دورية أكاديمية
Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.
| العنوان: | Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. |
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| المؤلفون: | Lui LM; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States., Majumder EL; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States., Smith HJ; Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States., Carlson HK; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States., von Netzer F; Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States., Fields MW; Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States., Stahl DA; Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States., Zhou J; Institute for Environmental Genomics, Department of Microbiology & Plant Biology, School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, United States., Hazen TC; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN, United States., Baliga NS; Institute for Systems Biology, Seattle, WA, United States., Adams PD; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States., Arkin AP; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States. |
| المصدر: | Frontiers in microbiology [Front Microbiol] 2021 Mar 24; Vol. 12, pp. 642422. Date of Electronic Publication: 2021 Mar 24 (Print Publication: 2021). |
| 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: | Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments. 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. (Copyright © 2021 Lui, Majumder, Smith, Carlson, von Netzer, Fields, Stahl, Zhou, Hazen, Baliga, Adams and Arkin.) |
| References: | Nat Rev Microbiol. 2020 Jun;18(6):313-314. (PMID: 32350400) Nat Commun. 2020 Sep 18;11(1):4717. (PMID: 32948774) J Bacteriol. 2012 Aug;194(16):4151-60. (PMID: 22661685) Environ Sci Technol. 2006 Apr 15;40(8):2601-7. (PMID: 16683598) mSystems. 2020 Jun 23;5(3):. (PMID: 32576650) ISME J. 2020 Jun;14(6):1520-1532. (PMID: 32203117) Front Microbiol. 2018 Jun 08;9:1234. (PMID: 29937762) Science. 2014 May 30;344(6187):1039-42. (PMID: 24789972) FEMS Microbiol Ecol. 2018 Dec 1;94(12):. (PMID: 30265315) ISME J. 2009 Jun;3(6):675-84. (PMID: 19242534) Front Microbiol. 2018 Oct 04;9:2305. (PMID: 30337913) Appl Environ Microbiol. 2017 Sep 29;83(20):. (PMID: 28778896) BMC Biol. 2014 Aug 22;12:69. (PMID: 25184604) Microb Biotechnol. 2009 Mar;2(2):274-86. (PMID: 21261921) Nature. 2017 Nov 23;551(7681):457-463. (PMID: 29088705) mBio. 2018 Jul 17;9(4):. (PMID: 30018110) Chem Rev. 2019 May 8;119(9):5954-5997. (PMID: 30747524) Philos Trans R Soc Lond B Biol Sci. 2020 May 11;375(1798):20190241. (PMID: 32200750) Environ Microbiol. 2019 Feb;21(2):784-799. (PMID: 30536693) Sci Rep. 2020 Nov 3;10(1):18886. (PMID: 33144634) Appl Environ Microbiol. 2015 Oct 09;82(1):51-61. (PMID: 26452555) J Contam Hydrol. 2016 Apr;187:55-64. (PMID: 26897652) mBio. 2016 Apr 05;7(2):e02234-15. (PMID: 27048805) Ground Water. 2005 Mar-Apr;43(2):169-77. (PMID: 15819938) Philos Trans A Math Phys Eng Sci. 2014 Feb 10;372(2011):20120488. (PMID: 24516181) Nat Commun. 2019 Jan 18;10(1):308. (PMID: 30659179) Environ Sci Technol. 2017 Apr 4;51(7):3609-3620. (PMID: 28300407) ACS Synth Biol. 2016 Jul 15;5(7):569-76. (PMID: 26885935) mSystems. 2021 Feb 9;6(1):. (PMID: 33563788) Curr Opin Syst Biol. 2017 Aug;4:92-96. (PMID: 36937228) Sci Data. 2016 Mar 15;3:160018. (PMID: 26978244) Biosens Bioelectron. 2016 Nov 15;85:915-923. (PMID: 27315516) Curr Opin Microbiol. 2017 Jun;37:35-41. (PMID: 28437664) Nat Methods. 2019 Jul;16(7):567-571. (PMID: 31227812) J Biol Chem. 2016 Apr 22;291(17):9190-202. (PMID: 26940877) Environ Microbiol. 2019 Jan;21(1):152-163. (PMID: 30289197) Nat Commun. 2020 Sep 29;11(1):4897. (PMID: 32994415) mBio. 2015 May 12;6(3):e00326-15. (PMID: 25968645) mBio. 2018 Feb 20;9(1):. (PMID: 29463661) Appl Environ Microbiol. 2005 Nov;71(11):6776-83. (PMID: 16269709) Annu Rev Microbiol. 2012;66:83-101. (PMID: 22994489) Proc Natl Acad Sci U S A. 2019 Dec 17;116(51):25900-25908. (PMID: 31772013) Appl Environ Microbiol. 2015 Aug;81(15):4976-83. (PMID: 25979890) BMC Microbiol. 2018 Sep 12;18(1):115. (PMID: 30208844) PLoS One. 2020 Sep 28;15(9):e0232437. (PMID: 32986713) ACS Chem Biol. 2016 Jun 17;11(6):1677-85. (PMID: 27045776) mBio. 2020 Jan 14;11(1):. (PMID: 31937646) ISME J. 2015 Jun;9(6):1295-305. (PMID: 25405978) Front Microbiol. 2020 Oct 19;11:587127. (PMID: 33193240) Environ Microbiol. 2017 Aug;19(8):3059-3069. (PMID: 28419704) mBio. 2013 Mar 05;4(2):. (PMID: 23462114) Nat Microbiol. 2018 Jul;3(7):767-772. (PMID: 29915204) ISME J. 2019 Aug;13(8):1997-2004. (PMID: 30936420) Front Microbiol. 2014 Jun 26;5:315. (PMID: 25071731) Chemosphere. 2020 Sep;255:126951. (PMID: 32417512) Nat Rev Microbiol. 2020 Sep;18(9):507-520. (PMID: 32472051) Front Microbiol. 2019 Jan 22;10:3. (PMID: 30723459) Nature. 2015 Oct 22;526(7574):513-4. (PMID: 26490616) Microb Biotechnol. 2009 Mar;2(2):154-6. (PMID: 21261909) Environ Sci Technol. 2015 Mar 17;49(6):3727-36. (PMID: 25698072) EMBO Rep. 2004 May;5(5):470-6. (PMID: 15184977) Nature. 2018 May;557(7706):503-509. (PMID: 29769716) ISME J. 2009 Jan;3(1):47-64. (PMID: 18769457) Environ Microbiol. 2018 Dec;20(12):4197-4209. (PMID: 30106224) Sci Total Environ. 2016 May 15;553:128-140. (PMID: 26909705) ACS Synth Biol. 2019 Feb 15;8(2):391-402. (PMID: 30681833) Environ Microbiol. 2015 Mar;17(3):622-36. (PMID: 24674078) Environ Sci Technol. 2015 Nov 3;49(21):12922-31. (PMID: 25835088) PLoS Comput Biol. 2021 May 7;17(5):e1008972. (PMID: 33961626) Cell. 2011 Mar 18;144(6):844-9. (PMID: 21414475) Nature. 2009 Oct 15;461(7266):976-9. (PMID: 19794413) Front Microbiol. 2013 Dec 06;4:365. (PMID: 24367356) ISME J. 2020 Feb;14(2):450-462. (PMID: 31659234) Front Microbiol. 2012 Feb 20;3:57. (PMID: 22363331) mSystems. 2019 Mar 26;4(2):. (PMID: 30944879) Nat Methods. 2020 Oct;17(10):953-954. (PMID: 32839599) Philos Trans R Soc Lond B Biol Sci. 2020 May 11;375(1798):20190240. (PMID: 32200745) ISME J. 2020 Aug;14(8):2034-2045. (PMID: 32372050) Water Res. 2019 Nov 1;164:114917. (PMID: 31387058) ISME J. 2011 Feb;5(2):305-16. (PMID: 20668487) Environ Sci Technol. 2017 Mar 7;51(5):2879-2889. (PMID: 28112946) Front Microbiol. 2011 May 02;2:94. (PMID: 21833332) Environ Microbiol. 2019 Apr;21(4):1395-1406. (PMID: 30807684) mSystems. 2018 Jan 16;3(1):. (PMID: 29359196) Microbiome. 2020 Apr 6;8(1):51. (PMID: 32252814) ISME J. 2020 Apr;14(4):999-1014. (PMID: 31953507) PLoS One. 2018 Mar 20;13(3):e0194663. (PMID: 29558522) Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):E836-45. (PMID: 24550501) ISME J. 2020 Nov;14(11):2862-2876. (PMID: 32934357) ISME J. 2019 Apr;13(4):937-949. (PMID: 30523276) Microbiol Mol Biol Rev. 2017 Oct 11;81(4):. (PMID: 29021219) Nat Biotechnol. 2018 Jul 6;36(7):566-569. (PMID: 29979655) Proc Natl Acad Sci U S A. 2020 Dec 29;117(52):33317-33324. (PMID: 33318221) F1000Res. 2017 Jun 29;6:1026. (PMID: 28721211) Biochem Soc Trans. 2018 Apr 17;46(2):403-412. (PMID: 29540507) Nat Commun. 2016 Jun 17;7:11965. (PMID: 27311813) Appl Environ Microbiol. 2019 Aug 14;85(17):. (PMID: 31253673) ISME J. 2015 Aug;9(8):1846-56. (PMID: 25647349) Science. 2018 Aug 3;361(6401):469-474. (PMID: 30072533) Appl Environ Microbiol. 2004 Nov;70(11):6525-34. (PMID: 15528515) ISME J. 2016 Nov;10(11):2557-2568. (PMID: 27022995) Appl Environ Microbiol. 2015 Jun 15;81(12):4164-72. (PMID: 25862231) Front Microbiol. 2017 Nov 28;8:2321. (PMID: 29234312) |
| فهرسة مساهمة: | Keywords: metabolic model; reactive transport modeling; species interaction network; subsurface microbial ecology; systems biology |
| تواريخ الأحداث: | Date Created: 20210412 Latest Revision: 20240407 |
| رمز التحديث: | 20240407 |
| مُعرف محوري في PubMed: | PMC8024649 |
| DOI: | 10.3389/fmicb.2021.642422 |
| PMID: | 33841364 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1664-302X |
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| DOI: | 10.3389/fmicb.2021.642422 |