Functional and Genomic Analysis of Rouxiella badensis SER3 as a Novel Biocontrol Agent of Fungal Pathogens

Abstract

In recent decades, various bacterial species have been characterized as biocontrol agents for plant crop diseases; however, only a few genera have been predominantly reported in the literature. Therefore, the identification of new antagonists against phytopathogens is essential for boosting sustainable food production systems. In this study, we evaluated the role of strain SER3 from the recently discovered Rouxiella badensis as a biocontrol agent. SER3 was isolated from the phyllosphere of decaying strawberry fruit (Fragaria × ananassa) and showed different grades of antagonism against 20 fungal pathogens of berries, based on confrontation assays, due to the action of its diffusible and volatile compounds. These fungal pathogens were isolated from decayed strawberry, blackberry, and blueberry fruit and were characterized through internal transcribed spacer (ITS) sequencing and homology searches, exhibiting similarity with well-known postharvest pathogens such as Botrytis, Fusarium, Geotrichum, Mucor, Penicillium, Alternaria, and Botryosphaeria. Koch’s postulates were confirmed for most pathogens by reinfecting berry fruit. SER3 showed good capacity to inhibit the growth of Botrytis cinerea and Fusarium brachygibbosum in strawberry fruit, affecting mycelial development. To gain better understanding of the genetic and metabolic capacities of the SER3 strain, its draft genome was determined and was found to comprise a single chromosome of 5.08 Mb, 52.8% G + C content, and 4,545 protein-coding genes. Phylogenetic analysis indicated that the SER3 strain is affiliated with the R. badensis species, with an average nucleotide identity >96% and a genome-to-genome distance >70%. A comparison of the genomic properties of R. badensis SER3 and other close bacterial relatives showed several genes with potential functions in biocontrol activities, such as those encoding siderophores, non-ribosomal peptide synthetases, and polyketide synthases. This is the first study to demonstrate a novel role of the recently discovered R. badensis species (and any other species of the genus Rouxiella) as a biocontrol agent against postharvest fungal pathogens.

Investigating the inoculum dynamics of Cladosporium on the surface of raspberry fruits and in the air

“…Strains in the Bacillus genus have been frequently used in commercial biopesticide development on soft fruits. Of particular interest is the genus Rouxiella ; an in vitro study showed that specific Rouxiella strains successfully controlled common pathogens of strawberries (Morales‐Cedeño et al, 2021). This genus was more prevalent on the later fruit development stages (when Cladosporium was noted to decrease); hence, further investigations into the antagonism of this genus against Cladosporium may be warranted.…”

Bacteria existing in pre-pollinated styles (silks) can defend the exposed male gamete fertilization channel of maize against an environmental Fusarium pathogen

“…R. badensis has not been previously reported to suppress GER disease in maize to the best of our knowledge. It has been reported as a novel biocontrol agent against the postharvest fungal pathogens Botrytis cinerea and Fusarium brachygibbosum in strawberry fruit, affecting mycelial development ( Morales-Cedeño et al., 2021 ). It also showed different levels of in vitro antagonism against 20 fungal pathogens in berries ( Morales-Cedeño et al., 2021 ).…”

“…It has been reported as a novel biocontrol agent against the postharvest fungal pathogens Botrytis cinerea and Fusarium brachygibbosum in strawberry fruit, affecting mycelial development ( Morales-Cedeño et al., 2021 ). It also showed different levels of in vitro antagonism against 20 fungal pathogens in berries ( Morales-Cedeño et al., 2021 ). Here, we showed that R. badensis (AS112) seemed to colonize wound sites on silks more than Fg hyphae.…”

Complete genome sequence of Australian soil bacterium Rouxiella badensis DAR84756 resolved with Oxford Nanopore long-read and Illumina sequences

“…Rouxiella badensis is a Gram-negative bacterium in the family Yersiniaceae ( 1 ) found associated with soil and plant ecosystems ( 2 ), with emerging applications including post-harvest preservation of berries ( 3 ), a human antidepressant probiotic ( 4 – 6 ), biosynthesis of L-asparaginase ( 7 ), and uncharacterized antibiotics ( 8 ). High-quality genome sequences, such as described here, allow improved identification of metabolic pathways and secondary metabolite prediction ( 9 , 10 ).…”