دورية أكاديمية
أعرض في EDS

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type.

التفاصيل البيبلوغرافية
العنوان: Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type.
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.)
References: Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432. (PMID: 30357350)
PLoS One. 2015 Jun 23;10(6):e0130659. (PMID: 26102275)
Biochim Biophys Acta. 2013 Jun;1830(6):3670-95. (PMID: 23428572)
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D115-9. (PMID: 14681372)
Proc Natl Acad Sci U S A. 2014 Mar 11;111(10):3757-62. (PMID: 24550451)
mSystems. 2020 Jan 14;5(1):. (PMID: 31937678)
Mol Biol Evol. 2015 Jan;32(1):268-74. (PMID: 25371430)
mBio. 2019 Oct 1;10(5):. (PMID: 31575762)
Proc Natl Acad Sci U S A. 2016 Dec 20;113(51):14811-14816. (PMID: 27911822)
Acc Chem Res. 2015 Jul 21;48(7):1909-19. (PMID: 26079760)
Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20759-64. (PMID: 24297932)
Glob Ecol Biogeogr. 2010 Jan;19(1):27-39. (PMID: 24443643)
Nat Microbiol. 2018 Jul;3(7):836-843. (PMID: 29807988)
Bioinformatics. 2015 May 15;31(10):1674-6. (PMID: 25609793)
Trends Microbiol. 2017 Apr;25(4):280-292. (PMID: 28038926)
Microbiome. 2019 May 22;7(1):78. (PMID: 31118083)
Curr Opin Chem Biol. 2012 Apr;16(1-2):117-23. (PMID: 22342766)
Appl Environ Microbiol. 2012 May;78(10):3744-52. (PMID: 22427492)
Bioinformatics. 2016 Feb 15;32(4):605-7. (PMID: 26515820)
Microbiol Mol Biol Rev. 2007 Sep;71(3):413-51. (PMID: 17804665)
Genome Biol. 2014;15(12):550. (PMID: 25516281)
Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):2664-2669. (PMID: 29490920)
Chem Biol. 2014 May 22;21(5):679-88. (PMID: 24768308)
Nat Methods. 2014 Nov;11(11):1144-6. (PMID: 25218180)
ISME J. 2017 Dec;11(12):2864-2868. (PMID: 28742071)
Bioinformatics. 2010 Oct 1;26(19):2460-1. (PMID: 20709691)
Genome Res. 2019 Aug;29(8):1352-1362. (PMID: 31160374)
Annu Rev Microbiol. 2004;58:453-88. (PMID: 15487945)
Antibiotics (Basel). 2018 Feb 13;7(1):. (PMID: 29438308)
Nat Rev Microbiol. 2010 Jan;8(1):15-25. (PMID: 19946288)
Biotechnol Adv. 2011 Mar-Apr;29(2):223-9. (PMID: 21130862)
Microbiol Mol Biol Rev. 2012 Sep;76(3):585-96. (PMID: 22933561)
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259. (PMID: 30931475)
Science. 2007 Feb 2;315(5812):640-2. (PMID: 17272720)
Chem Rev. 2017 Apr 26;117(8):5389-5456. (PMID: 28256131)
Nat Rev Microbiol. 2018 Oct;16(10):629-645. (PMID: 30181663)
Sci Rep. 2017 Apr 13;7(1):862. (PMID: 28408760)
Bioinformatics. 2016 Jul 1;32(13):1933-42. (PMID: 27153688)
mSystems. 2018 Dec 26;3(6):. (PMID: 30637337)
Nat Commun. 2016 Oct 24;7:13219. (PMID: 27774985)
Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):11615-11620. (PMID: 29078342)
Bioinformatics. 2012 Jun 1;28(11):1420-8. (PMID: 22495754)
Nat Methods. 2012 Mar 04;9(4):357-9. (PMID: 22388286)
mBio. 2020 Jun 16;11(3):. (PMID: 32546614)
Genome Res. 2015 Jul;25(7):1043-55. (PMID: 25977477)
Front Microbiol. 2018 Sep 24;9:2049. (PMID: 30319555)
PeerJ. 2016 Nov 8;4:e2687. (PMID: 27843720)
Bioinformatics. 2009 Aug 1;25(15):1972-3. (PMID: 19505945)
Annu Rev Biochem. 2012;81:479-505. (PMID: 22404629)
Nat Rev Microbiol. 2006 Apr;4(4):249-58. (PMID: 16501584)
Nat Microbiol. 2016 Apr 11;1:16048. (PMID: 27572647)
Nature. 2018 Jun;558(7710):440-444. (PMID: 29899444)
Nat Commun. 2019 Oct 8;10(1):4563. (PMID: 31594941)
BMC Bioinformatics. 2010 Mar 08;11:119. (PMID: 20211023)
Nucleic Acids Res. 2000 Jan 1;28(1):27-30. (PMID: 10592173)
PLoS One. 2016 Mar 14;11(3):e0151087. (PMID: 26975050)
Nucleic Acids Res. 2017 Jul 3;45(W1):W36-W41. (PMID: 28460038)
Nat Methods. 2017 Jun;14(6):587-589. (PMID: 28481363)
Nat Commun. 2017 Feb 06;8:14207. (PMID: 28165449)
Front Microbiol. 2019 Apr 26;10:893. (PMID: 31080444)
Nat Microbiol. 2019 Aug;4(8):1356-1367. (PMID: 31110364)
Nat Biotechnol. 2017 Aug 8;35(8):725-731. (PMID: 28787424)
PeerJ. 2015 Aug 27;3:e1165. (PMID: 26336640)
Nat Commun. 2019 Sep 13;10(1):4173. (PMID: 31519891)
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
الوصف
تدمد:2150-7511
DOI:10.1128/mBio.00416-20