دورية أكاديمية
Disentangling temporal associations in marine microbial networks.
العنوان: | Disentangling temporal associations in marine microbial networks. |
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المؤلفون: | Deutschmann IM; Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain. ina.m.deutschmann@gmail.com., Krabberød AK; Department of Biosciences/Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, p.b. 1066 Blindern, N-0316, Oslo, Norway., Latorre F; Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain., Delage E; Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France.; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France., Marrasé C; Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain., Balagué V; Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain., Gasol JM; Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain., Massana R; Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain., Eveillard D; Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France.; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France., Chaffron S; Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France.; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France., Logares R; Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain. ramiro.logares@icm.csic.es. |
المصدر: | Microbiome [Microbiome] 2023 Apr 21; Vol. 11 (1), pp. 83. Date of Electronic Publication: 2023 Apr 21. |
نوع المنشور: | Video-Audio Media; Journal Article; Research Support, Non-U.S. Gov't |
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* , Microbiota*, Bacteria/genetics ; Microbial Consortia ; Seasons ; Microbial Interactions |
مستخلص: | Background: Microbial interactions are fundamental for Earth's ecosystem functioning and biogeochemical cycling. Nevertheless, they are challenging to identify and remain barely known. Omics-based censuses are helpful in predicting microbial interactions through the statistical inference of single (static) association networks. Yet, microbial interactions are dynamic and we have limited knowledge of how they change over time. Here, we investigate the dynamics of microbial associations in a 10-year marine time series in the Mediterranean Sea using an approach inferring a time-resolved (temporal) network from a single static network. Results: A single static network including microbial eukaryotes and bacteria was built using metabarcoding data derived from 120 monthly samples. For the decade, we aimed to identify persistent, seasonal, and temporary microbial associations by determining a temporal network that captures the interactome of each individual sample. We found that the temporal network appears to follow an annual cycle, collapsing, and reassembling when transiting between colder and warmer waters. We observed higher association repeatability in colder than in warmer months. Only 16 associations could be validated using observations reported in literature, underlining our knowledge gap in marine microbial ecological interactions. Conclusions: Our results indicate that marine microbial associations follow recurrent temporal dynamics in temperate zones, which need to be accounted for to better understand the functioning of the ocean microbiome. The constructed marine temporal network may serve as a resource for testing season-specific microbial interaction hypotheses. The applied approach can be transferred to microbiome studies in other ecosystems. Video Abstract. (© 2023. The Author(s).) |
References: | BMC Syst Biol. 2011;5 Suppl 2:S15. (PMID: 22784572) ISME J. 2022 Jan;16(1):178-189. (PMID: 34285363) ISME J. 2011 Oct;5(10):1571-9. (PMID: 21472016) Bioinformatics. 2013 Jan 15;29(2):230-7. (PMID: 23178636) Environ Microbiol Rep. 2012 Feb;4(1):1-9. (PMID: 23757223) ISME J. 2011 Sep;5(9):1414-25. (PMID: 21430787) Bioinformatics. 2014 Oct;30(19):2811-2. (PMID: 24930139) BMC Bioinformatics. 2019 Jun 13;20(1):329. (PMID: 31195956) Science. 2008 May 23;320(5879):1034-9. (PMID: 18497287) Mar Pollut Bull. 2020 Nov;160:111691. (PMID: 33181960) ISME J. 2021 Jun;15(6):1722-1734. (PMID: 33452480) Trends Microbiol. 2017 Jun;25(6):494-505. (PMID: 28108182) Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6506-6511. (PMID: 29784790) Bioinformatics. 2004 Dec 12;20(18):3508-15. (PMID: 15284103) Sci Adv. 2021 Aug 27;7(35):. (PMID: 34452910) Microbiome. 2020 Apr 20;8(1):55. (PMID: 32312331) FEMS Microbiol Rev. 2018 Nov 1;42(6):761-780. (PMID: 30085090) Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16213-6. (PMID: 22927371) Science. 2015 May 22;348(6237):1262073. (PMID: 25999517) Mol Ecol. 2010 Mar;19 Suppl 1:21-31. (PMID: 20331767) Trends Microbiol. 2017 Mar;25(3):217-228. (PMID: 27916383) ISME J. 2017 Nov;11(11):2510-2525. (PMID: 28731479) Nat Rev Microbiol. 2015 Mar;13(3):133-46. (PMID: 25659323) Nucleic Acids Res. 2021 Jan 8;49(D1):D667-D676. (PMID: 33125079) Nat Methods. 2016 Jul;13(7):581-3. (PMID: 27214047) ISME J. 2017 Jul;11(7):1614-1629. (PMID: 28398348) Environ Microbiome. 2022 May 7;17(1):22. (PMID: 35526063) Nat Rev Microbiol. 2021 Apr;19(4):225-240. (PMID: 33093661) Cell. 2019 Dec 12;179(7):1451-1454. (PMID: 31835026) ISME J. 2014 Apr;8(4):816-29. (PMID: 24196323) Front Microbiol. 2017 Nov 15;8:2224. (PMID: 29187837) Appl Environ Microbiol. 2007 Aug;73(16):5261-7. (PMID: 17586664) Mol Ecol. 2019 Mar;28(5):923-935. (PMID: 30411822) Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6. (PMID: 23193283) Proc Natl Acad Sci U S A. 2016 May 24;113(21):5970-5. (PMID: 27140646) ISME J. 2020 Feb;14(2):544-559. (PMID: 31685936) Ecol Lett. 2012 Dec;15(12):1353-61. (PMID: 22994257) Environ Microbiol. 2012 Jan;14(1):4-12. (PMID: 22004523) Phys Rev Lett. 2002 Nov 11;89(20):208701. (PMID: 12443515) Microbiome. 2021 Nov 26;9(1):232. (PMID: 34823593) ISME J. 2015 Dec;9(12):2573-86. (PMID: 25989373) Front Microbiol. 2020 Jul 21;11:1590. (PMID: 32793139) Cell Syst. 2019 Sep 25;9(3):286-296.e8. (PMID: 31542415) mSystems. 2021 Jun 29;6(3):e0056521. (PMID: 34060911) ISME J. 2013 Dec;7(12):2259-73. (PMID: 23864126) ISME J. 2019 Feb;13(2):388-401. (PMID: 30254323) Nature. 2009 May 14;459(7244):200-6. (PMID: 19444206) ISME J. 2016 Jul;10(7):1669-81. (PMID: 26905627) PLoS One. 2017 May 11;12(5):e0176751. (PMID: 28493918) Nucleic Acids Res. 2013 Jan;41(Database issue):D597-604. (PMID: 23193267) Trends Ecol Evol. 2018 Jul;33(7):549-564. (PMID: 29807839) J Mol Biol. 1990 Oct 5;215(3):403-10. (PMID: 2231712) Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6578-83. (PMID: 9618454) Sci Total Environ. 2016 Dec 15;573:817-825. (PMID: 27595939) |
فهرسة مساهمة: | Keywords: Association network; Microbial interactions; Microorganisms; Ocean; Plankton; Temporal network; Time series |
تواريخ الأحداث: | Date Created: 20230420 Date Completed: 20230424 Latest Revision: 20231121 |
رمز التحديث: | 20231215 |
مُعرف محوري في PubMed: | PMC10120119 |
DOI: | 10.1186/s40168-023-01523-z |
PMID: | 37081491 |
قاعدة البيانات: | MEDLINE |
تدمد: | 2049-2618 |
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DOI: | 10.1186/s40168-023-01523-z |