Van Goethem, Marc W.Osborn, Andrew R.Bowen, Benjamin P.Andeer, Peter F.Swenson, Tami L.Clum, AliciaRiley, RobertHe, GuifenKoriabine, MaximSandor, LauraYan, MiDaum, Chris G.Yoshinaga, YukoMakhalanyane, Thulani PeterGarcia-Pichel, FerranVisel, AxelPennacchio, Len A.O’Malley, Ronan C.Northen, Trent R.2022-07-222022-07-222021-11-18Van Goethem, M.W., Osborn, A.R., Bowen, B.P. et al. Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics. Communications Biology 4, 1302 (2021). https://doi.org/10.1038/s42003-021-02809-4.2399-3642 (online)10.1038/s42003-021-02809-4https://repository.up.ac.za/handle/2263/86405Supplementary Data 1 : Description: Raw metagenome and metatranscriptome statistics.Supplementary Data 2 : Description: Assembly statistics of short- and long-read metagenomes as well as metatranscriptomes.Supplementary Data 3 : Description: Each biosynthetic gene cluster identified from the assembled metagenomes in this study.Supplementary Data 4 : Description: Each biosynthetic gene cluster identified in the metatranscriptomic assemblies.Supplementary Data 5 : Description: The genes used to calculate transcription of biosynthetic gene clusters and core bacterial genes.Supplementary Data 6 : Description: DESeq2 analysis of significantly transcribed genes between day and night-time transcription.Supplementary Data 7 : Description: Transcriptional scores for cation-related genes.Supplementary Data 8 : Description: Average abundance pattern for each phylum through time.Supplementary Data 9 : Description: Taxonomic composition of metagenomes and metatranscriptomes using fulllength 16S rRNA.Supplementary Data 10 : Description: Normalized sequence data showing scores of transcription at each time point with BGC type and Phylum shownMicrobial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.en© The Author(s) 2021. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License.Microbial biosynthetic gene clustersSoil crustsCyanobacteriaBiocrustsBacterial geneticsMetagenomicsMicrobial ecologyArticle