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<p><i>Lycopodium clavatum</i> L., a well-known medicinal herb, grows luxuriantly in the eroding nutrient-poor mountain terrain of Darjeeling Himalaya. Rhizospheric microbiomes mediated growth and development for the plant has not been studied. This is the first report deciphering the cross-talk of the untapped rhizomicrobiome of <i>L. clavatum.</i> Three potential PGPR (plant growth promoting rhizobacteria) bacteria viz. <i>Bacillus mycoides</i> KUR1107, <i>B. mycoides</i> KUR1109 and <i>Alcaligenes pakistanensis</i> subsp. <i>lycopodii</i> KUR1110<sup>T*</sup> were identified based on 16S rRNA sequencing. The subsp. nov. has strong Indole-3-acetic acid (IAA) producing (150.66 <i>±</i> 7.46&#xa0;µg/ml), phosphate solubilizing (11.9 <i>±</i> 0.21&#xa0;µg/ml) and siderophore producing (99.1 <i>±</i> 2.48 nmol/ml) property. It stimulates plant growth following root inoculation. Genome-wide data mining was performed for the unexplored <i>A. pakistanensis</i> subsp. <i>lycopodii</i> KUR1110 to find novel genes and metabolites. The genome of <i>A. pakistanensis</i> is ~ 3.99&#xa0;Mb in size, with 3607 protein-coding genes. Genomic characterization gives a deeper insight into a repertoire of genes associated with antibiotic resistance, secondary metabolite biosynthesis, heavy metal resistance, IAA synthesis, and metabolism of sulfur, nitrogen and phosphorus. Production of inorganic phosphate solubilizing organic acids, siderophore biosynthesis precursors, and the compounds involved in defence were detected by Liquid chromatography-Mass spectrometry (LC-MS) analysis. In silico analysis of two key genes viz. di-iron N-oxygenase (dnfA) of dirammox pathway and lysine decarboxylase of siderophore biosynthesis revealed that the proteins were stable to execute their functions. <i>A. pakistanensis</i> subsp. <i>lycopodii</i>, contributing to global biogeochemical cycling, is a potential bioinoculant in nutrient-poor/heavy metal-infested soil and can be developed for sustainable bioremediation and biomining technology. [*NCBI accession no and MTCC deposit no for all three strains are <i>B. mycoides</i> KUR1107 (NCBI OR 592244, MTCC 13924), <i>B. mycoides</i> KUR1109 (NCBI OR592282, MTCC 13925), and <i>A. pakistanensis</i> subsp. <i>lycopodii</i> KUR1110<sup>T</sup> (NCBI OR592286, MTCC 13945)].</p> Graphical Abstract <p></p>

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Genomic and functional insights into Alcaligenes pakistanensis subsp. lycopodii subsp. nov. -deciphering crosstalk with Lycopodium clavatum L. for bioinoculant potential

  • 期刊论文

  • 发表日期：

    2026年4月16日

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  • Raja Paul,
  • Kakali Sen,
  • Bejoysekhar Datta,
  • Sima Biswas

摘要

Lycopodium clavatum L., a well-known medicinal herb, grows luxuriantly in the eroding nutrient-poor mountain terrain of Darjeeling Himalaya. Rhizospheric microbiomes mediated growth and development for the plant has not been studied. This is the first report deciphering the cross-talk of the untapped rhizomicrobiome of L. clavatum. Three potential PGPR (plant growth promoting rhizobacteria) bacteria viz. Bacillus mycoides KUR1107, B. mycoides KUR1109 and Alcaligenes pakistanensis subsp. lycopodii KUR1110T* were identified based on 16S rRNA sequencing. The subsp. nov. has strong Indole-3-acetic acid (IAA) producing (150.66 ± 7.46 µg/ml), phosphate solubilizing (11.9 ± 0.21 µg/ml) and siderophore producing (99.1 ± 2.48 nmol/ml) property. It stimulates plant growth following root inoculation. Genome-wide data mining was performed for the unexplored A. pakistanensis subsp. lycopodii KUR1110 to find novel genes and metabolites. The genome of A. pakistanensis is ~ 3.99 Mb in size, with 3607 protein-coding genes. Genomic characterization gives a deeper insight into a repertoire of genes associated with antibiotic resistance, secondary metabolite biosynthesis, heavy metal resistance, IAA synthesis, and metabolism of sulfur, nitrogen and phosphorus. Production of inorganic phosphate solubilizing organic acids, siderophore biosynthesis precursors, and the compounds involved in defence were detected by Liquid chromatography-Mass spectrometry (LC-MS) analysis. In silico analysis of two key genes viz. di-iron N-oxygenase (dnfA) of dirammox pathway and lysine decarboxylase of siderophore biosynthesis revealed that the proteins were stable to execute their functions. A. pakistanensis subsp. lycopodii, contributing to global biogeochemical cycling, is a potential bioinoculant in nutrient-poor/heavy metal-infested soil and can be developed for sustainable bioremediation and biomining technology. [*NCBI accession no and MTCC deposit no for all three strains are B. mycoides KUR1107 (NCBI OR 592244, MTCC 13924), B. mycoides KUR1109 (NCBI OR592282, MTCC 13925), and A. pakistanensis subsp. lycopodii KUR1110T (NCBI OR592286, MTCC 13945)].

Graphical Abstract