Complete genome sequence of Nguyenibacter sp. L1, a phosphate solubilizing bacterium isolated from Lespedeza bicolor rhizosphere

Xiao Li Li; Xin Yang Lv; Jun Bin Ji; Wei Duo Wang; Ji Wang; Cong Wang; Hai Bin He; Ai Ling Ben; Ting Li Liu

doi:10.3389/fmicb.2023.1257442

Complete genome sequence of Nguyenibacter sp. L1, a phosphate solubilizing bacterium isolated from Lespedeza bicolor rhizosphere

Front Microbiol. 2023 Dec 11:14:1257442. doi: 10.3389/fmicb.2023.1257442. eCollection 2023.

Authors

Xiao Li Li¹, Xin Yang Lv¹, Jun Bin Ji¹, Wei Duo Wang¹, Ji Wang¹, Cong Wang², Hai Bin He³, Ai Ling Ben¹, Ting Li Liu¹

Affiliations

¹ School of Food Science, Nanjing Xiaozhuang University, Nanjing, China.
² College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China.
³ College of Forestry, Nanjing Forestry University, Nanjing, China.

Abstract

Phosphorus (P) deficiency is a predominant constraint on plant growth in acidified soils, largely due to the sequestration of P by toxic aluminum (Al) compounds. Indigenous phosphorus-solubilizing bacteria (PSBs) capable of mobilizing Al-P in these soils hold significant promise. A novel Al-P-solubilizing strain, Al-P Nguyenibacter sp. L1, was isolated from the rhizosphere soil of healthy Lespedeza bicolor plants indigenous to acidic terrains. However, our understanding of the genomic landscape of bacterial species within the genus Nguyenibacter remains in its infancy. To further explore its biotechnological potentialities, we sequenced the complete genome of this strain, employing an amalgamation of Oxford Nanopore ONT and Illumina sequencing platforms. The resultant genomic sequence of Nguyenibacter sp. L1 manifests as a singular, circular chromosome encompassing 4,294,433 nucleotides and displaying a GC content of 66.73%. The genome was found to host 3,820 protein-coding sequences, 12 rRNAs, and 55 tRNAs. Intriguingly, annotations derived from the eggNOG and KEGG databases indicate the presence of genes affiliated with phosphorus solubilization and nitrogen fixation, including iscU, glnA, and gltB/D associated with nitrogen fixation, and pqqBC associated with inorganic phosphate dissolution. Several bioactive secondary metabolite genes in the genome, including pqqCDE, phytoene synthase and squalene synthase predicted by antiSMASH. Moreover, we uncovered a complete metabolic pathway for ammonia, suggesting an ammonia-affinity property inherent to Nguyenibacter sp. L1. This study verifies the nitrogen-fixing and phosphate-dissolving abilities of Nguyenibacter sp. L1 at the molecular level through genetic screening and analysis. The insights gleaned from this study offer strategic guidance for future strain enhancement and establish a strong foundation for the potential incorporation of this bacterium into agricultural practices.

Keywords: Nguyenibacter sp. L1; gene functions; nitrogen fixation; phosphate dissolution; whole genome.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was funded by the Natural Science Foundation of Jiangsu Province (BK20221426); by Nanjing Key Laboratory of Quality and safety of agricultural products; by Excellent Scientific and Technological Innovation Team of Colleges and Universities of Jiangsu Province [SUJIAOKE (2021)]; and by the Key Subject of Ecology of Jiangsu Province [SUJIAOYANHAN (2022)].