ] used to classify mucilage isolate genomes in this study, the lack of species level assignment to described species of Raoultella for many mucilage derived Raoultella isolates using WGS similarity indicates the potential genomic novelty for Raoultella associated with Sierra Mixe maize and suggests that strain variation is important for these traits to be conferred in the microbiome.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2020

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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.

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“…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: 90%

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

Medina-Cordoba

Chande

Rishishwar

et al. 2019

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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...

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Raoultellasp. strain L03 fixes N₂in association with micropropagated sugarcane plants

Cited by 16 publications

References 20 publications

Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage

Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage

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

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

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Raoultellasp. strain L03 fixes N2in association with micropropagated sugarcane plants

Cited by 16 publications

References 20 publications

Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage

Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage

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

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

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Raoultellasp. strain L03 fixes N₂in association with micropropagated sugarcane plants