Vertical distribution of structure and function of the methanogenic archaeal community in Lake Dagow sediment

• Published in: Environmental microbiology Vol. 7; no. 8; pp. 1139 - 1149
• Main Authors: Chan, On Chim, Claus, Peter, Casper, Peter, Ulrich, Andreas, Lueders, Tillmann, Conrad, Ralf
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Science Ltd 01-08-2005
• Subjects: Archaea - classification; Archaea - growth & development; Archaea - metabolism; DNA, Archaeal - analysis; DNA, Ribosomal - analysis; Ecosystem; Fresh Water - microbiology; Genes, rRNA; Geologic Sediments - microbiology; Methane - metabolism; Methanomicrobiales - growth & development; Methanomicrobiales - metabolism; Methanosarcinales - growth & development; Methanosarcinales - metabolism; Molecular Sequence Data; Polymorphism, Restriction Fragment Length; RNA, Ribosomal, 16S - genetics; Sequence Analysis, DNA
• ISSN: 1462-2912; 1462-2920
• DOI: 10.1111/j.1462-2920.2005.00790.x

Summary
Detailed studies on the relation of structure and function of microbial communities in a sediment depth profile scarcely exist. We determined as functional aspect the vertical distribution of the acetotrophic and hydrogenotrophic CH4 production activity by measuring production rates and stable 13C/12C‐isotopic signatures of CH4 in the profundal sediment of Lake Dagow. The structural aspect was determined by the composition of the methanogenic community by quantifying the abundance of different archaeal groups using ‘real‐time’ polymerase chain reaction and analysis of terminal restriction fragment length polymorphism (T‐RFLP). Methane production rates in the surface sediment (0–3 cm depth) were higher in August than in May, but strongly decreased with depth (down to 20 cm). The δ13C of the produced CH4 and CO2 indicated an increase in isotopic fractionation with sediment depth. The relative contribution of hydrogenotrophic to total methanogenesis, which was calculated from the isotopic signatures, increased with depth from about 22% to 38%. Total numbers of microorganisms were higher in August than in May, but strongly decreased with depth. The increase of microorganisms from May to August mainly resulted from Bacteria. The Archaea, on the other hand, exhibited a rather constant abundance, but also decreased with depth from about 1 × 108 copies of the archaeal 16S rRNA gene per gram of dry sediment  at  the  surface  to  4 × 107 copies  per  gram at 15–20 cm depth. T‐RFLP analysis combined with phylogenetic analysis of cloned sequences of the archaeal 16S rRNA genes showed that the methanogenic community consisted mainly of Methanomicrobiales and Methanosaetaceae. The relative abundance of Methanosaetaceae decreased with depth, whereas that of Methanomicrobiales slightly increased. Hence, the vertical distribution of the functional characteristics (CH4 production from acetate versus H2/CO2) was reflected in the structure of the community consisting of acetotrophic (Methanosaetaceae) versus hydrogenotrophic (Methanomicrobiales) phenotypes.