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Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics.

التفاصيل البيبلوغرافية
العنوان: Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics.
المؤلفون: Van Goethem MW; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Osborn AR; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Bowen BP; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Andeer PF; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Swenson TL; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA.; Labcorp Drug Development, Covance, Madison, WI, USA., Clum A; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Riley R; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., He G; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Koriabine M; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Sandor L; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Yan M; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Daum CG; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Yoshinaga Y; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Makhalanyane TP; Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genomics and Microbiology, University of Pretoria, Lynnwood Rd, Hatfield, Pretoria, 0028, South Africa., Garcia-Pichel F; Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.; School of Life Sciences, Arizona State University, Tempe, AZ, USA., Visel A; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Pennacchio LA; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., O'Malley RC; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA.; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Northen TR; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA. TRNorthen@lbl.gov.; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA. TRNorthen@lbl.gov.
المصدر: Communications biology [Commun Biol] 2021 Nov 18; Vol. 4 (1), pp. 1302. Date of Electronic Publication: 2021 Nov 18.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Nature Publishing Group UK Country of Publication: England NLM ID: 101719179 Publication Model: Electronic Cited Medium: Internet ISSN: 2399-3642 (Electronic) Linking ISSN: 23993642 NLM ISO Abbreviation: Commun Biol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London, United Kingdom : Nature Publishing Group UK, [2018]-
مواضيع طبية MeSH: Metagenome* , Secondary Metabolism* , Soil Microbiology*, Bacteria/*metabolism , Microbiota/*genetics, Bacteria/genetics ; Metagenomics ; Multigene Family ; Utah
مستخلص: Microbial 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.
(© 2021. The Author(s).)
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معلومات مُعتمدة: DE-AC02-05CH11231 DOE | Office of Science (SC)
تواريخ الأحداث: Date Created: 20211119 Date Completed: 20211224 Latest Revision: 20230209
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC8602731
DOI: 10.1038/s42003-021-02809-4
PMID: 34795375
قاعدة البيانات: MEDLINE
الوصف
تدمد:2399-3642
DOI:10.1038/s42003-021-02809-4