Phosphorus (P) serves as an essential macronutrient underpinning plant growth and development (Tania et al., 2010), playing a key role in numerous physiological and biochemical processes. As per the United Nations’ latest forecasts, the global population will swell to an estimated 9.7 billion by 2050 (Goswami and Deka, 2020). To satiate the escalating demand for food and shelter, the agricultural industry often resorts to the excessive use of chemical fertilizers, notably phosphate fertilizers. However, this practice often results in the inefficient utilization or immobilization of these fertilizers in the soil. Acid soils blanket approximately 30% of ice-free land and encroach upon 70% of potential arable soils worldwide (von Uexküll and Mutert, 1995). In China, acid soils stretch across 2.18 million km², comprising 22.7% of the country’s total area (Huang and Zhao, 2014). Within these acid soils, most phosphates exist as insoluble iron and aluminum phosphates, rendering the majority of phosphorus from added fertilizer inaccessible to plants (Hemwall, 1957; Tian et al., 2021). Moreover, the protracted application of phosphorus fertilizers risks causing soil salinization and pollution, including groundwater contamination due to leaching and transpiration. These environmental quandaries threaten to diminish food production and potentially jeopardize human health (Wang et al., 2023). Unlike nitrogen (N), which has volatile atmospheric forms such as N₂ and N₂O, phosphorus lacks a soluble atmospheric supply (Yang and Post, 2017). In natural ecosystems, phosphorus primarily derives from rock weathering, cementing its status as an unrenewable resource and the world’s second-most limiting nutrient for plant growth (Walker and Syers, 1976). Therefore, unshackling soil-bound phosphorus and converting it into forms that are readily available to plants and microbes stand as paramount goals in the development and evolution of agriculture and forestry practices.

Soil microorganisms occupy a pivotal role in the facilitation of plant nutrient uptake and are the crux of an array of biological processes (Timofeeva et al., 2022). Abundant research illuminates the multifaceted capabilities of phosphate-solubilizing bacteria within the soil and rhizosphere, showcasing their potential to enhance host plant growth through mechanisms such as organic phosphate mineralization and inorganic phosphate dissolution (Li et al., 2016). These bacteria, commonly referred to as phosphate-solubilizing microorganisms (PSM), have been garnering significant attention due to their eco-friendly nature, cost-effectiveness, and high efficiency (Khan et al., 2007; Owen et al., 2015). PSM demonstrate their plant growth-promoting abilities by amplifying biological nitrogen fixation efficiency, stimulating phytohormone synthesis, and bolstering the bioavailability of specific micronutrients like zinc and iron (Wani et al., 2007). Concurrently, experiments with PSM inoculation have unequivocally evidenced increased plant yield and phosphorus uptake in both controlled pot experiments and field conditions (Wang et al., 2015). Given its economic and environmental benefits, the phosphate solubilization capacity of soil microorganisms is deemed a particularly promising research frontier. Therefore, the strategy of inoculating soil or crops with phosphate-solubilizing microorganisms is perceived as an advantageous approach to augmenting plant phosphorus uptake (Alori et al., 2012).

The advent and advancement of genetic tools and technology, particularly whole genome sequencing, have opened up promising avenues for investigating the physiological and ecological functions of rhizobacteria (Jana and Yaish, 2021). For instance, Soni et al. (2021) probed the draft genome of Paenibacillus polymyxa HK4, successfully identifying genes associated with phosphorus solubility and confirming its abilities in biological control and plant growth promotion. Similarly, Xu et al. (2022) shed light on the genetic attributes of Rahnella aceris ZF458 pertaining to plant growth, utilizing genome annotation and comparative genomics. This work laid the groundwork for investigating genes associated with phosphorus solubility. Leveraging molecular biology techniques allows the extraction of functional genes involved in siderophore synthesis, nitrogen fixation, and phosphorus dissolution. These genes play pivotal roles in elucidating key growth-promoting attributes (Cleton-Jansen et al., 1991; Straub et al., 2013; Kang et al., 2016; Silva et al., 2020). Therefore, the process of mining these functional genes is not only valuable but also instrumental in bolstering research on the growth-promoting traits of bacterial strains. It offers insights into the metabolic pathways of these strains and can potentially enhance the applicability and efficiency of PSM in plant growth promotion.

Within our laboratory, strain L1 has been identified as exhibiting high AlPO4 solubilizing capability and was initially classified as Nguyenibacter based on its 16S rRNA gene sequence (Li Q. et al., 2021). However, given the paucity of genomic information available for this species, a more comprehensive molecular examination of strain L1 is warranted.

Prior research indicated that the combined inoculation of two strains, L1 and S1, significantly bolstered soybean growth under greenhouse conditions (Li et al., 2023). Furthermore, previous studies proposed that Nguyenibacter possesses N-fixing capabilities (Thi Lan Vu et al., 2013). Nonetheless, the metabolic pathways and mechanisms underlying these functions remain enigmatic. We hypothesize that the biological control and plant growth-promoting attributes of strain L1 are intrinsically linked to key growth-promoting genes. Consequently, we undertook the sequencing of the L1 genome with the aim of unearthing and verifying its plethora of gene functions associated with growth-promoting properties and capabilities. The data generated from this investigation enriches our understanding of plant growth-promoting mechanisms, casting fresh light on the operative processes within this realm.

Plant-associated endophytic microbes have intricately evolved their biosynthetic pathways to facilitate symbiotic interactions with their hosts. The diverse metabolites derived from these endophytes contribute to plant growth promotion, thereby propelling significant interest towards their genomic studies in recent years (Patel et al., 2016; Kandel et al., 2022). Nguyenibacter, for instance, is documented as an N-fixing bacterium (Thi Lan Vu et al., 2013). An examination of the nitrogen metabolic pathway in Nguyenibacter sp. L1 reveals the bacterium’s proclivity towards ammonium, bolstered by the presence of nitrogen-fixing genes (iscU and nifU), and its capacity for ammonia metabolism. Our prior research led to the isolation of Nguyenibacter sp. L1, which displayed notable plant growth-promoting characteristics under low-phosphorus conditions (Li et al., 2023). The exploration and understanding of these inherent genes might pave the way for the development of commercial bioinoculants, potentially reducing the reliance on chemical fertilizers.

Phosphorus, an essential nutrient for plants, often emerges as a significant limiting factor for plant growth and development due to its low bioavailability (Zeng et al., 2017; Li et al., 2018). In this context, PSM play a pivotal role in the ecosystem as they catalyze the conversion of insoluble soil phosphates into forms accessible to plants, thereby mitigating the phosphorus deficit (Kour et al., 2021). Nguyenibacter sp. L1 was initially isolated based on its exceptional ability to solubilize AlPO4. Remarkably, when co-inoculated with Pseudomonas sp. S1, it exhibited considerable potential to enhance the total phosphorus content in soybean plants (Li et al., 2023). Despite these promising attributes, the intricacies of the mechanism underlying the phosphorus dissolution orchestrated by Nguyenibacter sp. L1 remain elusive. A comprehensive understanding of this mechanism could reveal significant insights into the sustainable management of phosphorus in agriculture.

Initial characterization of Nguyenibacter sp. L1 uncovered its robust ability to secrete gluconic acid, particularly in the presence of glucose as a carbon source (Li X. L. et al., 2021). In the present study, genome analysis of Nguyenibacter sp. L1 offered intriguing hints to the presence of distinct genes instrumental for phosphate solubilization. PSM enhances plant growth by transforming mineral phosphate into a form readily absorbed by plants. This is achieved via an array of solubilization mechanisms, including the production of extracellular enzymes and the release of organic acids, protons, and hydroxyl ions. Phosphate-solubilizing bacteria such as Bacillus, Pseudomonas, and Pantoea are renowned for their gluconic acid secretion (Rodríguez et al., 2007). It is noteworthy that Enterobacter asburiae mutants lacking glucose dehydrogenase (GDH) activity failed to solubilize phosphate (Gyaneshwar et al., 1999). GDH plays a pivotal role in the periplasmic oxidation of glucose to gluconic acid, a major metabolic pathway involved in inorganic phosphate solubilization in Gram-negative bacteria (Goldstein, 1994; de Werra et al., 2009). In the Nguyenibacter sp. L1 genome, we identified the presence of gcd and pqq genes, which are critical for the synthesis of gluconic acid and the solubilization of inorganic mineral phosphates. Meanwhile, secondary metabolite genes pqqCDE in the genome were predicted by antiSMASH. The gcd gene, encoding an enzyme that mediates inorganic P solubilization, was predominant across soil samples and was a major determinant of bioavailable soil P (Liang et al., 2020). These findings echo the previously reported high gluconic acid secretion capacity of this strain, thereby supporting the notion that Nguyenibacter sp. L1 could be a valuable biological tool in enhancing phosphate utilization in agriculture.

Microorganisms have adeptly evolved strategies to utilize alternative sources of phosphorus, such as phosphonates, particularly during phosphate scarcity. The enzymes pivotal to phosphonate catabolic pathways are conserved and encoded by orthologous genes in bacteria. Nguyenibacter sp. L1 harbors phn genes like phnP, integral to phosphate solubilization. Furthermore, the ugpQ and glpQ genes encode cytoplasmic glycerophosphoryl diester phosphodiesterase and periplasmic glycerophosphoryl diester phosphodiesterase, respectively, which facilitate the hydrolysis of organic phosphorus (Zeng et al., 2022). Notably, Nguyenibacter sp. L1 also possesses pstABCS genes, representing a prominent transporter system for inorganic phosphorus uptake (Hsieh and Wanner, 2010). Comparable gene clusters have also been reported for phosphonate binding, transport, and degradation in Rahnella victoriana JZ-GX1 and Pantoea agglomerans strain P5 (Shariati et al., 2017; Kong et al., 2022).

This study represents the inaugural whole-genome sequencing of Nguyenibacter sp. L1 and genome-wide analysis of the genes associated with plant growth promotion, such as nitrogen fixation and phosphorus dissolution. The genetic screening and analysis conducted in this study offer significant insights into the functioning and potential enhancement of Nguyenibacter. This, in turn, might pave the way for practical applications of the stain as a biofertilizer in agriculture, thereby providing a sustainable and environmentally friendly alternative to chemical fertilizers.

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found at: https://www.ncbi.nlm.nih.gov/, PRJNA975354.

XLi: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Writing – original draft. XLv: Data curation, Investigation, Writing – review & editing. JJ: Writing – review & editing. WW: Writing – review & editing. JW: Supervision, Writing – review & editing. CW: Data curation, Investigation, Visualization, Writing – review & editing. HH: Data curation, Investigation, Writing – review & editing. AB: Funding acquisition, Supervision, Writing – review & editing. TL: Conceptualization, Funding acquisition, Project administration, Resources, Supervision, Writing – review & editing.