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Community analysis of methanogenic archaea within a riparian flooding gradient.
Environ Microbiol. 2004 May; 6(5):449-61.EM

Abstract

Anoxic soils in river floodplains (or riparian soils) are a source of methane emission. However, little is known about the ecology and community structure of archaeal methanogenic microbes, which are a crucial component of methane flux in those habitats. We studied the archaeal community in the vertical profile of four different sites along the River Waal in the Netherlands. These sites differ in their annual flooding regime ranging from never or seldom to permanently flooded. The archaeal community structure has been characterized by terminal restriction fragment length polymorphism (T-RFLP) and comparative sequence analysis of the archaeal SSU rRNA gene and the mcrA gene. The latter gene codes for the alpha-subunit of methyl-coenzyme M reductase. Additionally, the potential methanogenic activity was determined by incubation of soil slurries under anoxic conditions. The community composition differed only slightly with the depth of the soil (0-20 cm). However, the diversity of archaeal SSU rRNA genes increased with the frequency of flooding. Terminal restriction fragment length polymorphism analysis of mcrA gene amplicons confirmed the results concerning methanogenic archaea. In the never and rarely flooded soils, crenarchaeotal sequences were the dominant group. In the frequently and permanently flooded soils, Methanomicrobiaceae, Methanobacteriaceae, Methanosarcinaceae and the uncultured Rice Clusters IV and VI (Crenarchaeota) were detectable independently from duration of anoxic conditions. Methanosaetaceae, on the other hand, were only found in the permanently and frequently flooded soils under conditions where concentrations of acetate were < 30 microM. The results indicate that methanogens as well as other archaea occupy characteristic niches according to the flooding conditions in the field. Methanosaetaceae, in particular, seem to be adapted (or proliferate at) to low acetate concentrations.

Authors+Show Affiliations

Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Str., 35043 Marburg, Germany.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

15049918

Citation

Kemnitz, Dana, et al. "Community Analysis of Methanogenic Archaea Within a Riparian Flooding Gradient." Environmental Microbiology, vol. 6, no. 5, 2004, pp. 449-61.
Kemnitz D, Chin KJ, Bodelier P, et al. Community analysis of methanogenic archaea within a riparian flooding gradient. Environ Microbiol. 2004;6(5):449-61.
Kemnitz, D., Chin, K. J., Bodelier, P., & Conrad, R. (2004). Community analysis of methanogenic archaea within a riparian flooding gradient. Environmental Microbiology, 6(5), 449-61.
Kemnitz D, et al. Community Analysis of Methanogenic Archaea Within a Riparian Flooding Gradient. Environ Microbiol. 2004;6(5):449-61. PubMed PMID: 15049918.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Community analysis of methanogenic archaea within a riparian flooding gradient. AU - Kemnitz,Dana, AU - Chin,Kuk-Jeong, AU - Bodelier,Paul, AU - Conrad,Ralf, PY - 2004/3/31/pubmed PY - 2004/6/23/medline PY - 2004/3/31/entrez SP - 449 EP - 61 JF - Environmental microbiology JO - Environ Microbiol VL - 6 IS - 5 N2 - Anoxic soils in river floodplains (or riparian soils) are a source of methane emission. However, little is known about the ecology and community structure of archaeal methanogenic microbes, which are a crucial component of methane flux in those habitats. We studied the archaeal community in the vertical profile of four different sites along the River Waal in the Netherlands. These sites differ in their annual flooding regime ranging from never or seldom to permanently flooded. The archaeal community structure has been characterized by terminal restriction fragment length polymorphism (T-RFLP) and comparative sequence analysis of the archaeal SSU rRNA gene and the mcrA gene. The latter gene codes for the alpha-subunit of methyl-coenzyme M reductase. Additionally, the potential methanogenic activity was determined by incubation of soil slurries under anoxic conditions. The community composition differed only slightly with the depth of the soil (0-20 cm). However, the diversity of archaeal SSU rRNA genes increased with the frequency of flooding. Terminal restriction fragment length polymorphism analysis of mcrA gene amplicons confirmed the results concerning methanogenic archaea. In the never and rarely flooded soils, crenarchaeotal sequences were the dominant group. In the frequently and permanently flooded soils, Methanomicrobiaceae, Methanobacteriaceae, Methanosarcinaceae and the uncultured Rice Clusters IV and VI (Crenarchaeota) were detectable independently from duration of anoxic conditions. Methanosaetaceae, on the other hand, were only found in the permanently and frequently flooded soils under conditions where concentrations of acetate were < 30 microM. The results indicate that methanogens as well as other archaea occupy characteristic niches according to the flooding conditions in the field. Methanosaetaceae, in particular, seem to be adapted (or proliferate at) to low acetate concentrations. SN - 1462-2912 UR - https://www.unboundmedicine.com/medline/citation/15049918/Community_analysis_of_methanogenic_archaea_within_a_riparian_flooding_gradient_ DB - PRIME DP - Unbound Medicine ER -