Biological characteristics and genome-wide sequence analysis of endophytic nitrogen-fixing bacteria Klebsiella variicola GN02

Abstract

The biological characteristics and genome-wide sequence analysis of highly efficient endophytic nitrogen-fixing bacteria Klebsiella variicola GN02 isolated from the roots of Pennisetum sinense Roxb. were studied by the combination of second-generation and third-generation sequencing techniques. The cell cultivation characteristics, microscopic morphological observation and infrared spectroscopic analysis of this GN02 strain were performed and its genome assembly, gene prediction and functional annotation, eggNOG/GO clustering analysis and co-linearity analysis were conducted through corresponding software. The results showed that the GN02 strain had the basic morphological characteristics of genus Klebsiella and it had the characteristic absorption peak of marker C-N group and the characteristic absorption peaks of carbonyl and amide groups in nitrogen-fixing bacteria. The GN02 genome size was 5,599,366 bp with GC content of 57.41%, 5,261 ORF, 25 rRNA, 87 tRNA, 125 other ncRNA, 7 CRISPR repeats, and 54 GIs. Gene function annotations indicate that there were a large number of genes closely related to cellular nitrogen metabolism and the genes with high abundance are associated with amino acid metabolism. The genome-wide sequence has been submitted to the GenBank database under the accession number of CP31061. The basic characteristics of GN02 genome are similar to those of other K. variicola. Several strains of K. variicola have good co-linearity. The GN02 strain has a complete nitrogen-fixing gene group and 57 nitrogen-fixing genes have been identified.

Complete Genome Sequence of Enterobacter roggenkampii ED5, a Nitrogen Fixing Plant Growth Promoting Endophytic Bacterium With Biocontrol and Stress Tolerance Properties, Isolated From Sugarcane Root

“…SA187 genome includes dissimilatory nitrate reduction genes apart from genes coding for the nitrogenase enzyme (nifDHK). Klebsiella variicola GN02 and K. variicola DX120E genome hold numerous genes associated with nitrogen fixation, for example, nif gene cluster (nifHDK and nifLA), nitrogen metabolism-regulatory genes (ntrBC and glnD), and ammonium carrier gene (amtB) (Lin et al, 2012(Lin et al, , 2015Biaosheng et al, 2019).…”

Molecular mechanism of endophytic bacteria DX120E regulating polyamine metabolism and promoting plant growth in sugarcane

“…Research on sugarcane endophytic bacteria has been mostly focused on biological nitrogen fixing bacteria ( Trivedi et al., 2021 ). Bacteria of the genus Klebsiella belonging to the family Enterobacteriaceae stimulated plant growth via an array of direct and indirect mechanisms that are of increasing biotechnological interest due to their potential bio-inoculants for plant growth ( Lin et al., 2019 ; Medina-Cordoba et al., 2021 ). Carolina et al.…”

Complete genome analysis of sugarcane root associated endophytic diazotroph Pseudomonas aeruginosa DJ06 revealing versatile molecular mechanism involved in sugarcane development

“…SA187 genome. The genomes of Klebsiella variicola GN02, K. variicola DX120E, Enterobacter roggenkampii ED5, and streptomyces chartreuses WZS021 also contain several nitrogen fixation-related genes, such as nif gene clusters, nifHDK, iscU , and nifLA ; nitrogen metabolism regulator genes, ntrBC and glnD ; and ammonia assimilation cycle gene, amtB (Lin et al, 2015 , 2019 ; Wang et al, 2019 ; Guo et al, 2020 ). In this study, DNDH-GDH, GS, and NR activities were examined with the inoculated strain DJ06, and the results showed that sugarcane nitrogen metabolism enzyme activities were changed after inoculation of the DJ06 strain.…”