Draft genome sequence and metabolomics data for Streptomyces sp. ADLamb9 isolated from the rhizosphere of Lavandula dentata

TL;DR

This paper reports the genome sequence and metabolite profile of a Streptomyces strain from lavender rhizosphere, revealing its potential for producing siderophores and aiding in bioremediation.

Contribution

The study identifies novel siderophore metabolites and gene clusters in Streptomyces sp. ADLamb9, including the effect of rare earth elements on their biosynthesis.

Findings

Streptomyces sp. ADLamb9 produces multiple siderophores including desferrioxamine B, IC202C, mirubactin, and desferrioxamine A1C.

The presence of cerium differentially affects the accumulation of catecholate and hydroxamate siderophores.

Genomic analysis identified four putative siderophore biosynthetic gene clusters in the 8.2 Mb genome.

Abstract

Iron-chelating molecules or siderophores play pivotal roles in soil ecosystems, particularly in facilitating plant iron uptake as well as the phytoremediation of metal-polluted environments. Lavandula dentata, commonly referred to as French Lavender, is a valuable species for siderophore production due to its ability to thrive in iron-deficient Mediterranean soils by forming symbiotic relationships with siderophore-producing rhizosphere microbes. Here, we used a Chrome Azurol S (CAS) overlay assay to isolate a yellow-pigmented L. dentata rhizosphere siderophore-producing bacterium. This isolate also demonstrated antibacterial and antifungal activities against Bacillus subtilis and Aspergillus flavus, respectively. Genomic sequencing revealed that the isolate was Streptomyces sp. ADLamb9 with a genome size of 8.2 Mb and 71.77% GC content. antiSMASH analysis of the Streptomyces sp. ADLamb9 genome identified four putative siderophore biosynthetic gene clusters as well as the catecholate siderophore mirubactin. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) masses consistent with desferrioxamine B (561.3604 m/z), IC202C (517.3342 m/z), mirubactin (605.2207 m/z), as well as previously unreported desferrioxamine A1C. Notably, the presence of the rare earth element cerium differentially affected the accumulation of catecholate and hydroxamate siderophores, highlighting our incomplete understanding of the complex regulation and relationship between siderophore biosynthesis genes. These datasets, deposited at NCBI under the BioProject accession number PRJNA1224804, contribute to the broader scientific understanding of metabolite diversity and genomic features of Streptomyces sp. ADLamb9, providing insight into its use in bioremediation, especially in the presence of rare earth elements.

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