Genome-Driven Functional Validation of Bacillus amyloliquefaciens Strain MEPW12: A Multifunctional Endophyte for Sustainable Sweet Potato Cultivation

Abstract

Sweet potato (Ipomoea batatas (L.) Lam.), as an important crop, is rich in polyphenols, vitamins, minerals, and other nutrients in its roots and leaves and is gradually gaining popularity. The use of endophytic bacteria to improve the quality of sweet potato can protect the environment and effectively promote the sustainable development of the sweet potato industry. In this study, 12 strains of endophytic bacteria were isolated from sweet potato. Through nitrogen fixation, phosphorus solubilization, indoleacetic acid production, siderophore production, ACC deaminase production, and carboxymethyl cellulose production, three strains with multiple biological activities were screened out. Among them, MEPW12 had the most plant growth-promoting functions. In addition, MEPW12 promoted host chlorophyll accumulation and inhibited pathogen growth and colonization in sweet potato roots and can utilize various carbon sources and salts for growth. It can also grow in extreme environments of high salt and weak acid. MEPW12 was identified as Bacillus amyloliquefaciens with a genome size of 3,928,046 bp and a GC content of 46.59%. After the annotation of multiple databases, it was found that MEPW12 had multiple enzymatic activities and metabolic potential. Comparative genomics and pan-genomics analyses revealed that other Bacillus sp. strains of MEPW12 have similar functions. However, due to adaptation to different growth environments, there are still genomic differences and changes. Inoculation with MEPW12 induced the high expression of IbGH3.10, IbERF1, and other genes, thereby promoting the growth of sweet potatoes. Bacillus amyloliquefaciens strain MEPW12 is a sweet potato endophyte with multiple growth-promoting functions, which can promote the growth of sweet potato seedlings. This study provides new microbial resources for developing microbial agents and improving the quality of sweet potatoes.

Keywords: endophyte; genome; growth promoting bacteria; pan-genomic analysis; sweet potato.

Figure 1

Functional identification of endophytic bacteria. (A) Nitrogen fixation capacity testing; (B) ACC deaminase detection; (C) Solubilization of phosphate testing; (D) Detection of CMC cellulase production capacity; (E) Siderophore production capacity testing; (F) IAA quantification.

Figure 2

Effect of endophytes on the growth of sweet potato seedlings. (A) Growth appearance of sweet potato seedlings inoculated with different strains; (B) The effects of endophytes on the root length of sweet potato seedlings; (C) Effects of endophytes on the weight of sweet potato seedlings. (D) Chlorophyll a contents of leaves; (E) Chlorophyll b contents of leaves; Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Figure 3

Identification of physiological and biochemical functions of MEPW12, and detection of antibacterial and colonization ability. (A) Physiological and biochemical analysis of MEPW12; (B) The inhibitory effect of MEPW12 on sweet potato pathogens; (C) Expression of gyrA in the samples; Significance levels: *** p < 0.001.

Figure 4

Phylogenetic tree of MEPW12 constructed based on the maximum likelihood method of MEGA 11.

Figure 5

Genome circle mapping and COG annotation of MEPW12. (A) Genomic circle diagram of strain MEPW12; (B) COG database annotations for strain MEPW12.

Figure 6

Pfam database annotations and NR database annotations for MEPW12. (A) Pfam database annotations for strain MEPW12; (B) NR database annotations for strain MEPW12.

Figure 7

GO functional annotation and KEGG signaling pathways annotation for MEPW12 (A) GO functional annotation map of strain MEPW12; (B) Results of KEGG signal pathway enrichment analysis of strain MEPW12.

Figure 8

Comparative genomics and pan-genomic analysis. (A) Collinearity analysis; (B) ANI analysis; (C) Pan-genome, core genome, and gene cluster relationship chart; (D) Pan-genome map based on COG annotation.

Figure 9

Changes in gene expression involved in the plant hormone signaling pathway. Significance levels: * p < 0.05,** p < 0.01, **** p < 0.0001.