Abstract
BackgroundBacteria within the genus Streptomyces remain a major source of new natural product discovery and as soil inoculants in agriculture where they promote plant growth and protect from disease. Recently, Streptomyces spp. have been implicated as important members of naturally disease-suppressive soils. To shine more light on the ecology and evolution of disease-suppressive microbial communities, we have sequenced the genome of three Streptomyces strains isolated from disease-suppressive soils and compared them to previously sequenced isolates. Strains selected for sequencing had previously showed strong phenotypes in competition or signaling assays.ResultsHere we present the de novo sequencing of three strains of the genus Streptomyces isolated from disease-suppressive soils to produce high-quality complete genomes. Streptomyces sp. GS93–23, Streptomyces sp. 3211–3, and Streptomyces sp. S3–4 were found to have linear chromosomes of 8.24 Mb, 8.23 Mb, and greater than 7.5 Mb, respectively. In addition, two of the strains were found to have large, linear plasmids. Each strain harbors between 26 and 38 natural product biosynthetic gene clusters, on par with previously sequenced Streptomyces spp. We compared these newly sequenced genomes with those of previously sequenced organisms. We see substantial natural product biosynthetic diversity between closely related strains, with the gain/loss of episomal DNA elements being a primary driver of genome evolution.ConclusionsLong read sequencing data facilitates large contig assembly for high-GC Streptomyces genomes. While the sample number is too small for a definitive conclusion, we do not see evidence that disease suppressive soil isolates are particularly privileged in terms of numbers of biosynthetic gene clusters. The strong sequence similarity between GS93–23 and previously isolated Streptomyces lydicus suggests that species recruitment may contribute to the evolution of disease-suppressive microbial communities.
Highlights
Bacteria within the genus Streptomyces remain a major source of new natural product discovery and as soil inoculants in agriculture where they promote plant growth and protect from disease
Isolation and phenotypic characterization of strains Each of the strains sequenced for this study were selected because (i) they were isolated from soils with measurable disease-suppressive characteristics, and (ii) they displayed strong phenotypes in competition or signaling assays
GS93–23 was isolated from a potato scab-suppressive plot in Grand Rapids, MN using the Anderson Air Sampler isolation method [21, 22]
Summary
Bacteria within the genus Streptomyces remain a major source of new natural product discovery and as soil inoculants in agriculture where they promote plant growth and protect from disease. Ninety percent of the 2000 major diseases of the 31 principle crops in the US are caused by soil-borne pathogens [2, 3], and soil microbial communities can have a protective effect [4]. Natural and agricultural disease-suppressive soils (DSSs) have been identified that provide long-lasting and stable protection against numerous bacterial and fungal pathogens [7]. In addition to preventing crop loss, DSSs can lower the cost of production by removing the need for pesticide application. They have been reported against many major crop pathogens, including wheat take-all disease, potato scab, and wilt on melon [8,9,10,11,12]. Diseasesuppression is correlated with increased antagonistic or competitive capacities in one or more isolates from the soil microbial community, and this behavior can emerge in a soil following long-term monoculture [7, 13,14,15,16]
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