دورية أكاديمية
Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type.
العنوان: | Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type. |
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المؤلفون: | Sharrar AM; Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, USA., Crits-Christoph A; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA., Méheust R; Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, USA.; Innovative Genomics Institute, Berkeley, California, USA., Diamond S; Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, USA., Starr EP; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA., Banfield JF; Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, USA jbanfield@berkeley.edu.; Innovative Genomics Institute, Berkeley, California, USA. |
المصدر: | MBio [mBio] 2020 Jun 16; Vol. 11 (3). Date of Electronic Publication: 2020 Jun 16. |
نوع المنشور: | Journal Article; Research Support, U.S. Gov't, Non-P.H.S. |
اللغة: | English |
بيانات الدورية: | Publisher: American Society for Microbiology Country of Publication: United States NLM ID: 101519231 Publication Model: Electronic Cited Medium: Internet ISSN: 2150-7511 (Electronic) NLM ISO Abbreviation: mBio Subsets: MEDLINE |
أسماء مطبوعة: | Original Publication: Washington, D.C. : American Society for Microbiology |
مواضيع طبية MeSH: | Microbiota* , Secondary Metabolism* , Soil* , Soil Microbiology*, Bacteria/*metabolism, Bacteria/classification ; Biosynthetic Pathways ; California ; Metagenome ; Multigene Family ; Phylogeny ; Trees |
مستخلص: | Bacteria isolated from soils are major sources of specialized metabolites, including antibiotics and other compounds with clinical value that likely shape interactions among microbial community members and impact biogeochemical cycles. Yet, isolated lineages represent a small fraction of all soil bacterial diversity. It remains unclear how the production of specialized metabolites varies across the phylogenetic diversity of bacterial species in soils and whether the genetic potential for production of these metabolites differs with soil depth and vegetation type within a geographic region. We sampled soils and saprolite from three sites in a northern California Critical Zone Observatory with various vegetation and bedrock characteristics and reconstructed 1,334 metagenome-assembled genomes containing diverse biosynthetic gene clusters (BGCs) for secondary metabolite production. We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria , Chloroflexi , and candidate phylum " Candidatus Dormibacteraeota." Surprisingly, one genome of a candidate phyla radiation (CPR) bacterium coded for a ribosomally synthesized linear azole/azoline-containing peptide, a capacity we found in other publicly available CPR bacterial genomes. Overall, bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy. IMPORTANCE Microbes produce specialized compounds to compete or communicate with one another and their environment. Some of these compounds, such as antibiotics, are also useful in medicine and biotechnology. Historically, most antibiotics have come from soil bacteria which can be isolated and grown in the lab. Though the vast majority of soil bacteria cannot be isolated, we can extract their genetic information and search it for genes which produce these specialized compounds. These understudied soil bacteria offer a wealth of potential for the discovery of new and important microbial products. Here, we identified the ability to produce these specialized compounds in diverse and novel bacteria in a range of soil environments. This information will be useful to other researchers who wish to isolate certain products. Beyond their use to humans, understanding the distribution and function of microbial products is key to understanding microbial communities and their effects on biogeochemical cycles. (Copyright © 2020 Sharrar et al.) |
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فهرسة مساهمة: | Keywords: metagenomics; secondary metabolism; soil microbiology |
سلسلة جزيئية: | figshare 10.6084/m9.figshare.10045988 |
المشرفين على المادة: | 0 (Soil) |
تواريخ الأحداث: | Date Created: 20200618 Date Completed: 20210409 Latest Revision: 20240329 |
رمز التحديث: | 20240329 |
مُعرف محوري في PubMed: | PMC7298704 |
DOI: | 10.1128/mBio.00416-20 |
PMID: | 32546614 |
قاعدة البيانات: | MEDLINE |
تدمد: | 2150-7511 |
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DOI: | 10.1128/mBio.00416-20 |