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Investigation of the methanogen population structure and activity in a brackish lake sediment.
Environ Microbiol. 2005 Jul; 7(7):947-60.EM

Abstract

The methanogen community in sediment from the edge of a small brackish lake connected to the Beaulieu Estuary (Hampshire, UK) was investigated by analysis of 16S rRNA gene diversity using new methanogen-specific primers plus Archaea-specific primers. 16S rRNA gene primers previously used for polymerase chain reaction (PCR) detection of methanogenic Archaea from a variety of environments were evaluated by in silico testing. The primers displayed variable coverage of the four main orders of methanogens, highlighting the importance of this type of primer evaluation. Three PCR primer sets were designed using novel reverse primers to facilitate specific amplification of the orders Methanomicrobiales/Methanosarcinales, Methanobacteriales and Methanococcales. Diversity of the methanogen functional gene, methyl coenzyme M reductase (mcrA), was also studied. All gene libraries constructed from this sediment indicated that Methanomicrobiales and Methanosarcinales were the only methanogens detected. There was good agreement between the relative sequence abundances in the methanogen-specific 16S rRNA gene library and terminal restriction fragment length polymorphism (T-RFLP) profiling, suggesting that the population was dominated by putative H2 CO2 utilizing Methanomicrobiales, although acetate-utilizing methanogens were also present. The methanogen population analyses were in agreement with methanogenic activity measurements, which indicated that bicarbonate methanogenesis was higher than acetate methanogenesis at all depths measured and overall there was a significant difference (P = 0.001) between the rates of the two pathways. This study demonstrates the utility of new 16S rRNA gene PCR primers targeting specific methanogenic orders, and the combined results suggest that the CO2 reduction pathway dominates methanogenesis in the brackish sediment investigated.

Authors+Show Affiliations

Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, PO Box 915, Cardiff CF10 3TL, Wales, UK.No affiliation info availableNo affiliation info availableNo 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

15946291

Citation

Banning, Natasha, et al. "Investigation of the Methanogen Population Structure and Activity in a Brackish Lake Sediment." Environmental Microbiology, vol. 7, no. 7, 2005, pp. 947-60.
Banning N, Brock F, Fry JC, et al. Investigation of the methanogen population structure and activity in a brackish lake sediment. Environ Microbiol. 2005;7(7):947-60.
Banning, N., Brock, F., Fry, J. C., Parkes, R. J., Hornibrook, E. R., & Weightman, A. J. (2005). Investigation of the methanogen population structure and activity in a brackish lake sediment. Environmental Microbiology, 7(7), 947-60.
Banning N, et al. Investigation of the Methanogen Population Structure and Activity in a Brackish Lake Sediment. Environ Microbiol. 2005;7(7):947-60. PubMed PMID: 15946291.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Investigation of the methanogen population structure and activity in a brackish lake sediment. AU - Banning,Natasha, AU - Brock,Fiona, AU - Fry,John C, AU - Parkes,R John, AU - Hornibrook,Edward R C, AU - Weightman,Andrew J, PY - 2005/6/11/pubmed PY - 2005/8/3/medline PY - 2005/6/11/entrez SP - 947 EP - 60 JF - Environmental microbiology JO - Environ Microbiol VL - 7 IS - 7 N2 - The methanogen community in sediment from the edge of a small brackish lake connected to the Beaulieu Estuary (Hampshire, UK) was investigated by analysis of 16S rRNA gene diversity using new methanogen-specific primers plus Archaea-specific primers. 16S rRNA gene primers previously used for polymerase chain reaction (PCR) detection of methanogenic Archaea from a variety of environments were evaluated by in silico testing. The primers displayed variable coverage of the four main orders of methanogens, highlighting the importance of this type of primer evaluation. Three PCR primer sets were designed using novel reverse primers to facilitate specific amplification of the orders Methanomicrobiales/Methanosarcinales, Methanobacteriales and Methanococcales. Diversity of the methanogen functional gene, methyl coenzyme M reductase (mcrA), was also studied. All gene libraries constructed from this sediment indicated that Methanomicrobiales and Methanosarcinales were the only methanogens detected. There was good agreement between the relative sequence abundances in the methanogen-specific 16S rRNA gene library and terminal restriction fragment length polymorphism (T-RFLP) profiling, suggesting that the population was dominated by putative H2 CO2 utilizing Methanomicrobiales, although acetate-utilizing methanogens were also present. The methanogen population analyses were in agreement with methanogenic activity measurements, which indicated that bicarbonate methanogenesis was higher than acetate methanogenesis at all depths measured and overall there was a significant difference (P = 0.001) between the rates of the two pathways. This study demonstrates the utility of new 16S rRNA gene PCR primers targeting specific methanogenic orders, and the combined results suggest that the CO2 reduction pathway dominates methanogenesis in the brackish sediment investigated. SN - 1462-2912 UR - https://www.unboundmedicine.com/medline/citation/15946291/Investigation_of_the_methanogen_population_structure_and_activity_in_a_brackish_lake_sediment_ L2 - https://doi.org/10.1111/j.1462-2920.2004.00766.x DB - PRIME DP - Unbound Medicine ER -