Functional Analysis and Genome Mining Reveal High Potential of Biocontrol and Plant Growth Promotion in Nodule-Inhabiting Bacteria Within Paenibacillus polymyxa Complex

Abstract

Bacteria belonging to the genus <i>Paenibacillus</i> were frequently isolated from legume nodules. The nodule-inhabiting <i>Paenibacillus</i> as a resource of biocontrol and plant growth-promoting endophytes has rarely been explored. This study explored the nodule-inhabiting <i>Paenibacillus</i>' antifungal activities and biocontrol potentials against broad-spectrum important phytopathogenic fungi. We collected strains which were isolated from nodules of <i>Robinia pseudoacacia</i>, <i>Dendrolobium triangulare</i>, <i>Ormosia semicastrata</i>, <i>Cicer arietinum</i>, <i>Acacia crassicarpa</i>, or <i>Acacia implexa</i> and belong to <i>P. peoriae</i>, <i>P. kribbensis</i>, <i>P. endophyticus</i>, <i>P. enshidis</i>, <i>P. puldeungensis</i>, <i>P. taichungensis</i>, or closely related to <i>P. kribbensis</i>, or <i>P. anseongense</i>. These nodule-inhabiting <i>Paenibacillus</i> showed diverse antagonistic activities against five phytopathogenic fungi (<i>Fusarium graminearum</i>, <i>Magnaporthe oryzae</i>, <i>Rhizoctonia solani</i>, <i>Sclerotinia sclerotiorum</i>, and <i>Botrytis cinerea</i>). Six strains within the <i>P. polymyxa</i> complex showed broad-spectrum and potent activities against all the five pathogens, and produced multiple hydrolytic enzymes, siderophores, and lipopeptide fusaricidins. Fusaricidins are likely the key antimicrobials responsible for the broad-spectrum antifungal activities. The nodule-inhabiting strains within the <i>P. polymyxa</i> complex were able to epiphytically and endophytically colonize the non-host wheat plants, produce indole acetic acids (IAA), and dissolve calcium phosphate and calcium phytate. <i>P. peoriae</i> strains RP20, RP51, and RP62 could fix N₂. <i>P. peoriae</i> RP51 and <i>Paenibacillus</i> sp. RP31, which showed potent plant colonization and plant growth-promotion competence, effectively control fungal infection <i>in planta</i>. Genome mining revealed that all strains (<i>n</i> = 76) within the <i>P. polymyxa</i> complex contain <i>ipdC</i> gene encoding indole-3-pyruvate decarboxylase for biosynthesis of IAA, 96% (<i>n</i> = 73) contain the <i>fus</i> cluster for biosynthesis of fusaricidins, and 43% (<i>n</i> = 33) contain the <i>nif</i> cluster for nitrogen fixation. Together, our study highlights that endophytic strains within the <i>P. polymyxa</i> complex have a high probability to be effective biocontrol agents and biofertilizers and we propose an effective approach to screen strains within the <i>P. polymyxa</i> complex.