Microbial community drivers of PK/NRP gene diversity in selected global soils

Abstract

Background The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natural products allowing the exploitation of a larger fraction of the microbial community. Polyketide (PK) and non-ribosomal pepetide (NRP) natural products have been reported to be related to compounds with antimicrobial and anticancer activities. We report here a new culture-independent approach to explore bacterial biosynthetic diversity and determine bacterial phyla in the microbial community associated with PK and NRP diversity in selected soils. Results Through amplicon sequencing, we explored the microbial diversity (16S rRNA gene) of 13 soils from Antarctica, Africa, Europe and a Caribbean island and correlated this with the amplicon diversity of the adenylation (A) and ketosynthase (KS) domains within functional genes coding for non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), which are involved in the production of NRP and PK, respectively. Mantel and Procrustes correlation analyses with microbial taxonomic data identified not only the well-studied phyla Actinobacteria and Proteobacteria , but also, interestingly, the less biotechnologically exploited phyla Verrucomicrobia and Bacteroidetes , as potential sources harbouring diverse A and KS domains. Some soils, notably that from Antarctica, provided evidence of endemic diversity, whilst others, such as those from Europe, clustered together. In particular, the majority of the domain reads from Antarctica remained unmatched to known sequences suggesting they could encode enzymes for potentially novel PK and NRP. Conclusions The approach presented here highlights potential sources of metabolic novelty in the environment which will be a useful precursor to metagenomic biosynthetic gene cluster mining for PKs and NRPs which could provide leads for new antimicrobial metabolites. Electronic supplementary material The online version of this article (10.1186/s40168-019-0692-8) contains supplementary material, which is available to authorized users.

Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica

“…comparable with Benaud and co-worker's study [12] due to different methodological procedures, they are in agreement with the ones presented by Borsetto [13].…”

“…In comparison with similar studies in different ecosystems, such as American desert soil [8], urban park soils [34], and even from soils distributed at a global scale [7] the biosynthetic diversity observed in Maxwell Bay (Tables S2 and S3) is clearly inferior, which is expected for a continent with extreme environmental constraints [13]. Very recently, Benaud [12] and Borsetto [13] have assessed biosynthetic diversity in Antarctica, and while diversity indices presented here are not directly comparable with Benaud and co-worker's study [12] due to different methodological procedures, they are in agreement with the ones presented by Borsetto [13].…”

“…A positive correlation between the diversity of biosynthetic genes and the diversity of the known-producers Proteobacteria, Actinobacteria, and Planctomycetes and for the less known Acidobacteria and Gemmatimonadetes bacterial phyla was observed ( Table 1). Recently Borsetto and co-workers [13] also found the Gemmatimonadetes phylum to be positively correlated with biosynthetic genes' diversity. Curiously, samples 72 and TC3, the most biosynthetically diverse ( Figure 2), are located geographically very closely to sample 54 (Figure 1), the least biosynthetically diverse ( Figure 2).…”

“…A large percentage (from 19% to 59% of relative abundance by sample) of the assembled KS OTUs were most closely related to environmental sample sequences, likely obtained from metagenome surveys as well as biosynthetic gene mining studies across the globe [13,59,60]. Regarding Actinobacteria, the chemically rich order Strepromycetales is widely distributed and accounts for 58% of KS domains sequences in sample 54 ( Figure 6C).…”

“…As such, metabarcoding approaches to study PKS and NRPS diversity in Antarctic ecosystems represent a simple and effective strategy to understand the biosynthetic potential of a large number of sampling sites [7]. A couple of such studies have been carried out very recently in Antarctica [12,13] revealing that soils at different Antarctica locations harbor multiple endemic PKS and NRPS genes, likely to be involved in the synthesis of new chemical diversity. In Antarctic soils, the percentage of yet-uncultured genera is expected to be much higher [14] than the 82% described for general soils [15].…”