title: Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge.
abstract: Methanogens play a critical role in the decomposition of organics under anaerobic conditions. The methanogenic consortia in saturated wetland soils are often subjected to large temperature fluctuations and acidic conditions, imposing a selective pressure for psychro- and acidotolerant community members; however, methanogenic communities in engineered digesters are frequently maintained within a narrow range of mesophilic and circumneutral conditions to retain system stability. To investigate the hypothesis that these two disparate environments have distinct methanogenic communities, the methanogens in an oligotrophic acidic fen and a mesophilic anaerobic digester treating municipal wastewater sludge were characterized by creating clone libraries for the 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes. A quantitative framework was developed to assess the differences between these two communities by calculating the average sequence similarity for 16S rRNA genes and mcrA within a genus and family using sequences of isolated and characterized methanogens within the approved methanogen taxonomy. The average sequence similarities for 16S rRNA genes within a genus and family were 96.0 and 93.5%, respectively, and the average sequence similarities for mcrA within a genus and family were 88.9 and 79%, respectively. The clone libraries of the bog and digester environments showed no overlap at the species level and almost no overlap at the family level. Both libraries were dominated by clones related to uncultured methanogen groups within the Methanomicrobiales, although members of the Methanosarcinales and Methanobacteriales were also found in both libraries. Diversity indices for the 16S rRNA gene library of the bog and both mcrA libraries were similar, but these indices indicated much lower diversity in the 16S digester library than in the other three libraries.
authors.affiliation: Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Steinberg
authors.forename: John M
authors.initials: JM
authors.lastname: Regan
mesh_terms: D000693:Anaerobiosis; D044822:Biodiversity; D016000:Cluster Analysis; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D004783:Environmental Microbiology; D008697:Methane / Q000378:metabolism; D017012:Methanobacteriales / Q000145:classification / Q000302:isolation & purification*; D017018:Methanomicrobiales / Q000145:classification / Q000302:isolation & purification*; D019640:Methanosarcinales / Q000145:classification / Q000302:isolation & purification*; D008969:Molecular Sequence Data; D010088:Oxidoreductases / Q000235:genetics; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D012722:Sewage / Q000382:microbiology*
chemical_list: D019641:DNA, Archaeal; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012722:Sewage; D010088:Oxidoreductases; C021572:methyl coenzyme M reductase; D008697:Methane
references.citation: Appl Environ Microbiol. 1994 Apr;60(4):1232-40
references.pmid: 7517128
references.citation: Water Res. 2004 Feb;38(3):619-30
references.pmid: 14723931
references.citation: Res Microbiol. 2006 Dec;157(10):914-21
references.pmid: 17070673
references.citation: Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5685-9
references.pmid: 1608980
references.citation: Environ Microbiol. 2001 Mar;3(3):194-204
references.pmid: 11321536
references.citation: Archaea. 2005 May;1(5):353-63
references.pmid: 15876569
references.citation: Environ Microbiol. 2005 Jul;7(7):947-60
references.pmid: 15946291
references.citation: Environ Microbiol. 2005 Aug;7(8):1104-15
references.pmid: 16011748
references.citation: Appl Environ Microbiol. 2006 Feb;72(2):1623-30
references.pmid: 16461718
references.citation: Appl Environ Microbiol. 1997 Aug;63(8):3043-50
references.pmid: 9251192
references.citation: Appl Environ Microbiol. 2003 Sep;69(9):5483-91
references.pmid: 12957937
references.citation: FEMS Microbiol Ecol. 2005 Jun 1;53(1):89-101
references.pmid: 16329932
references.citation: Appl Environ Microbiol. 2003 Jun;69(6):3181-91
references.pmid: 12788715
references.citation: Environ Microbiol. 2005 Aug;7(8):1139-49
references.pmid: 16011751
references.citation: Appl Environ Microbiol. 2005 Apr;71(4):2195-8
references.pmid: 15812059
references.citation: Nature. 2006 Jul 13;442(7099):192-4
references.pmid: 16699521
references.citation: Microbiology (Reading). 2002 Nov;148(Pt 11):3521-3530
references.pmid: 12427943
references.citation: Bioresour Technol. 2003 Apr;87(2):147-53
references.pmid: 12765353
references.citation: Appl Environ Microbiol. 1996 Feb;62(2):668-75
references.pmid: 8593069
references.citation: FEMS Microbiol Ecol. 2001 Jan;34(3):221-228
references.pmid: 11137602
references.citation: Appl Environ Microbiol. 2001 Oct;67(10):4399-406
references.pmid: 11571135
references.citation: Biotechnol Bioeng. 1998 Feb 5;57(3):342-55
references.pmid: 10099211
references.citation: FEMS Microbiol Ecol. 2002 Dec 1;42(3):441-9
references.pmid: 19709303
references.citation: Appl Environ Microbiol. 2003 Sep;69(9):5472-82
references.pmid: 12957936
references.citation: Appl Environ Microbiol. 2005 Mar;71(3):1501-6
references.pmid: 15746353
references.citation: Environ Microbiol. 2005 Jan;7(1):118-32
references.pmid: 15643942
references.citation: Environ Microbiol. 2001 Jul;3(7):460-70
references.pmid: 11553236
references.citation: Environ Microbiol. 2006 Aug;8(8):1428-40
references.pmid: 16872405
references.citation: Appl Environ Microbiol. 2006 Apr;72(4):2400-6
references.pmid: 16597937
references.citation: Anaerobe. 2000 Aug;6(4):205-26
references.pmid: 16887666
references.citation: Appl Environ Microbiol. 1994 Sep;60(9):3112-9
references.pmid: 7524440
references.citation: Brief Bioinform. 2004 Jun;5(2):150-63
references.pmid: 15260895
references.citation: Appl Environ Microbiol. 1998 Dec;64(12):4983-9
references.pmid: 9835592
references.citation: Appl Environ Microbiol. 2003 Jan;69(1):320-6
references.pmid: 12514011
references.citation: Appl Environ Microbiol. 1999 Apr;65(4):1696-702
references.pmid: 10103270
references.citation: FEMS Microbiol Ecol. 2002 Oct 1;42(1):119-29
references.pmid: 19709271
references.citation: Water Res. 2002 Jul;36(13):3203-10
references.pmid: 12188116
references.citation: Appl Environ Microbiol. 2004 Nov;70(11):6559-68
references.pmid: 15528519
references.citation: Environ Microbiol. 2005 Oct;7(10):1547-57
references.pmid: 16156728
references.citation: Microb Ecol. 2000 Apr;39(3):246-262
references.pmid: 12035101
references.citation: FEMS Microbiol Lett. 2003 Feb 28;219(2):297-304
references.pmid: 12620635
references.citation: Biotechnol Bioeng. 2004 Sep 30;87(7):823-34
references.pmid: 15334409
references.citation: FEMS Microbiol Ecol. 2003 Nov 1;46(2):159-70
references.pmid: 19719569
references.citation: Appl Environ Microbiol. 1999 May;65(5):2222-9
references.pmid: 10224023
references.citation: Appl Environ Microbiol. 1999 Oct;65(10):4375-84
references.pmid: 10508063
references.citation: Microb Ecol. 2003 Aug;46(2):270-8
references.pmid: 14708751
references.citation: Environ Microbiol. 2005 Oct;7(10):1582-92
references.pmid: 16156731
references.citation: Water Res. 2006 Nov;40(19):3653-9
references.pmid: 16904720
references.citation: Trends Microbiol. 2007 Apr;15(4):150-5
references.pmid: 17320399
references.citation: Microb Ecol. 2005 Feb;49(2):209-17
references.pmid: 15965727
references.citation: Trends Biotechnol. 2001 Sep;19(9):363-70
references.pmid: 11514000
references.citation: Environ Microbiol. 2007 Mar;9(3):612-24
references.pmid: 17298362
references.citation: Int J Syst Bacteriol. 1995 Jul;45(3):554-9
references.pmid: 8590683
references.citation: FEMS Microbiol Ecol. 2003 Aug 1;45(3):301-15
references.pmid: 19719599