دورية أكاديمية
The Evolution of Ecological Diversity in Acidobacteria .
| العنوان: | The Evolution of Ecological Diversity in Acidobacteria . |
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| المؤلفون: | Sikorski J; Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany., Baumgartner V; Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany., Birkhofer K; Department of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany., Boeddinghaus RS; Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany., Bunk B; Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany., Fischer M; Institute of Plant Sciences, University of Bern, Bern, Switzerland., Fösel BU; Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany., Friedrich MW; Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany., Göker M; Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany., Hölzel N; Biodiversity and Ecosystem Research Group, Institute of Landscape Ecology, University Münster, Münster, Germany., Huang S; Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany., Huber KJ; Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany., Kandeler E; Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany., Klaus VH; Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland., Kleinebecker T; Institute of Landscape Ecology and Resources Management, University of GieBen, GieBen, Germany., Marhan S; Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany., von Mering C; Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland., Oelmann Y; Geoecology, University of Tübingen, Tübingen, Germany., Prati D; Institute of Plant Sciences, University of Bern, Bern, Switzerland., Regan KM; Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany., Richter-Heitmann T; Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany., Rodrigues JFM; Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland., Schmitt B; Institute of Plant Sciences, University of Bern, Bern, Switzerland., Schöning I; Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany., Schrumpf M; Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany., Schurig E; Geoecology, University of Tübingen, Tübingen, Germany., Solly EF; Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany., Wolters V; Tierökologie, Justus-Liebig-Universität, GieBen, Germany., Overmann J; Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.; Microbiology, Faculty of Life Sciences, Technische Universität Braunschweig, Braunschweig, Germany. |
| المصدر: | Frontiers in microbiology [Front Microbiol] 2022 Feb 02; Vol. 13, pp. 715637. Date of Electronic Publication: 2022 Feb 02 (Print Publication: 2022). |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Frontiers Research Foundation Country of Publication: Switzerland NLM ID: 101548977 Publication Model: eCollection Cited Medium: Print ISSN: 1664-302X (Print) Linking ISSN: 1664302X NLM ISO Abbreviation: Front Microbiol Subsets: PubMed not MEDLINE |
| أسماء مطبوعة: | Original Publication: Lausanne : Frontiers Research Foundation |
| مستخلص: | Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to elucidate ecological adaptations and their evolution for 4,154 operational taxonomic units (OTUs) of Acidobacteria across 150 different, comprehensively characterized grassland soils in Germany. Using the relative abundances of their 16S rRNA gene transcripts, the responses of active OTUs along gradients of 41 environmental variables were modeled using hierarchical logistic regression (HOF), which allowed to determine values for optimum activity for each variable (niche optima). By linking 16S rRNA transcripts to the phylogeny of full 16S rRNA gene sequences, we could trace the evolution of the different ecological adaptations during the diversification of Acidobacteria . This approach revealed a pronounced ecological diversification even among acidobacterial sister clades. Although the evolution of habitat adaptation was mainly cladogenic, it was disrupted by recurrent events of convergent evolution that resulted in frequent habitat switching within individual clades. Our findings indicate that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation even at the level of closely related species. A comparison of niche optima of individual OTUs with the phenotypic properties of their cultivated representatives showed that our niche modeling approach (1) correctly predicts those physiological properties that have been determined for cultivated species of Acidobacteria but (2) also provides ample information on ecological adaptations that cannot be inferred from standard taxonomic descriptions of bacterial isolates. These novel information on specific adaptations of not-yet-cultivated Acidobacteria can therefore guide future cultivation trials and likely will increase their cultivation success. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer IB declared a shared affiliation with one of the authors, NH, to the handling editor at the time of review. (Copyright © 2022 Sikorski, Baumgartner, Birkhofer, Boeddinghaus, Bunk, Fischer, Fösel, Friedrich, Göker, Hölzel, Huang, Huber, Kandeler, Klaus, Kleinebecker, Marhan, von Mering, Oelmann, Prati, Regan, Richter-Heitmann, Rodrigues, Schmitt, Schöning, Schrumpf, Schurig, Solly, Wolters and Overmann.) |
| References: | Front Microbiol. 2019 Jul 30;10:1680. (PMID: 31417506) Appl Environ Microbiol. 2007 May;73(9):3113-6. (PMID: 17337544) BMC Bioinformatics. 2011 Nov 24;12:455. (PMID: 22115179) Annu Rev Microbiol. 2017 Sep 8;71:711-730. (PMID: 28731846) ISME J. 2018 Apr;12(4):1072-1083. (PMID: 29515169) Environ Microbiol. 2011 Mar;13(3):798-805. (PMID: 21108723) Appl Environ Microbiol. 2015 Nov 06;82(2):560-9. (PMID: 26546425) Appl Environ Microbiol. 1993 Mar;59(3):695-700. (PMID: 7683183) Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. (PMID: 9254694) Nucleic Acids Res. 2019 Jan 8;47(D1):D631-D636. (PMID: 30256983) Bioinformatics. 2011 Aug 15;27(16):2194-200. (PMID: 21700674) Appl Environ Microbiol. 2011 Jun;77(11):3846-52. (PMID: 21460107) Bioinformatics. 2014 Jan 15;30(2):287-8. (PMID: 24215029) FEMS Microbiol Lett. 2020 Sep 25;367(18):. (PMID: 32897365) Int J Syst Evol Microbiol. 2014 Jun;64(Pt 6):1866-1875. (PMID: 24573163) Syst Biol. 2008 Oct;57(5):758-71. (PMID: 18853362) Evolution. 2003 Apr;57(4):717-45. (PMID: 12778543) Int J Syst Evol Microbiol. 2018 Dec;68(12):3796-3806. (PMID: 30325293) PLoS One. 2020 Mar 17;15(3):e0230157. (PMID: 32182280) Front Microbiol. 2020 Jun 30;11:1391. (PMID: 32695081) ISME J. 2021 Feb;15(2):363-376. (PMID: 33024291) Evolution. 1998 Oct;52(5):1247-1262. (PMID: 28565378) Science. 2004 Jun 11;304(5677):1629-33. (PMID: 15192218) Front Microbiol. 2016 May 31;7:744. (PMID: 27303369) Appl Environ Microbiol. 2016 Apr 18;82(9):2595-2607. (PMID: 26896137) Environ Microbiol. 2018 Mar;20(3):1041-1063. (PMID: 29327410) Bioinformatics. 2010 Jun 1;26(11):1463-4. (PMID: 20395285) Genet Mol Biol. 2015 Jul-Sep;38(3):396-400. (PMID: 26500445) Appl Environ Microbiol. 2011 Jan;77(2):586-96. (PMID: 21097594) Syst Biol. 2016 Jan;65(1):82-97. (PMID: 26424727) Nat Rev Microbiol. 2017 Oct;15(10):579-590. (PMID: 28824177) Environ Microbiol. 2004 Jan;6(1):73-8. (PMID: 14686943) Appl Environ Microbiol. 2007 Aug;73(16):5261-7. (PMID: 17586664) ISME J. 2020 Feb;14(2):463-475. (PMID: 31659233) Environ Microbiol. 2014 Mar;16(3):658-75. (PMID: 23802854) Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6. (PMID: 23193283) Evolution. 2012 Apr;66(4):1079-90. (PMID: 22486690) Front Microbiol. 2018 Nov 19;9:2775. (PMID: 30510549) Arch Microbiol. 2016 Dec;198(10):987-993. (PMID: 27339258) Biom J. 2008 Jun;50(3):346-63. (PMID: 18481363) ISME J. 2009 Apr;3(4):442-53. (PMID: 19129864) Front Microbiol. 2021 Jul 19;12:682886. (PMID: 34349739) PLoS One. 2010 Mar 29;5(3):e9788. (PMID: 20360960) Science. 2018 Jan 19;359(6373):320-325. (PMID: 29348236) Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5. (PMID: 19004872) Int J Syst Evol Microbiol. 2020 Nov;70(11):5607-5612. (PMID: 32701423) Syst Appl Microbiol. 2013 Mar;36(2):82-9. (PMID: 23266188) Front Microbiol. 2016 Jan 22;6:1567. (PMID: 26834718) Int J Syst Evol Microbiol. 2017 Nov;67(11):4487-4493. (PMID: 28945537) Nat Commun. 2020 Feb 6;11(1):754. (PMID: 32029713) Appl Environ Microbiol. 2012 Oct;78(20):7398-406. (PMID: 22885760) Bioinformatics. 2013 Nov 15;29(22):2933-5. (PMID: 24008419) ISME J. 2018 Jun;12(7):1729-1742. (PMID: 29476143) |
| فهرسة مساهمة: | Keywords: 16S rRNA gene transcripts; Acidobacteria; adaptation; ecological diversity; evolution; optimum niche modeling; physiological traits |
| تواريخ الأحداث: | Date Created: 20220221 Latest Revision: 20231103 |
| رمز التحديث: | 20240628 |
| مُعرف محوري في PubMed: | PMC8847707 |
| DOI: | 10.3389/fmicb.2022.715637 |
| PMID: | 35185839 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1664-302X |
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| DOI: | 10.3389/fmicb.2022.715637 |