Article (Scientific journals)
Vertical distribution of ammonia-oxidizing crenarchaeota and methanogens in the epipelagic waters of Lake Kivu (Rwanda-Democratic Republic of the Congo)
Llirós, M.; Gich, F.; Plasencia, A. et al.
2010In Applied and Environmental Microbiology, 76 (20), p. 6853-6863
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Keywords :
Anoxic water; Archaea; Archaeal; Copy number; Crenarchaeota; Denaturing gradient gel electrophoresis; Fluorescence in situ hybridization; Methanosarcinales; Microscopic counts; Monooxygenases; Nitrification process; Operational taxonomic units; Phylogenetic analysis; Phylotypes; Planktonic community; Quantitative PCR; Signature genes; Stratified basin; Transition zones; Vertical distributions; Ammonia; Analytical geochemistry; Electrophoresis; Fluorescence microscopy; Lakes; Microorganisms; Nitrification; Polymerase chain reaction; RNA; Genes; RNA 16S; Democratic Republic Congo; DNA denaturation; DNA fingerprinting; DNA sequence; RNA gene; Animals; Biodiversity; Cluster Analysis; Democratic Republic of the Congo; DNA, Archaeal; DNA, Ribosomal; Electrophoresis, Polyacrylamide Gel; Genes, rRNA; In Situ Hybridization, Fluorescence; Methane; Molecular Sequence Data; Nucleic Acid Denaturation; Oxidation-Reduction; Phylogeny; RNA, Archaeal; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid; Water Microbiology; East African Lakes; Lake Kivu; Euryarchaeota; Methanosarcina; Otus
Abstract :
[en] Four stratified basins in Lake Kivu (Rwanda-Democratic Republic of theCongo) 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-oxidizingarchaea (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 theoxic-anoxic transition zone (∼50-m depth). Phylogenetic analysis of the archaeal planktonic community revealed a higher level of richnessof 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. © 2010, American Society for Microbiology.
Disciplines :
Microbiology
Author, co-author :
Llirós, M.;  Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Campus Montilivi, E-17071 Girona, Spain
Gich, F.;  Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Campus Montilivi, E-17071 Girona, Spain
Plasencia, A.;  Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Campus Montilivi, E-17071 Girona, Spain
Auguet, J.-C.;  Department of Continental Ecology, Group of Limnology, Centre D'Estudis Avançats de Blanes-CSIC, Accés Cala Sant Francesc 14, E-17300 Blanes, Spain
Darchambeau, François ;  Université de Liège - ULiège > Département d'astrophys., géophysique et océanographie (AGO) > Unité d'Océanographie chimique (UOC)
Casamayor, E. O.;  Department of Continental Ecology, Group of Limnology, Centre D'Estudis Avançats de Blanes-CSIC, Accés Cala Sant Francesc 14, E-17300 Blanes, Spain
Descy, Jean-Pierre ;  Laboratory of Freshwater Ecology-URBO, Facultés Universitaires Notre-Dame de la Paix, University of Namur, B-5000 Namur, Belgium
Borrego, C.;  Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Campus Montilivi, E-17071 Girona, Spain
Language :
English
Title :
Vertical distribution of ammonia-oxidizing crenarchaeota and methanogens in the epipelagic waters of Lake Kivu (Rwanda-Democratic Republic of the Congo)
Publication date :
2010
Journal title :
Applied and Environmental Microbiology
ISSN :
0099-2240
eISSN :
1098-5336
Publisher :
American Society for Microbiology, Washington, United States - District of Columbia
Volume :
76
Issue :
20
Pages :
6853-6863
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 18 December 2012

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