Revealing the role of Plant Growth Promoting Rhizobacteria in suppressive soils against Fusarium oxysporum f.sp. cubense based on metagenomic analysis

Abstract

Fusarium oxysporum f.sp. cubense (Foc) is a soil-borne pathogen causing fusarium wilt banana disease. Management of soil-borne disease generally required the application of toxic pesticides or fungicides strongly affect the soil microbiomes ecosystem. Suppressive soil is a promising method for controlling soil-borne pathogens in which soil microbiomes may affect the suppressiveness. The comparative analysis of microbial diversity was conducted from suppressive and conducive soils by analyzing whole shotgun metagenomic DNA data. Two suppressive soil samples and two conducive soil samples were collected from a banana plantation in Sukabumi, West Java, Indonesia. Each soil sample was prepared by mixing the soil samples collected from three points sampling sites with 20 cm depth. Analysis of microbial abundance, diversity, co-occurrence network using Metagenome Analyzer 6 (MEGAN6) and functional analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed. Data showed the abundance of Actinobacteria, Betaproteobacteria, Rhizobiales, Burkholderiales, Bradyrhizobiaceae, Methylobacteriaceae, Rhodopseudomonas palustri s, and Methylobacterium nodulans were higher in the suppressive than conducive soils. Interestingly, those bacteria groups are known functionally as members of Plant Growth Promoting Rhizobacteria (PGPR). The co-occurrence analysis showed Pseudomonas, Burkholderia , and Streptomyces were present in the suppressive soils, while Bacillus and more Streptomyces were found in the conducive soils. Furthermore, the relative abundance of Pseudomonas , Burkholderia , Bacillus , and Streptomyces was performed. The analysis showed that the relative abundance of Pseudomonas and Burkholderia was higher in the suppressive than conducive soils. Therefore, it assumed Pseudomonas and Burkholderia play a role in suppressing Foc based on co-occurrence and abundance analysis. Functional analysis of Pseudomonas and Burkholderia showed that the zinc/manganese transport system was higher in the suppressive than conducive soils. In contrast, the phosphate transport system was not found in conducive soils. Both functions are may be responsible for the synthesis of a siderophore and phosphate solubilization. In conclusion, this study provides information that PGPR may be contributing to Foc growth suppressing by releasing secondary metabolites.

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

“…Microbiome‐based studies have shown an abundance of various PGPR communities in disease suppressive soils than conducive soils. For example, several rhizobacteria belonging to Actinobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Rhizobiales, Burkholderiales, Bradyrhizobiaceae, Methylobacteriaceae, have been found as major predictors for soil suppressiveness against Fusarium oxysporum (Nisrina et al, 2021; Trivedi et al, 2017; Zheng et al, 2020). In addition, higher Zn/Mn and phosphate transport systems of Pseudomonas and Burkholderia having a role in siderophore and P solubilization were linked with the suppressiveness of soils (Nisrina et al, 2021).…”

“…For example, several rhizobacteria belonging to Actinobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Rhizobiales, Burkholderiales, Bradyrhizobiaceae, Methylobacteriaceae, have been found as major predictors for soil suppressiveness against Fusarium oxysporum (Nisrina et al, 2021; Trivedi et al, 2017; Zheng et al, 2020). In addition, higher Zn/Mn and phosphate transport systems of Pseudomonas and Burkholderia having a role in siderophore and P solubilization were linked with the suppressiveness of soils (Nisrina et al, 2021). Similarly, microbial communities ( Pseudomonas in Proteobacteria and Streptomyces in Actinobacteria ) harbouring nonribosomal peptide (NRP)‐synthesizing genes were abundant in the suppressive soil than in the conducive soils to banana Fusarium wilt disease (Zhao et al, 2018).…”

Characterization of the Soil Bacterial Community from Selected Boxwood Gardens across the United States

“…Second, 66 bacterial species known to have strains with antagonistic activities against plant pathogens (BCA candidates) were also identified. The bacterial orders and BCA candidates observed resemble those in the suppressive soils from other environments [ 21 , 59 , 60 , 61 , 62 ]. They are important components of a healthy soil microbiome [ 3 , 4 , 63 , 64 ], and likely have contributed to the decline of the Cps population in these garden soils [ 33 ].…”

“…Specifically, Pseudomonas , Bacillus , Paenibacillus , and Streptomyces species are well known to inhibit the formation and germination of microsclerotia by Verticillium spp. or increase their mortality [ 80 , 81 , 82 , 83 ], by producing volatile organic compounds [ 81 ] or chitin lysis enzymes [ 62 , 79 ]. Some of the same genera identified in this study likely have contributed to the decline of Cps , which also produces microsclerotia for survival in soils [ 84 ].…”

mgPGPT: Metagenomic analysis of plant growth-promoting traits

“…Here, for instance, the metagenome analysis pipeline DIAMOND+MEGAN6 (26, 27, 28, 29, 30) can be used, as it comes up with the conservative read alignment approach against NCBInr proteins that are further mapped to NCBI (31) or GTDB (32) taxonomy and various functional classifications, including KEGG. For example, Nisrina and coworkers applied a MEGAN approach for PGPT screening of PGPBs in fungi suppressive soils (33). Recently, the AnnoTree assignment approach was added to MEGAN, that showed higher accuracy especially for environmental samples like soil, addressing a huge amount of uncultured strains as it relies on additional protein sequences derived from metagenome-assembled-genomes (MAGS) (34, 35).…”