دورية أكاديمية
Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism.
| العنوان: | Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism. |
|---|---|
| المؤلفون: | Valentin-Alvarado LE; Graduate Group in Microbiology, University of California, Berkeley, CA, USA.; Innovative Genomics Institute, University of California, Berkeley, CA, USA., Fakra SC; Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Probst AJ; Earth and Planetary Science, University of California, Berkeley, CA, USA.; Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry,, University of Duisburg-Essen, Essen, Essen, Germany., Giska JR; Earth and Planetary Science, University of California, Berkeley, CA, USA.; Cleaner Air Oregon Program, Oregon Department of Environmental Quality, Portland, USA., Jaffe AL; Graduate Group in Microbiology, University of California, Berkeley, CA, USA., Oltrogge LM; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.; Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA., West-Roberts J; Environmental Science, Policy and Management, University of California, Berkeley, CA, USA., Rowland J; Earth and Planetary Science, University of California, Berkeley, CA, USA.; Earth and Env. Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA., Manga M; Earth and Planetary Science, University of California, Berkeley, CA, USA.; University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany., Savage DF; Innovative Genomics Institute, University of California, Berkeley, CA, USA.; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.; Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA., Greening C; Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia., Baker BJ; Department of Integrative Biology, University of Texas, Austin, USA.; Department of Marine Science, University of Texas, Austin, USA., Banfield JF; Innovative Genomics Institute, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.; Earth and Planetary Science, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.; Environmental Science, Policy and Management, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.; Department of Marine Science, University of Texas, Austin, USA. jbanfield@berkeley.edu.; Energy Geoscience Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. jbanfield@berkeley.edu. |
| المصدر: | Microbiome [Microbiome] 2024 Jan 26; Vol. 12 (1), pp. 15. Date of Electronic Publication: 2024 Jan 26. |
| نوع المنشور: | Video-Audio Media; Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: BioMed Central Country of Publication: England NLM ID: 101615147 Publication Model: Electronic Cited Medium: Internet ISSN: 2049-2618 (Electronic) Linking ISSN: 20492618 NLM ISO Abbreviation: Microbiome Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: London: BioMed Central, 2013- |
| مواضيع طبية MeSH: | Ecosystem* , Groundwater*/microbiology, Bacteria/genetics ; Bacteria/metabolism ; Sulfides/metabolism ; Oxidation-Reduction ; Sulfur/metabolism ; Biofilms ; Hydrogen/metabolism ; Phylogeny |
| مستخلص: | Background: Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling. Results: Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa, dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L Conclusions: Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix, and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling. Video Abstract. (© 2024. The Author(s).) |
| References: | Nat Biotechnol. 2018 Nov;36(10):996-1004. (PMID: 30148503) Int J Syst Evol Microbiol. 2004 Sep;54(Pt 5):1477-1482. (PMID: 15388698) ISME J. 2020 Sep;14(9):2261-2274. (PMID: 32457501) Bioinformatics. 2021 Aug 25;37(16):2473-2475. (PMID: 33459763) J Biol Chem. 2017 Aug 25;292(34):14026-14038. (PMID: 28684420) Microbiome. 2021 Feb 16;9(1):46. (PMID: 33593438) FEMS Microbiol Ecol. 2004 Dec 27;51(1):31-53. (PMID: 16329854) Appl Environ Microbiol. 2007 Nov;73(21):7013-22. (PMID: 17766448) ISME J. 2015 Jun;9(6):1434-45. (PMID: 25489728) PeerJ. 2019 Jul 26;7:e7359. (PMID: 31388474) FEMS Microbiol Lett. 2016 Aug;363(16):. (PMID: 27324397) Microbiology (Reading). 1995 Feb;141 ( Pt 2):449-58. (PMID: 7704275) Environ Microbiol. 2000 Aug;2(4):389-98. (PMID: 11234927) Nature. 2011 Oct 16;479(7372):249-52. (PMID: 22002606) Science. 2012 Sep 28;337(6102):1661-5. (PMID: 23019650) ISME J. 2022 Aug;16(8):2056-2059. (PMID: 35440729) Microbiome. 2017 Sep 2;5(1):112. (PMID: 28865481) Nat Microbiol. 2018 Jul;3(7):836-843. (PMID: 29807988) Microbiome. 2022 Feb 16;10(1):33. (PMID: 35172890) Mol Biol Evol. 2013 Apr;30(4):772-80. (PMID: 23329690) Appl Environ Microbiol. 2004 Dec;70(12):7487-96. (PMID: 15574952) Nat Commun. 2019 Jan 28;10(1):463. (PMID: 30692531) Proc Natl Acad Sci U S A. 2015 Jan 6;112(1):244-9. (PMID: 25535390) Bioinformatics. 2016 Feb 15;32(4):605-7. (PMID: 26515820) J Synchrotron Radiat. 2004 May 1;11(Pt 3):239-47. (PMID: 15103110) Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5341-4. (PMID: 8389482) Front Microbiol. 2012 Jan 09;2:276. (PMID: 22291687) Science. 2002 Nov 29;298(5599):1788-90. (PMID: 12459589) Adv Microb Physiol. 2009;54:103-200. (PMID: 18929068) Science. 2007 Nov 30;318(5855):1449-52. (PMID: 17947550) J Synchrotron Radiat. 2010 Sep;17(5):676-82. (PMID: 20724789) Appl Environ Microbiol. 1985 Apr;49(4):887-98. (PMID: 4004221) Appl Environ Microbiol. 2006 Aug;72(8):5596-609. (PMID: 16885314) mBio. 2022 Apr 26;13(2):e0001622. (PMID: 35258328) ISME J. 2016 Nov;10(11):2702-2714. (PMID: 27137126) Science. 2007 Feb 16;315(5814):1003-6. (PMID: 17303759) Proc Natl Acad Sci U S A. 2022 Jan 11;119(2):. (PMID: 34992141) Elife. 2015 Mar 03;4:. (PMID: 25735037) Nat Commun. 2015 Feb 27;6:6372. (PMID: 25721682) Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844) Appl Environ Microbiol. 2005 Nov;71(11):7310-20. (PMID: 16269773) Appl Environ Microbiol. 2001 Apr;67(4):1663-74. (PMID: 11282619) Front Microbiol. 2017 May 08;8:791. (PMID: 28533768) Nucleic Acids Res. 2021 Jul 2;49(W1):W293-W296. (PMID: 33885785) Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):11479-84. (PMID: 25049411) Nat Rev Microbiol. 2018 Oct;16(10):629-645. (PMID: 30181663) Nat Methods. 2023 Aug;20(8):1203-1212. (PMID: 37500759) J Struct Biol. 2005 Dec;152(3):149-56. (PMID: 16198601) Int J Syst Evol Microbiol. 2003 Sep;53(Pt 5):1271-1276. (PMID: 13130005) Environ Sci Technol. 2018 Jan 16;52(2):503-512. (PMID: 26371540) Nat Commun. 2016 Oct 24;7:13219. (PMID: 27774985) Environ Microbiol. 2021 Jul;23(7):3710-3726. (PMID: 33350070) Stand Genomic Sci. 2013 Apr 15;8(1):58-68. (PMID: 23961312) Environ Microbiol. 2014 Nov;16(11):3443-62. (PMID: 24628880) Appl Environ Microbiol. 1998 Jan;64(1):119-25. (PMID: 9435068) Bioinformatics. 2012 Jun 1;28(11):1420-8. (PMID: 22495754) Nat Methods. 2012 Mar 04;9(4):357-9. (PMID: 22388286) Nat Biotechnol. 2019 Nov;37(11):1314-1321. (PMID: 31570900) J Biomater Sci Polym Ed. 2002;13(8):919-37. (PMID: 12463511) J Synchrotron Radiat. 2005 Jul;12(Pt 4):537-41. (PMID: 15968136) J Dent Res. 2020 Jun;99(6):685-694. (PMID: 32075512) Mol Biol Evol. 2015 Jan;32(1):268-74. (PMID: 25371430) Curr Opin Microbiol. 2005 Jun;8(3):253-9. (PMID: 15939347) Bioinformatics. 2009 Aug 1;25(15):1972-3. (PMID: 19505945) Science. 1992 Nov 6;258(5084):972-5. (PMID: 1439809) Nat Commun. 2021 Apr 28;12(1):2454. (PMID: 33911080) Stand Genomic Sci. 2011 Dec 31;5(3):398-406. (PMID: 22675589) J Phys Chem B. 2008 Nov 6;112(44):13711-6. (PMID: 18842017) J Synchrotron Radiat. 2003 May 1;10(Pt 3):280-3. (PMID: 12714762) Nat Microbiol. 2021 Mar;6(3):354-365. (PMID: 33495623) BMC Biol. 2020 Jun 19;18(1):69. (PMID: 32560683) Nat Microbiol. 2016 Apr 11;1:16048. (PMID: 27572647) Nature. 2015 Jul 9;523(7559):208-11. (PMID: 26083755) Sci Rep. 2016 Sep 27;6:34212. (PMID: 27670643) ISME J. 2008 Jun;2(6):590-601. (PMID: 18356823) mBio. 2022 Oct 26;13(5):e0171122. (PMID: 36043790) Nat Biotechnol. 2021 May;39(5):555-560. (PMID: 33398153) J Dent Res. 2019 May;98(5):500-509. (PMID: 30894042) Environ Microbiome. 2021 Dec 14;16(1):24. (PMID: 34906246) Front Microbiol. 2015 Jan 08;5:756. (PMID: 25620962) Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):506-10. (PMID: 22203982) J Phys Chem B. 2007 Jul 5;111(26):7691-9. (PMID: 17559260) ISME J. 2018 Jun;12(7):1715-1728. (PMID: 29467397) J Synchrotron Radiat. 2003 Mar 1;10(Pt 2):125-36. (PMID: 12606790) Q Rev Biophys. 1995 Feb;28(1):33-130. (PMID: 7676009) Nature. 2002 Jan 17;415(6869):312-5. (PMID: 11797006) Appl Environ Microbiol. 1986 Aug;52(2):225-33. (PMID: 16347121) ISME J. 2012 Jan;6(1):158-70. (PMID: 21716305) Mol Biol Evol. 2013 May;30(5):1188-95. (PMID: 23418397) |
| معلومات مُعتمدة: | 1R01GM12763 United States NH NIH HHS; 1R01GM12763 United States NH NIH HHS |
| فهرسة مساهمة: | Keywords: Candidate phyla radiation; Groundwater microbiome; Synchrotron-based spectromicroscopy |
| المشرفين على المادة: | 0 (Sulfides) 70FD1KFU70 (Sulfur) 7YNJ3PO35Z (Hydrogen) |
| تواريخ الأحداث: | Date Created: 20240125 Date Completed: 20240129 Latest Revision: 20240129 |
| رمز التحديث: | 20240129 |
| مُعرف محوري في PubMed: | PMC10811913 |
| DOI: | 10.1186/s40168-023-01704-w |
| PMID: | 38273328 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 2049-2618 |
|---|---|
| DOI: | 10.1186/s40168-023-01704-w |