{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T00:22:58Z","timestamp":1774398178573,"version":"3.50.1"},"reference-count":56,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,12,11]],"date-time":"2023-12-11T00:00:00Z","timestamp":1702252800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004608","name":"Natural Science Foundation of Jiangsu Province","doi-asserted-by":"publisher","award":["BK20221426"],"award-info":[{"award-number":["BK20221426"]}],"id":[{"id":"10.13039\/501100004608","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>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 <jats:italic>Nguyenibacter<\/jats:italic> sp. L1, was isolated from the rhizosphere soil of healthy <jats:italic>Lespedeza bicolor<\/jats:italic> plants indigenous to acidic terrains. However, our understanding of the genomic landscape of bacterial species within the genus <jats:italic>Nguyenibacter<\/jats:italic> 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 <jats:italic>Nguyenibacter<\/jats:italic> 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 <jats:italic>isc<\/jats:italic>U, <jats:italic>gln<\/jats:italic>A, and <jats:italic>glt<\/jats:italic>B\/D associated with nitrogen fixation, and <jats:italic>pqq<\/jats:italic>BC associated with inorganic phosphate dissolution. Several bioactive secondary metabolite genes in the genome, including <jats:italic>pqq<\/jats:italic>CDE, phytoene synthase and squalene synthase predicted by antiSMASH. Moreover, we uncovered a complete metabolic pathway for ammonia, suggesting an ammonia-affinity property inherent to <jats:italic>Nguyenibacter<\/jats:italic> sp. L1. This study verifies the nitrogen-fixing and phosphate-dissolving abilities of <jats:italic>Nguyenibacter<\/jats:italic> 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.<\/jats:p>","DOI":"10.3389\/fmicb.2023.1257442","type":"journal-article","created":{"date-parts":[[2023,12,11]],"date-time":"2023-12-11T04:27:13Z","timestamp":1702268833000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":9,"title":["Complete genome sequence of Nguyenibacter sp. L1, a phosphate solubilizing bacterium isolated from Lespedeza bicolor rhizosphere"],"prefix":"10.3389","volume":"14","author":[{"given":"Xiao Li","family":"Li","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin Yang","family":"Lv","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun Bin","family":"Ji","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei Duo","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ji","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hai Bin","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ai Ling","family":"Ben","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ting Li","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2023,12,11]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"13","DOI":"10.5539\/jas.v4n7p13","article-title":"Characterization of arbuscular mycorrhizal spores isolated from southern Guinea savanna of Nigeria","volume":"4","author":"Alori","year":"2012","journal-title":"J. Agric. Sci."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"2607","DOI":"10.1371\/journal.pone.0017473","article-title":"GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions","volume":"29","author":"Besemer","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"667339","DOI":"10.3389\/fagro.2021.667339","article-title":"Study of pyrroloquinoline quinine from phosphate-solubilizing microbes responsible for plant growth: in silico approach","volume":"3","author":"Bhanja","year":"2021","journal-title":"Front. 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Soil Ecol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"744","DOI":"10.1007\/s00284-016-1012-1","article-title":"Simultaneous detection and quantification of phytohormones by a sensitive method of separation in culture of Pseudomonas sp","volume":"72","author":"Patel","year":"2016","journal-title":"Curr. Microbiol."},{"key":"ref9003","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1177\/1082013206063838","article-title":"Gluconic Acid: Properties, Applications and Microbial Production","volume":"44","author":"Ramachandran","year":"2006","journal-title":"Food Technol. Biotechnol."},{"key":"ref32","author":"Rodr\u00edguez","year":"2007"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"15610","DOI":"10.1038\/s41598-017-15820-9","article-title":"Comprehensive genomic analysis of a plant growth promoting rhizobacterium Pantoea agglomerans strain P5","volume":"7","author":"Shariati","year":"2017","journal-title":"Sci. Rep."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/s43008-020-00035-x","article-title":"Molecular characterization of siderophore biosynthesis in Paracoccidioides brasiliensis","volume":"11","author":"Silva","year":"2020","journal-title":"IMA Fungus"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"126734","DOI":"10.1016\/j.micres.2021.126734","article-title":"Genomics assisted functional characterization of Paenibacillus polymyxa HK4 as a biocontrol and plant growth promoting bacterium","volume":"248","author":"Soni","year":"2021","journal-title":"Microbiol. Res."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"4603","DOI":"10.1093\/jxb\/ert276","article-title":"Root ethylene signalling is involved in Miscanthus sinensis growth promotion by the bacterial endophyte Herbaspirillum frisingense GSF30(T)","volume":"64","author":"Straub","year":"2013","journal-title":"J. Exp. Bot."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1007\/s11104-009-0168-x","article-title":"Phosphate-solubilizing peanut associated bacteria: screening for plant growth promoting activities","volume":"329","author":"Tania","year":"2010","journal-title":"Plant Soil"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/1471-2105-4-41","article-title":"The COG database: an updated version includes eukaryotes","volume":"4","author":"Tatusov","year":"2003","journal-title":"BMC Bioinform."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"153","DOI":"10.2323\/jgam.59.2_153","article-title":"Nguyenibacter vanlangensis gen. nov., sp. nov., an unusual acetic acid bacterium in the \u03b1-Proteobacteria","volume":"59","author":"Thi Lan Vu","year":"2013","journal-title":"J. Gen. Appl. Microbiol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"158","DOI":"10.3390\/biology10020158","article-title":"Roles of phosphate solubilizing microorganisms from managing soil phosphorus deficiency to mediating biogeochemical P cycle","volume":"10","author":"Tian","year":"2021","journal-title":"Biology"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"2119","DOI":"10.3390\/plants11162119","article-title":"Prospects for using phosphate-solubilizing microorganisms as natural fertilizers in agriculture","volume":"11","author":"Timofeeva","year":"2022","journal-title":"Plan. Theory"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/BF00009558","article-title":"Global extent, development and economic impact of acid soils","volume":"171","author":"von Uexk\u00fcll","year":"1995","journal-title":"Plant Soil"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"e0112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PLoS One"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0016-7061(76)90066-5","article-title":"The fate of phosphorus during pedogenesis","volume":"15","author":"Walker","year":"1976","journal-title":"Geoderma"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1016\/S2095-3119(14)60760-7","article-title":"Preparation and utilization of phosphate biofertilizers using agricultural waste","volume":"14","author":"Wang","year":"2015","journal-title":"J. Integr. Agric."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"21548","DOI":"10.1007\/s11356-022-23564-x","article-title":"Whole genome analysis of Enterobacter cloacae Rs-2 and screening of genes related to plant-growth promotion","volume":"30","author":"Wang","year":"2023","journal-title":"Environ. Sci. Pollut. Res. Int."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1556\/aagr.55.2007.3.7","article-title":"Co-inoculation of nitrogen-fixing and phosphate-solubilizing bacteria to promote growth, yield and nutrient uptake in chickpea","volume":"55","author":"Wani","year":"2007","journal-title":"Acta Agron. Hung."},{"key":"ref9004","doi-asserted-by":"publisher","first-page":"21329","DOI":"10.1038\/srep21329","article-title":"Comparative genomic and functional analysis reveal conservation of plant growth promoting traitsin Paenibacillus polymyxa and its closely related species","volume":"6","author":"Xie","year":"2016","journal-title":"Sci. Rep."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"850084","DOI":"10.3389\/fmicb.2022.850084","article-title":"Comparative genomics assisted functional characterization of Rahnella aceris ZF458 as a novel plant growth promoting rhizobacterium","volume":"13","author":"Xu","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"2907","DOI":"10.5194\/bg-8-2907-2011","article-title":"Phosphorus transformations as a function of pedogenesis: a synthesis of soil phosphorus data using Hedley fractionation method","volume":"8","author":"Yang","year":"2017","journal-title":"Biogeosciences"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"892533","DOI":"10.3389\/fmicb.2022.892533","article-title":"Identification of the phosphorus-solubilizing bacteria strain JP233 and its effects on soil phosphorus leaching loss and crop growth","volume":"13","author":"Yu","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1186\/s40168-022-01292-1","article-title":"PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes","volume":"10","author":"Zeng","year":"2022","journal-title":"Microbiome"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"844","DOI":"10.4014\/jmb.1611.11057","article-title":"Phosphate solubilization and gene expression of phosphate-solubilizing bacterium Burkholderia multivorans WS-FJ9 under different levels of soluble phosphate","volume":"27","author":"Zeng","year":"2017","journal-title":"J. Microbiol. 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