A panoramic view of the genomic landscape of the genus Streptomyces

Pangenome mining of the Streptomyces genus redefines species' biosynthetic potential

BACKGROUND

Streptomyces is a highly diverse genus known for the production of secondary or specialized metabolites with a wide range of applications in the medical and agricultural industries. Several thousand complete or nearly complete Streptomyces genome sequences are now available, affording the opportunity to deeply investigate the biosynthetic potential within these organisms and to advance natural product discovery initiatives.

RESULTS

We perform pangenome analysis on 2371 Streptomyces genomes, including approximately 1200 complete assemblies. Employing a data-driven approach based on genome similarities, the Streptomyces genus was classified into 7 primary and 42 secondary Mash-clusters, forming the basis for comprehensive pangenome mining. A refined workflow for grouping biosynthetic gene clusters (BGCs) redefines their diversity across different Mash-clusters. This workflow also reassigns 2729 known BGC families to only 440 families, a reduction caused by inaccuracies in BGC boundary detections. When the genomic location of BGCs is included in the analysis, a conserved genomic structure, or synteny, among BGCs becomes apparent within species and Mash-clusters. This synteny suggests that vertical inheritance is a major factor in the diversification of BGCs.

CONCLUSIONS

Our analysis of a genomic dataset at a scale of thousands of genomes refines predictions of BGC diversity using Mash-clusters as a basis for pangenome analysis. The observed conservation in the order of BGCs' genomic locations shows that the BGCs are vertically inherited. The presented workflow and the in-depth analysis pave the way for large-scale pangenome investigations and enhance our understanding of the biosynthetic potential of the Streptomyces genus.

Biodiversity and Antifungal Activities of Amazonian Actinomycetes Isolated from Rhizospheres of Inga edulis Plants

BACKGROUND

Actinobacteria are major producers of antibacterial and antifungal metabolites and are growing their search for substances of biotechnological interest, especially for use in agriculture, among other applications. The Amazon is potentially rich in actinobacteria; however, almost no research studies exist. Thus, we present a study of the occurrence and antifungal potential of actinobacteria from the rhizosphere of Inga edulis, a native South American plant and one that is economically useful in the whole of the Amazon.

METHODS

Among the 64 actinobacteria strains isolated from the rhizosphere of three Inga edulis plants, 20 strains were selected and submitted to dual-culture assays against five important phytopathogenic fungi and morphological and 16S rRNA gene analyses. Two strains, LaBMicrA B270 and B280, were also studied for production curves of metabolic extracts and antifungal activities, including their minimum inhibitory concentration (MIC) against phytopathogenic fungi.

RESULTS

Among the 20 strains, 90% were identified as Streptomyces and 10% as Kitasatospora. All the strains showed antagonisms against two or more of five phytopathogens: Corynespora cassiicola, Colletotrichum guaranicola, Colletotrichum sp., Pestalotiopsis sp., and Sclerotium coffeicola. Streptomyces spp. strains LaBMicrA B270 and B280 were active against phytopathogens of the guarana plant (Paullinia cupana). Furthermore, AcOEt/2-propanol 9:1 extract from the 10-day strain LaBMicrA B280 cultured medium presented activity against all the phytopathogens tested, with a minimum inhibitory concentration of 125 μg/mL.

CONCLUSIONS

The results revealed various actinomycetes in three rhizospheres of I. edulis in the Amazon and the high potential of metabolic extracts from some of these bacterial strains against phytopathogenic fungi that destroy numerous crops.

Streptomyces castrisilvae sp. nov. and Streptomyces glycanivorans sp. nov., novel soil streptomycetes metabolizing mutan and alternan

Six bacterial strains, Mut1T, Mut2, Alt1, Alt2, Alt3T, and Alt4, were isolated from soil samples collected in parks in Gothenburg, Sweden, based on their ability to utilize the insoluble polysaccharides α-1,3-glucan (mutan; Mut strains) or the mixed-linkage α-1,3/α-1,6-glucan (alternan; Alt strains). Analysis of 16S rRNA gene sequences identified all strains as members of the genus Streptomyces. The genomes of the strains were sequenced and subsequent phylogenetic analyses identified Mut2 as a strain of Streptomyces laculatispora and Alt1, Alt2 and Alt4 as strains of Streptomyces poriferorum, while Mut1T and Alt3T were most closely related to the type strains Streptomyces drozdowiczii NBRC 101007T and Streptomyces atroolivaceus NRRL ISP-5137T, respectively. Comprehensive genomic and biochemical characterizations were conducted, highlighting typical features of Streptomyces, such as large genomes (8.0-9.6 Mb) with high G+C content (70.5-72.0%). All six strains also encode a wide repertoire of putative carbohydrate-active enzymes, indicating a capability to utilize various complex polysaccharides as carbon sources such as starch, mutan, and cellulose, which was confirmed experimentally. Based on phylogenetic and phenotypic characterization, our study suggests that strains Mut1T and Alt3T represent novel species in the genus Streptomyces for which the names Streptomyces castrisilvae sp. nov. and Streptomyces glycanivorans sp. nov. are proposed, with strains Mut1T (=DSM 117248T=CCUG 77596T) and Alt3T (=DSM 117252T=CCUG 77600T) representing the respective type strains.

Whole genome-based comparative analysis of the genus Streptomyces reveals many misclassifications

Streptomyces species are experts in the production of bioactive secondary metabolites; however, their taxonomy has fallen victim of the tremendous interest shown by the scientific community, evident in the discovery of numerous synonymous in public repositories. Based on genomic data from NCBI Datasets and nomenclature from the LPSN database, we compiled a dataset of 600 Streptomyces species along with their annotations and metadata. To pinpoint the most suitable taxonomic classification method, we conducted a comprehensive assessment comparing multiple methodologies, including analysis of 16S rRNA, individual housekeeping genes, multilocus sequence analysis (MLSA), and Fast Average Nucleotide Identity (FastANI) on a subset of 409 species with complete data. Due to insufficient resolution of 16S rRNA and inconsistency observed in individual housekeeping genes, we performed a more in-depth analysis, comparing only FastANI and MLSA, which expanded our dataset to include 502 species. With FastANI validated as the preferred method, we conducted pairwise analysis on the entire dataset identifying 59 non-unique species among the 600, and subsequently refined the dataset to 541 unique species. Additionally, we collected data on 724 uncharacterized Streptomyces strains to investigate the uniqueness potential of the unannotated fraction of the Streptomyces genus. Utilizing FastANI, 289 strains could be successfully classified into one of the 541 Streptomyces species. KEY POINTS: • Evaluation of taxonomic classification methods for Streptomyces species. • Whole genome analysis, specifically FastANI, has been chosen as preferred method. • Various reclassifications are proposed within the Streptomyces genus.

Harnessing co-evolutionary interactions between plants and Streptomyces to combat drought stress

Streptomyces is a drought-tolerant bacterial genus in soils, which forms close associations with plants to provide host resilience to drought stress. Here we synthesize the emerging research that illuminates the multifaceted interactions of Streptomyces spp. in both plant and soil environments. It also explores the potential co-evolutionary relationship between plants and Streptomyces spp. to forge mutualistic relationships, providing drought tolerance to plants. We propose that further advancement in fundamental knowledge of eco-evolutionary interactions between plants and Streptomyces spp. is crucial and holds substantial promise for developing effective strategies to combat drought stress, ensuring sustainable agriculture and environmental sustainability in the face of climate change.

Ecology shapes the genomic and biosynthetic diversification of Streptomyces bacteria from insectivorous bats

Streptomyces are prolific producers of secondary metabolites from which many clinically useful compounds have been derived. They inhabit diverse habitats but have rarely been reported in vertebrates. Here, we aim to determine to what extent the ecological source (bat host species and cave sites) influence the genomic and biosynthetic diversity of Streptomyces bacteria. We analysed draft genomes of 132 Streptomyces isolates sampled from 11 species of insectivorous bats from six cave sites in Arizona and New Mexico, USA. We delineated 55 species based on the genome-wide average nucleotide identity and core genome phylogenetic tree. Streptomyces isolates that colonize the same bat species or inhabit the same site exhibit greater overall genomic similarity than they do with Streptomyces from other bat species or sites. However, when considering biosynthetic gene clusters (BGCs) alone, BGC distribution is not structured by the ecological or geographical source of the Streptomyces that carry them. Each genome carried between 19-65 BGCs (median=42.5) and varied even among members of the same Streptomyces species. Nine major classes of BGCs were detected in ten of the 11 bat species and in all sites: terpene, non-ribosomal peptide synthetase, polyketide synthase, siderophore, RiPP-like, butyrolactone, lanthipeptide, ectoine, melanin. Finally, Streptomyces genomes carry multiple hybrid BGCs consisting of signature domains from two to seven distinct BGC classes. Taken together, our results bring critical insights to understanding Streptomyces-bat ecology and BGC diversity that may contribute to bat health and in augmenting current efforts in natural product discovery, especially from underexplored or overlooked environments.

Genomic analysis of lignocellulolytic enzyme producing novel Streptomyces sp.MS2A for the bioethanol applications

The conversion of lignocellulosic waste to energy offers a cost-effective biofuel. The current study discusses the utilization of cellulose in rice husks by lichen-associated Streptomyces sp. MS2A via carbohydrate metabolism. Out of 39 actinobacteria, one actinobacterial strain MS2A, showed CMCase, FPase, and cellobiohydrolase activity. The whole genome analysis of Streptomyces sp. MS2A showed maximum similarity with Streptomyces sp. CCM_MD2014. The genome analysis confirmed the presence of cellulose-degrading genes along with xylan-degrading genes that code for GH3, GH6, GH9, GH11, GH43, GH51, and 15 other GH families with glycosyl transferase, carbohydrate-binding modules, and energy metabolism groups. Protein family analysis corroborates the enzyme family. Among the 19,402 genes of Streptomyces sp. MS2A, approximately 70 GH family codes for lignocellulose degradation enzymes. The structure of cellulase was modeled and validated. Scanning electron microscopy and gas chromatography-mass spectrometry (GCMS) was performed to analyze the lignocellulosic degradation of rice husk and the end product bioethanol.

A panoramic view of the genomic landscape of the genus Streptomyces

We delineate the evolutionary plasticity of the ecologically and biotechnologically important genus Streptomyces, by analysing the genomes of 213 species. Streptomycetes genomes demonstrate high levels of internal homology, whereas the genome of their last common ancestor was already complex. Importantly, we identify the species-specific fingerprint proteins that characterize each species. Even among closely related species, we observed high interspecies variability of chromosomal protein-coding genes, species-level core genes, accessory genes and fingerprints. Notably, secondary metabolite biosynthetic gene clusters (smBGCs), carbohydrate-active enzymes (CAZymes) and protein-coding genes bearing the rare TTA codon demonstrate high intraspecies and interspecies variability, which emphasizes the need for strain-specific genomic mining. Highly conserved genes, such as those specifying genus-level core proteins, tend to occur in the central region of the chromosome, whereas those encoding proteins with evolutionarily volatile species-level fingerprints, smBGCs, CAZymes and TTA-codon-bearing genes are often found towards the ends of the linear chromosome. Thus, the chromosomal arms emerge as the part of the genome that is mainly responsible for rapid adaptation at the species and strain level. Finally, we observed a moderate, but statistically significant, correlation between the total number of CAZymes and three categories of smBGCs (siderophores, e-Polylysin and type III lanthipeptides) that are related to competition among bacteria.