Abstract
The terrestrial subsurface microbiome has gained considerable amount of interests in the recent years because of its rich potential resource for biomining novel genes coding for metabolites possessing antimicrobial activities. In our previous study, we identified two Streptomyces isolates, designated as ICC1 and ICC4, from the Iron Curtain Cave, Chilliwack, Canada that exhibited antagonistic activities against the multidrug resistant strains of Escherichia coli. In this study, the genomes of these two isolates were sequenced by Illumina MiSeq, assembled and annotated. The genes associated with secondary metabolite production were identified and annotated using the bioinformatics platforms antiSMASH and BAGEL. ICC1 and ICC4 were then cultivated and ICC1 metabolome characterized by UHPLC-ESI-HRMS. The Global Natural Products Social Molecular Networking was used to identify metabolites based on the MS/MS spectral data. ICC1 and ICC4 showed a high level of sequence identity with the terrestrial bacteria Streptomyces lavendulae; however, they possess a greater secondary metabolite potential as estimated by the total number of identified biosynthetic gene clusters (BGCs). In particular, ICC1 and ICC4 had a greater number of polyketide and non-ribosomal peptide BGCs. The most frequently detected BGCs were those predicted to generate terpenes, small and low complexity dipeptides and lipids. Spectral analysis clearly identified a number of diketopiperazine products through matched reference spectra for cyclo (Leu-Pro), cyclo (Pro-Val) and cyclo [(4-hydroxyPro)-Leu]. One of the terpenes gene clusters predicted by antiSMASH possesses a seven-gene pathway consistent with diazepinomicin biosynthesis. This molecule contains a very rare core structure and its BGC, to date, has only been identified from a single bacterial genome. The tetrapeptide siderophore coelichelin BGC was unambiguously identified in the genome, however, the metabolite could not be identified from the culture extracts. Two type III polyketides, 2′, 5′ – dimethoxyflavone and nordentatin, were identified from the UHPLC-HRMS data of the aqueous and n-butanolic fractions of Streptomyces sp. ICC1, respectively. A BGC likely encoding these metabolites was predicted in both genomes. The predicted similarities in molecule production and genome shared by these two strains could be an indicative of a cooperative mode of living in extreme habitats instead of a competitive one. This secondary metabolite potential may contribute to the fitness of ICC1 and ICC4 in the Iron Curtain Cave.
Highlights
Microbial life is ubiquitous in the Earth’s crust
Preliminary 16S rDNA sequencing of ICC1 and ICC4 indicated that both organisms belong to the genus Streptomyces, which is supported by morphology and growth characteristics of the bacteria
Whole genome sequencing by Illumina MiSeq (Illumina, United States) and de novo genome assembly by PATRIC (Wattam et al, 2017) generated draft genomes of 9,034,309 bp for ICC1 and 9,010,404 bp for ICC4, with a G+C content of 72% for both strains
Summary
Microbial life is ubiquitous in the Earth’s crust. As early as 1980s, the presence of viable microbes were found in various shallow aquifers, caves, and mines, among other subsurface environments (Ghiorse and Wilson, 1988; Yates et al, 1988; Lovley, 1997). Many subsurface environments are challenging to access, representative data is obtained from samples collected from mines and caves (Bonis and Gralnick, 2015; Kutvonen et al, 2015; Miettinen et al, 2015; Rajala et al, 2015), from water seeping through mine walls (Borgonie et al, 2015), by collecting rock material and scrapings from cave (Wu et al, 2015) and mines surfaces (Dziewit et al, 2015) Studies of such environments have shown that metals play a pivotal role in determining subsurface living communities (Parnell et al, 2015). Their biological activity, combined with mass transport of solubilized Fe(II) by groundwater, contribute to speleogenesis of banded iron formations (Parker et al, 2018)
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