title: Vertical distribution of ammonia-oxidizing crenarchaeota and methanogens in the epipelagic waters of Lake Kivu (Rwanda-Democratic Republic of the Congo).
abstract: Four stratified basins in Lake Kivu (Rwanda-Democratic Republic of the Congo) were sampled in March 2007 to investigate the abundance, distribution, and potential biogeochemical role of planktonic archaea. We used fluorescence in situ hybridization with catalyzed-reported deposition microscopic counts (CARD-FISH), denaturing gradient gel electrophoresis (DGGE) fingerprinting, and quantitative PCR (qPCR) of signature genes for ammonia-oxidizing archaea (16S rRNA for marine Crenarchaeota group 1.1a [MCG1] and ammonia monooxygenase subunit A [amoA]). Abundance of archaea ranged from 1 to 4.5% of total DAPI (4',6-diamidino-2-phenylindole) counts with maximal concentrations at the oxic-anoxic transition zone (∼50-m depth). Phylogenetic analysis of the archaeal planktonic community revealed a higher level of richness of crenarchaeal 16S rRNA gene sequences (21 of the 28 operational taxonomic units [OTUs] identified [75%]) over euryarchaeotal ones (7 OTUs). Sequences affiliated with the kingdom Euryarchaeota were mainly recovered from the anoxic water compartment and mostly grouped into methanogenic lineages (Methanosarcinales and Methanocellales). In turn, crenarchaeal phylotypes were recovered throughout the sampled epipelagic waters (0- to 100-m depth), with clear phylogenetic segregation along the transition from oxic to anoxic water masses. Thus, whereas in the anoxic hypolimnion crenarchaeotal OTUs were mainly assigned to the miscellaneous crenarchaeotic group, the OTUs from the oxic-anoxic transition and above belonged to Crenarchaeota groups 1.1a and 1.1b, two lineages containing most of the ammonia-oxidizing representatives known so far. The concomitant vertical distribution of both nitrite and nitrate maxima and the copy numbers of both MCG1 16S rRNA and amoA genes suggest the potential implication of Crenarchaeota in nitrification processes occurring in the epilimnetic waters of the lake.
authors.affiliation: Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Campus Montilivi, E-17071 Girona, Spain.
authors.forename: Marc
authors.initials: M
authors.lastname: Llirós
authors.forename: Frederic
authors.initials: F
authors.lastname: Gich
authors.forename: Anna
authors.initials: A
authors.lastname: Plasencia
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Auguet
authors.forename: François
authors.initials: F
authors.lastname: Darchambeau
authors.forename: Emilio O
authors.initials: EO
authors.lastname: Casamayor
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Descy
authors.forename: Carles
authors.initials: C
authors.lastname: Borrego
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D000818:Animals; D044822:Biodiversity; D016000:Cluster Analysis; D019615:Crenarchaeota / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D016172:DNA Fingerprinting; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D015023:Democratic Republic of the Congo; D004591:Electrophoresis, Polyacrylamide Gel; D020459:Genes, rRNA; D017404:In Situ Hybridization, Fluorescence; D008697:Methane / Q000378:metabolism*; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation; D010084:Oxidation-Reduction; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D019642:RNA, Archaeal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D014871:Water Microbiology
chemical_list: D019641:DNA, Archaeal; D004275:DNA, Ribosomal; D019642:RNA, Archaeal; D012336:RNA, Ribosomal, 16S; D000641:Ammonia; D008697:Methane
references.citation: Proc Natl Acad Sci U S A. 1997 Jan 7;94(1):277-82
references.pmid: 8990199
references.citation: FEMS Microbiol Ecol. 2007 Dec;62(3):242-57
references.pmid: 17991018
references.citation: Appl Environ Microbiol. 2000 Feb;66(2):499-508
references.pmid: 10653710
references.citation: ISME J. 2009 Feb;3(2):147-58
references.pmid: 18818711
references.citation: Nature. 2005 Sep 22;437(7058):543-6
references.pmid: 16177789
references.citation: Science. 1973 Jul 6;181(4094):51-4
references.pmid: 17769824
references.citation: Appl Environ Microbiol. 2007 Mar;73(6):2016-9
references.pmid: 17261512
references.citation: Microb Ecol. 2003 Aug;46(2):238-48
references.pmid: 14708748
references.citation: Appl Environ Microbiol. 2006 Apr;72(4):2679-90
references.pmid: 16597973
references.citation: Environ Microbiol. 2008 Apr;10(4):1080-6
references.pmid: 18215160
references.citation: ISME J. 2007 Nov;1(7):660-2
references.pmid: 18043673
references.citation: Science. 2004 Apr 2;304(5667):66-74
references.pmid: 15001713
references.citation: ISME J. 2008 Jan;2(1):3-18
references.pmid: 18180743
references.citation: Environ Microbiol. 2008 Nov;10(11):3002-16
references.pmid: 18973621
references.citation: Appl Environ Microbiol. 2004 Apr;70(4):2404-13
references.pmid: 15066838
references.citation: Environ Microbiol. 2010 Sep;12(9):2450-65
references.pmid: 20406296
references.citation: Appl Environ Microbiol. 2001 Aug;67(8):3618-29
references.pmid: 11472939
references.citation: Syst Biol. 2001 Aug;50(4):470-8
references.pmid: 12116647
references.citation: Environ Microbiol. 2005 Dec;7(12):1985-95
references.pmid: 16309395
references.citation: Trends Microbiol. 2009 Sep;17(9):414-22
references.pmid: 19726194
references.citation: Appl Environ Microbiol. 2009 Dec;75(23):7537-41
references.pmid: 19801464
references.citation: Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5685-9
references.pmid: 1608980
references.citation: Nucleic Acids Res. 2004 Feb 25;32(4):1363-71
references.pmid: 14985472
references.citation: Appl Environ Microbiol. 2003 Dec;69(12):7224-35
references.pmid: 14660370
references.citation: Appl Environ Microbiol. 1990 Jun;56(6):1919-25
references.pmid: 2200342
references.citation: Science. 2008 Oct 10;322(5899):252-5
references.pmid: 18787132
references.citation: Environ Microbiol. 2008 Nov;10(11):2931-41
references.pmid: 18973620
references.citation: Environ Microbiol. 2009 Sep;11(9):2434-45
references.pmid: 19601959
references.citation: Syst Appl Microbiol. 1999 Sep;22(3):434-44
references.pmid: 10553296
references.citation: Appl Environ Microbiol. 2006 Jul;72(7):5069-72
references.pmid: 16820507
references.citation: Appl Environ Microbiol. 1998 Nov;64(11):4299-306
references.pmid: 9797280
references.citation: Mol Biol Evol. 1987 Jul;4(4):406-25
references.pmid: 3447015
references.citation: ISME J. 2008 Apr;2(4):429-41
references.pmid: 18200070
references.citation: Trends Microbiol. 2006 May;14(5):207-12
references.pmid: 16603359
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4752-7
references.pmid: 19255441
references.citation: Environ Microbiol. 2010 Mar;12(3):679-88
references.pmid: 20002133
references.citation: Appl Environ Microbiol. 2004 Jul;70(7):4411-4
references.pmid: 15240332
references.citation: Environ Microbiol. 2009 Mar;11(3):687-99
references.pmid: 19207564
references.citation: Can J Microbiol. 2006 Feb;52(2):73-116
references.pmid: 16541146
references.citation: PLoS Biol. 2006 Apr;4(4):e95
references.pmid: 16533068
references.citation: Environ Microbiol. 2008 Apr;10(4):1068-79
references.pmid: 18266758
references.citation: Environ Microbiol. 2007 May;9(5):1162-75
references.pmid: 17472632
references.citation: Appl Environ Microbiol. 2006 Dec;72(12):7767-77
references.pmid: 17012598
references.citation: Nature. 2009 Oct 15;461(7266):976-9
references.pmid: 19794413
references.citation: Environ Microbiol. 2007 Apr;9(4):1001-16
references.pmid: 17359272
references.citation: Genetics. 1999 Aug;152(4):1285-97
references.pmid: 10430559
references.citation: Environ Microbiol. 2003 Sep;5(9):787-97
references.pmid: 12919414
references.citation: FEMS Microbiol Ecol. 2000 Oct 1;34(1):45-56
references.pmid: 11053735
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12317-22
references.pmid: 16894176
references.citation: Appl Environ Microbiol. 1993 Mar;59(3):695-700
references.pmid: 7683183
references.citation: Nat Rev Microbiol. 2005 Jun;3(6):479-88
references.pmid: 15931166
references.citation: Mol Biol Evol. 2007 Aug;24(8):1596-9
references.pmid: 17488738
references.citation: Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7104-9
references.pmid: 17420469
references.citation: Curr Opin Genet Dev. 1998 Dec;8(6):649-54
references.pmid: 9914204
references.citation: Environ Microbiol. 2009 Apr;11(4):971-80
references.pmid: 19077007
references.citation: FEMS Microbiol Ecol. 2008 Nov;66(2):331-42
references.pmid: 18754782
references.citation: ISME J. 2010 Feb;4(2):182-90
references.pmid: 19847207
references.citation: Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14683-8
references.pmid: 16186488
references.citation: Anaerobe. 2008 Oct;14(4):209-18
references.pmid: 18634895
references.citation: Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3846-51
references.pmid: 16505362
references.citation: FEMS Microbiol Ecol. 2008 Nov;66(2):181-96
references.pmid: 18752622