Genomic characterization of Nitrospirillum amazonense strain CBAmC, a nitrogen-fixing bacterium isolated from surface-sterilized sugarcane stems

Abstract

Nitrospirillum amazonense is a nitrogen-fixing bacterium that shows potential to promote plant growth when inoculated into sugarcane and rice plants. This microorganism has been the subject of biochemical and genetic characterization to elucidate important functions related to host plant interaction and growth promotion, including the determination of draft genome sequences of two strains, Y2 and CBAmC, the second of which is the aim of the present study. CBAmC has been isolated from sugarcane (Saccharum spp.), and is currently used in a sugarcane consortium inoculant with four other nitrogen-fixing bacterial strains. The present paper describes a significant improvement in the genome sequence and assembly for the N. amazonense strain CBAmC, and determination for the first time of a complete genome sequence for this bacterial species, using PacBio technology. The analysis of the genomic data obtained allowed the discovery of genes coding for metabolic pathways and cellular structures that may be determinant for the success of the bacterial establishment and colonization into the host sugarcane plant, besides conferring important characteristics to the inoculant. These include genes for the use of sucrose and N-glycans, biosynthesis of autoinducer molecules, siderophore production and acquisition, auxin and polyamine biosynthesis, flagellum, σ-fimbriae, a variety of secretion systems, and a complete denitrification system. Concerning genes for nitrogenase and auxiliary proteins, it was possible to corroborate literature data that in N. amazonense these probably had originated from horizontal gene transfer, from bacteria of the Rhizobiales order. The complete genomic sequence of the CBAmC strain of N. amazonense revealed that the bacterium harbors four replicons, including three chromosomes and one chromid, a profile that coincides with that of other two strains, according to literature data, suggesting that as a replicon pattern for the species. Finally, results of phylogenomic analyses in this work support the recent reclassification of the species, separating it from the Azospirillum genus. More importantly, results of the present work shall guide subsequent studies on strain CBAmC as well as the development of a sugarcane inoculant.

Functional Investigation of Plant Growth Promoting Rhizobacterial Communities in Sugarcane

“…Over the last two decades, while knowledge of associated nitrogen fixation with sugarcane has greatly improved, most of this work focused on specific nitrogen fixing bacteria and lacked a systematic investigation of sugarcane associated communities ( da Silva et al, 2018 ; Singh et al, 2019 ). Recently, with the development of high throughput sequencing technology, the structure and activities of sugarcane microbiome components have been gradually revealed ( Bertalan et al, 2009 ; Pedrosa et al, 2011 ; Sant’Anna et al, 2011 ; Zhu et al, 2012 ; de Souza et al, 2016 ; Yeoh et al, 2016 ; da Silva et al, 2018 ; Dong et al, 2018 ; Schwab et al, 2018 ). In this study, we decipher the composition of a bacterial community in the root and rhizosphere of sugarcane using 16S rDNA sequencing.…”

AGRONOMIC PERFORMANCE OF SUGARCANE INOCULATED WITH Nitrospirillum amazonense (BR11145)

“…Although biological nitrogen fixation has been the main explanation for the benefits of inoculation, it is possible that bacteria can stimulate ion absorption and nutrient transport in plants; however, the physiological explanation of the bacterial mixture is still little understood (SCHWAB;TERRA;BALDANI, 2018;SANTOS et al, 2019). Reis Junior et al (2008) found no increase in nitrogen accumulation by maize plants after inoculation with Azospirillum amazonensis.…”

The Neolithic site “La Marmotta”: DNA metabarcoding to identify the microbial deterioration of waterlogged archeological wood

“…The association encountered is among fungi ( Barbatospora ambicaudata and Xylaria sp.) and nitrogen-fixing bacteria [ Azospirillum, ( Steenhoudt and Vanderleyden, 2000 ) and Nitrospirillum amazonense ( Schwab et al, 2018 )]. Nitrogen availability in deadwood is highly restricted, therefore fungi may take advantage from associations with nitrogen-fixing bacteria for their growth ( Gómez-Brandón et al, 2020 ).…”