Sorgoleone degradation by sorghum-associated bacteria; an opportunity for enforcing plant growth promotion

Abstract

Metabolite exchange between plant roots and their associated rhizosphere microbiomes underpins plant growth promotion by microbes. Sorghum bicolor is a cereal crop that feeds animals and humans and is used for bioethanol production. Its root tips exude large amounts of a lipophilic benzoquinone called sorgoleone. Sorgoleone is an allelochemical that suppresses the growth of competing plant seedlings and is mineralized by microbes in soil. As an avenue to understand how sorghum and its root microbiome may be connected through root exudates, we identified the molecular determinants of microbial sorgoleone degradation and the distribution of this trait among microbes. We isolated and studied from sorghum-associated soils, three bacterial strains classified as Acinetobacter, Burkholderia, and Pseudomonas species that grow with sorgoleone as a sole carbon and energy source. The genomes of these strains were sequenced and subjected to transcriptomic and gene fitness analyses to identify candidate sorgoleone degradation genes. Follow up mutational analysis showed that sorgoleone catabolism is dependent on four contiguous genes that are conserved among the species we sequenced. Phylogenetic analysis of the sorgoleone degradation gene cluster showed that sorgoleone catabolism is enriched in sorghum-associated Streptomyces strains. The discovery of bacteria that grow on a compound like sorgoleone that is plant specific and not widely distributed in the environment, provides an opportunity to study how a plant exudate can enforce the development of a rhizosphere specific microbiome for the mutual benefit of plant and microbe.

Defined synthetic microbial communities colonize and benefit field-grown sorghum

“…Alternatively, this observation could be explained by strain-level competition for resources. Ongoing work from our group suggests that Streptomyces are good solubilizers of a wide variety of novel metabolites (Oda et al, 2023). We propose that Streptomyces may directly use sorghum-specific root exudate compounds such as sorgoleone and introduction of other utilizers creates competition for these carbon sources.…”

Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders inAcinetobacter pittii

“…Global proteomics results showed that all four gene members of the Srg gene cluster implicated in sorgoleone catabolism were readily identified and were more abundant in culturing conditions with sorgoleone compared to acetate. 18 From this pathway, OH685_09420 was identified as a protein binder of sorgoleone through competitive labeling with SoDA-PAL and purified sorgoleone. Recent technological advances in structural bioinformatics software, which has enabled faster and more accurate protein structure prediction through artificial intelligence, provide new opportunities to combine experimental and computational approaches for elucidation of protein functions and interactions.…”

“…This pathway is encoded by a gene cluster containing a putative monooxygenase, two putative α/β fold hydrolases, and a cytosine deaminase (Figure 5A). 18 Initially our global proteomic analysis revealed a marked difference in coverage of this pathway between carbon sources, where the lowest pathway member coverage was observed in the acetate culture (A), with higher coverage observed with the acetate to sorgoleone (AS) culture and sorgoleone only culture (S) (Figure 5B). This trend was further reinforced with competitive SoDA-PAL labelling of the acetate to sorgoleone cultures, as competition was observed for all four pathway members with the two putative α/β fold hydrolases (OH685_09415, OH685_09420) exhibiting significant competition, implying a direct interaction of those protein targets with sorgoleone (Figure 5C).…”

“…The sorghum rhizosphere associated bacterium Acinetobacter pittii SO1 was found to utilize sorgoleone as a carbon source and was selected as an ideal bacterium for this study. 18 We evaluated three different culturing strategies that reflect A. pittii growth on acetate, sorgoleone, or both (started on acetate then Scheme 1. SoDA-PAL probe synthesis.…”

“…Recently, our group has identified specific genes response for utilization of sorgoleone as a sole carbon source in bacterial isolates from the sorghum rhizosphere and specifically in Acinetobacter pittii strain SO1 (TaxonID:48296). 18 Acinetobacter have been shown to be beneficial for plant growth by engaging in beneficial nutrient cycling and by protecting against pathogens and abiotic stress. 19,20 These previous studies demonstrate that sorgoleone can have disparate impacts on the growth and functions of different microbial species, highlighting the potential of sorgoleone as a promising modulator of microbial functions and interactions in the sorghum rhizosphere.…”