title: Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters.
abstract: A replicate long-term experiment was conducted using anaerobic digestion (AD) as a model process to determine the relative role of niche and neutral theory on microbial community assembly, and to link community dynamics to system performance. AD is performed by a complex network of microorganisms and process stability relies entirely on the synergistic interactions between populations belonging to different functional guilds. In this study, three independent replicate anaerobic digesters were seeded with the same diverse inoculum, supplied with a model substrate, α-cellulose, and operated for 362 days at a 10-day hydraulic residence time under mesophilic conditions. Selective pressure imposed by the operational conditions and model substrate caused large reproducible changes in community composition including an overall decrease in richness in the first month of operation, followed by synchronised population dynamics that correlated with changes in reactor performance. This included the synchronised emergence and decline of distinct Ruminococcus phylotypes at day 148, and emergence of a Clostridium and Methanosaeta phylotype at day 178, when performance became stable in all reactors. These data suggest that many dynamic functional niches are predictably filled by phylogenetically coherent populations over long time scales. Neutral theory would predict that a complex community with a high degree of recognised functional redundancy would lead to stochastic changes in populations and community divergence over time. We conclude that deterministic processes may play a larger role in microbial community dynamics than currently appreciated, and under controlled conditions it may be possible to reliably predict community structural and functional changes over time.
authors.affiliation: 1] Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Queensland, Australia [2] Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia.
authors.forename: Inka
authors.initials: I
authors.lastname: Vanwonterghem
authors.affiliation: Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Queensland, Australia.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Jensen
authors.affiliation: 1] Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Queensland, Australia [2] Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia [3] School of Agriculture and Food Sciences, University of Queensland, St Lucia, Queensland, Australia.
authors.forename: Paul G
authors.initials: PG
authors.lastname: Dennis
authors.affiliation: Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia.
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
authors.affiliation: 1] Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Queensland, Australia [2] Laboratory for Microbial Ecology and Technology (LabMET), Ghent University, Ghent, Belgium.
authors.forename: Korneel
authors.initials: K
authors.lastname: Rabaey
authors.affiliation: 1] Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Queensland, Australia [2] Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia.
authors.forename: Gene W
authors.initials: GW
authors.lastname: Tyson
mesh_terms: D000693:Anaerobiosis; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D044822:Biodiversity; D019149:Bioreactors / Q000382:microbiology*; D002482:Cellulose / Q000378:metabolism; D010802:Phylogeny
chemical_list: D002482:Cellulose
references.citation: FEMS Microbiol Ecol. 2013 Sep;85(3):612-26
references.pmid: 23678985
references.citation: Appl Microbiol Biotechnol. 2013 Jun;97(11):5161-74
references.pmid: 23624683
references.citation: Int J Syst Bacteriol. 1996 Oct;46(4):1145-52
references.pmid: 8863449
references.citation: Appl Environ Microbiol. 2012 Oct;78(19):7160-2
references.pmid: 22843532
references.citation: Environ Microbiol Rep. 2010 Aug;2(4):489-99
references.pmid: 23766220
references.citation: Appl Environ Microbiol. 1999 Aug;65(8):3697-704
references.pmid: 10427068
references.citation: Nat Methods. 2010 May;7(5):335-6
references.pmid: 20383131
references.citation: Water Sci Technol. 2005;52(1-2):515-23
references.pmid: 16180472
references.citation: Water Res. 2011 Feb;45(4):1597-606
references.pmid: 21185054
references.citation: PLoS One. 2012;7(8):e42524
references.pmid: 22880016
references.citation: Bioresour Technol. 2011 Oct;102(19):8790-8
references.pmid: 21824765
references.citation: Int J Syst Evol Microbiol. 2006 Jan;56(Pt 1):127-31
references.pmid: 16403877
references.citation: Biotechnol Bioeng. 1998 Feb 5;57(3):342-55
references.pmid: 10099211
references.citation: Nat Methods. 2012 Apr 27;9(5):425-6
references.pmid: 22543370
references.citation: Appl Microbiol Biotechnol. 2008 Apr;78(6):1045-55
references.pmid: 18305937
references.citation: Water Res. 2007 Apr;41(7):1554-68
references.pmid: 17291558
references.citation: Proc Natl Acad Sci U S A. 2008 Aug 12;105 Suppl 1:11512-9
references.pmid: 18695234
references.citation: Oecologia. 2001 Oct;129(2):271-280
references.pmid: 28547606
references.citation: Water Res. 2009 Jan;43(1):157-65
references.pmid: 18945471
references.citation: Environ Sci Technol. 2006 Feb 15;40(4):1096-103
references.pmid: 16572761
references.citation: Microbiologyopen. 2013 Feb;2(1):35-53
references.pmid: 23239474
references.citation: Nature. 2004 Mar 4;428(6978):37-43
references.pmid: 14961025
references.citation: Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15345-50
references.pmid: 20705897
references.citation: Annu Rev Microbiol. 2004;58:521-54
references.pmid: 15487947
references.citation: ISME J. 2011 Sep;5(9):1406-13
references.pmid: 21368908
references.citation: Syst Appl Microbiol. 1999 Sep;22(3):434-44
references.pmid: 10553296
references.citation: Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4158-63
references.pmid: 21368115
references.citation: Appl Environ Microbiol. 2006 Jul;72(7):5069-72
references.pmid: 16820507
references.citation: Bioresour Technol. 2011 Feb;102(4):3730-9
references.pmid: 21194932
references.citation: Ann N Y Acad Sci. 2008 Mar;1125:171-89
references.pmid: 18378594
references.citation: PLoS One. 2011 Jan 26;6(1):e14519
references.pmid: 21297863
references.citation: Bioinformatics. 2010 Oct 1;26(19):2460-1
references.pmid: 20709691
references.citation: Int J Syst Bacteriol. 1992 Jul;42(3):463-8
references.pmid: 1380291
references.citation: mBio. 2013 Mar 05;4(2):
references.pmid: 23462114
references.citation: ISME J. 2007 Dec;1(8):714-28
references.pmid: 18059495
references.citation: Water Res. 2009 Feb;43(3):842-52
references.pmid: 19084250
references.citation: Environ Sci Technol. 2006 Jan 15;40(2):509-15
references.pmid: 16468396
references.citation: Curr Opin Biotechnol. 2003 Jun;14(3):270-6
references.pmid: 12849779
references.citation: Bioresour Technol. 2009 Nov;100(21):5219-25
references.pmid: 19520570
references.citation: Water Res. 2013 Dec 1;47(19):7098-108
references.pmid: 24216229
references.citation: Acc Chem Res. 2009 Dec 21;42(12):1899-909
references.pmid: 19757805
references.citation: Bioresour Technol. 2013 Feb;129:599-605
references.pmid: 23313735
references.citation: Appl Microbiol Biotechnol. 2010 Jan;85(4):849-60
references.pmid: 19777226
references.citation: J Biotechnol. 2008 Aug 31;136(1-2):77-90
references.pmid: 18597880
references.citation: FEMS Microbiol Ecol. 2012 Apr;80(1):159-67
references.pmid: 22224860
references.citation: ISME J. 2010 May;4(5):642-7
references.pmid: 20090784
references.citation: Water Sci Technol. 2011;64(4):880-6
references.pmid: 22097074
references.citation: Water Res. 2002 Feb;36(3):638-46
references.pmid: 11827326
references.citation: ISME J. 2013 Jul;7(7):1310-21
references.pmid: 23446837
references.citation: J Bacteriol. 1994 Nov;176(22):6952-6
references.pmid: 7961457
references.citation: Environ Microbiol. 2006 Apr;8(4):732-40
references.pmid: 16584484
references.citation: Nat Biotechnol. 2013 Jun;31(6):533-8
references.pmid: 23707974
references.citation: Appl Environ Microbiol. 2008 Mar;74(5):1305-15
references.pmid: 18165358
references.citation: FEMS Microbiol Ecol. 2008 Sep;65(3):544-54
references.pmid: 18647356
references.citation: Front Microbiol. 2013 May 01;4:68
references.pmid: 23641236
references.citation: BMC Genomics. 2011 Sep 07;12:444
references.pmid: 21899761
references.citation: Microbiol Res. 2012 Dec 20;167(10):581-9
references.pmid: 22770715
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Microbiol Rev. 1995 Mar;59(1):143-69
references.pmid: 7535888
references.citation: Bioinformatics. 2011 Aug 15;27(16):2194-200
references.pmid: 21700674