Studies on methanogenesis from freshwater sediments have so far primarily focused on lake sediments. To expand our knowledge on the community composition of methanogenic archaea in river sediments, we studied the abundance and diversity of methanogenic archaea at two localities along a vertical profile (top 50 cm) obtained from sediment samples from Sitka stream (the Czech Republic). In this study, we compare two sites which previously have been shown to have a 10-fold different methane emission. Archaeal and methanogen abundance were analyzed by real-time PCR and T-RFLP. Our results show that the absolute numbers for the methanogenic community (qPCR) are relatively stable along a vertical profile as well as for both study sites. This was also true for the archaeal community and for the three major methanogenic orders in our samples (Methanosarcinales, Methanomicrobiales, and Methanobacteriales). However, the underlying community structure (T-RFLP) reveals different community compositions of the methanogens for both locations as well as for different depth layers and over different sampling times. In general, our data confirm that Methanosarcinales together with Methanomicrobiales are the two dominant methanogenic orders in river sediments, while members of Methanobacteriales contribute a smaller community and Methanocellales are only rarely present in this sediment. Our results show that the previously observed 10-fold difference in methane emission of the two sites could not be explained by molecular methods alone.

Department of Biogeochemistry Max Planck Institute for Terrestrial Microbiology Marburg Germany

Department of Ecology and Environmental Sciences Faculty of Science Laboratory of Aquatic Microbial Ecology Palacky University Olomouc Czech Republic

Department of Internal Medicine University of Michigan Ann Arbor MI USA

Zobrazit více v PubMed

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, 947–960. PubMed

Barreto, D. P. , Conrad, R. , Klose, M. , Claus, P. , & Enrich‐Prast, A . (2014). Distance‐decay and taxa‐area relationships for bacteria, archaea and methanogenic archaea in a tropical lake sediment. PLoS ONE, 9, e110128 1–9. PubMed PMC

Bastviken, D. , Cole, J. , Pace, M. , & Tranvik, L . (2004). Methane emissions from lakes: Dependence of lake characteristics, two regional assessments, and a global estimate. Global Biogeochemical Cycles, 18, GB4009 doi:10.1029/2004GB002238. DOI

Borrel, G. , O'Toole, P. W. , Harris, H. M. B. , Peyret, P. , Brugere, J. F. , & Gribaldo, S. (2013). Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis. Genome Biology and Evolution, 5, 1769–1780. PubMed PMC

Borrel, G. , Parisot, N. , Harris, H. M. B. , Peyretaillade, E. , Gaci, N. , Tottey, W. , … Brugere, J. F . (2014). Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales‐related seventh order of methanogenic archaea that encodes pyrrolysine. Bmc Genomics, 15, 679. PubMed PMC

Brablcova, L. , Buriankova, I. , Badurova, P. , Chaudhary, P. P. , & Rulik, M. (2014). Methanogenic archaea diversity in hyporheic sediments of a small lowland stream. Anaerobe, 32C, 24–31. PubMed

Bretschko, G. , & Klemens, W. E. (1986). Quantitative methods and aspects in the study of the interstitial fauna of running waters. Stygologia, 2, 297–316.

Buriankova, I. , Brablcova, L. , Mach, V. , Dvorak, P. , Chaudhary, P. P. , & Rulik, M. (2013). Identification of methanogenic archaea in the hyporheic sediment of Sitka Stream. PLoS ONE, 8, e80804. PubMed PMC

Buriankova, I. , Brablcova, L. , Mach, V. , Hyblova, A. , Badurova, P. , Cupalova, J. , … Rulik, M. (2012). Methanogens and methanotrophs distribution in the hyporheic sediments of a small lowland stream. Fundamental and Applied Limnology, 181, 87–102.

Capone, D. G. , & Kiene, R. P. (1988). Comparison of microbial dynamics in marine and fresh‐water sediments ‐ contrasts in anaerobic carbon catabolism. Limnology and Oceanography, 33, 725–749.

Castro, H. , Newman, S. , Reddy, K. R. , & Ogram, A. (2005). Distribution and stability of sulfate‐reducing prokaryotic and hydrogenotrophic methanogenic assemblages in nutrient‐impacted regions of the Florida everglades. Applied and Environmental Microbiology, 71, 2695–2704. PubMed PMC

Castro, H. , Ogram, A. , & Reddy, K. R. (2004). Phylogenetic characterization of methanogenic assemblages in eutrophic and oligotrophic areas of the Florida Everglades. Applied and Environmental Microbiology, 70, 6559–6568. PubMed PMC

Chan, O. C. , Claus, P. , Casper, P. , Ulrich, A. , Lueders, T. , & Conrad, R. (2005). Vertical distribution of structure and function of the methanogenic archaeal community in Lake Dagow sediment. Environmental Microbiology, 7, 1139–1149. PubMed

Chaudhary, P. P. , Wright, A. D. , Brablcova, L. , Buriankova, I. , Bednarik, A. , & Rulik, M. (2014). Dominance of Methanosarcinales phylotypes and depth‐wise distribution of methanogenic community in fresh water sediments of Sitka stream from Czech Republic. Current Microbiology, 69, 809–816. PubMed

Chin, K. J. , Lueders, T. , Friedrich, M. W. , Klose, M. , & Conrad, R. (2004). Archaeal community structure and pathway of methane formation on rice roots. Microbial Ecology, 47, 59–67. PubMed

Chunleuchanon, S. , Sooksawang, A. , Teaumroong, N. , & Boonkerd, N. (2003). Diversity of nitrogen‐fixing cyanobacteria under various ecosystems of Thailand: Population dynamics as affected by environmental factors. World Journal of Microbiology and Biotechnology, 19, 167–173.

Ciais, P. , Sabine, C. , Bala, G. , Bopp, L. , Brovkin, V. , Canadell, J. , … Thornton, P . (2014). Carbon and other biogeochemical cycles In Stocker T. F., Qin D., Plattner G.‐K., Tignor M., Allen S. K., Boschung J., Nauels A., Xia Y., Bex V. & Midgley P. M. (Eds.), IPCC, 2013: Climate Change 2013: The Physical Science Basis Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (pp. 465–570). United Kingdom and New York, NY, USA: Cambridge University Press, Cambridge.

Cicerone, R. J. , & Oremland, R. S. (1988). Biogeochemical aspects of atmospheric methane. Global Biogeochemical Cycles, 2, 299–327.

Conrad, R. (2009). The global methane cycle: Recent advances in understanding the microbial processes involved. Environmental Microbiology Reports, 1, 285–292. PubMed

Conrad, R. , Ji, Y. , Noll, M. , Klose, M. , Claus, P. , & Enrich‐Prast, A. (2014). Response of the methanogenic microbial communities in Amazonian oxbow lake sediments to desiccation stress. Environmental Microbiology, 16, 1682–1694. PubMed

Conrad, R. , Klose, M. , Noll, M. , Kemnitz, D. , & Bodelier, P. L. E. (2008). Soil type links microbial colonization of rice roots to methane emission. Global Change Biology, 14, 657–669.

Delong, E. F. (1992). Archaea in coastal marine environments. Proceedings of the National Academy of Sciences, 89, 5685–5689. PubMed PMC

Dhillon, A. , Lever, M. , Lloyd, K. G. , Albert, D. B. , Sogin, M. L. , & Teske, A. (2005). Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin. Applied and Environmental Microbiology, 71, 4592–4601. PubMed PMC

Falz, K. Z. , Holliger, C. , Grosskopf, R. , Liesack, W. , Nozhevnikova, A. N. , Muller, B. , … Hahn, D. (1999). Vertical distribution of methanogens in the anoxic sediment of Rotsee (Switzerland). Applied and Environmental Microbiology, 65, 2402–2408. PubMed PMC

Galand, P. E. , Fritze, H. , Conrad, R. , & Yrjala, K. (2005). Pathways for methanogenesis and diversity of methanogenic archaea in three boreal peatland ecosystems. Applied and Environmental Microbiology, 71, 2195–2198. PubMed PMC

Hlavacova, E. , Rulik, M. , & Cap, L. (2005). Anaerobic microbial metabolism in hyporheic sediment of a gravel bar in a small lowland stream. River Research and Applications, 21, 1003–1011.

Kemnitz, D. , Chin, K. J. , Bodelier, P. , & Conrad, R. (2004). Community analysis of methanogenic archaea within a riparian flooding gradient. Environmental Microbiology, 6, 449–461. PubMed

Kleikemper, J. , Pombo, S. A. , Schroth, M. H. , Sigler, W. V. , Pesaro, M. , & Zeyer, J. (2005). Activity and diversity of methanogens in a petroleum hydrocarbon‐contaminated aquifer. Applied and Environmental Microbiology, 71, 149–158. PubMed PMC

Koizumi, Y. , Takii, S. , & Fukui, M. (2004). Depth‐related change in archaeal community structure in a freshwater lake sediment as determined with denaturing gradient gel electrophoresis of amplified 16S rRNA genes and reversely transcribed rRNA fragments. FEMS Microbiology Ecology, 48, 285–292. PubMed

Kotsyurbenko, O. R. , Chin, K. J. , Glagolev, M. V. , Stubner, S. , Simankova, M. V. , Nozhevnikova, A. N. , & Conrad, R. (2004). Acetoclastic and hydrogenotrophic methane production and methanogenic populations in an acidic West‐Siberian peat bog. Environmental Microbiology, 6, 1159–1173. PubMed

Lang, K. , Schuldes, J. , Klingl, A. , Poehlein, A. , Daniel, R. , & Brune, A. (2015). New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus Methanoplasma termitum”. Applied and Environmental Microbiology, 81, 1338–1352. PubMed PMC

Leichtfried, M. (1988). Bacterial substrates in gravel beds of a second order alpine stream (Project Ritrodas‐Lunz, Austria). Verhandlungen des Internationalen Verein Limnologie, 23, 1325–1332.

Lueders, T. , Chin, K. J. , Conrad, R. , & Friedrich, M. (2001). Molecular analyses of methyl‐coenzyme M reductase alpha‐subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environmental Microbiology, 3, 194–204. PubMed

Lueders, T. , & Friedrich, M. W. (2003). Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small‐subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Applied and Environment Microbiology, 69, 320–326. PubMed PMC

Luton, P. E. , Wayne, J. M. , Sharp, R. J. , & Riley, P. W. (2002). The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology, 148, 3521–3530. PubMed

Mach, V. , Blaser, M. B. , Claus, P. , Chaudhary, P. P. , & Rulik, M. (2015). Methane production potentials, pathways, and communities of methanogens in vertical sediment profiles of river Sitka. Frontiers in Microbiology, 6, 506. PubMed PMC

Munson, M. A. , Nedwell, D. B. , & Embley, T. M. (1997). Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Applied and Environmental Microbiology, 63, 4729–4733. PubMed PMC

Newberry, C. J. , Webster, G. , Cragg, B. A. , Parkes, R. J. , Weightman, A. J. , & Fry, J. C. (2004). Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environmental Microbiology, 6, 274–287. PubMed

Orphan, V. J. , Jahnke, L. L. , Embaye, T. , Turk, K. A. , Pernthaler, A. , Summons, R. E. , & Des Marais, D. J. (2008). Characterization and spatial distribution of methanogens and methanogenic biosignatures in hypersaline microbial mats of Baja California. Geobiology, 6, 376–393. PubMed

Ovreas, L. , Forney, L. , Daae, F. L. , & Torsvik, V. (1997). Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR‐amplified gene fragments coding for 16S rRNA. Applied and Environment Microbiology, 63, 3367–3373. PubMed PMC

Purdy, K. J. , Munson, M. A. , Nedwell, D. B. , & Embley, T. M. (2002). Comparison of the molecular diversity of the methanogenic community at the brackish and marine ends of a UK estuary. FEMS Microbiology Ecology, 39, 17–21. PubMed

Ramakrishnan, B. , Lueders, T. , Conrad, R. , & Friedrich, M. (2000). Effect of soil aggregate size on methanogenesis and archaeal community structure in anoxic rice field soil. FEMS Microbiology Ecology, 32, 261–270. PubMed

Ramakrishnan, B. , Lueders, T. , Dunfield, P. , Conrad, R. , & Friedrich, M. W. (2001). Archaeal community structures in rice soils from different geographical regions before and after initiation of methane production. FEMS Microbiology Ecology, 37, 175–186.

Rulik, M. , Bednarik, A. , Mach, V. , Brablcova, L. , Buriankova, I. , Badurova, P. , & Gratzova, K . (2013). Methanogenic system of a small lowland stream Sitka In Matovic M. D. (Eds.), Biomass now ‐ cultivation and utilization (pp. 395–426). Czech Republic: InTech.

Saarnio, S. , Winiwarter, W. , & Leitao, J. (2009). Methane release from wetlands and watercourses in Europe. Atmospheric Environment, 43, 1421–1429.

Schink, B. (1997). Energetics of syntrophic cooperation in methanogenic degradation. Microbiology and Molecular Biology Reviews, 61, 262–280. PubMed PMC

Schwarz, J. I. K. , Eckert, W. , & Conrad, R. (2007). Community structure of archaea and bacteria in a profundal lake sediment Lake Kinneret (Israel). Systematic and Applied Microbiology, 30, 239–254. PubMed

Springer, E. , Sachs, M. S. , Woese, C. R. , & Boone, D. R. (1995). Partial gene sequences for the A subunit of methyl‐coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae. International Journal of Systematic Bacteriology, 45, 554–559. PubMed

Stanley, E. H. , Casson, N. J. , Christel, S. T. , Crawford, J. T. , Loken, L. C. , & Oliver, S. K. (2016). The ecology of methane in streams and rivers: Patterns, controls, and global significance. Ecological Monographs, 86, 146–171.

Wuebbles, D. J. , & Hayhoe, K. (2002). Atmospheric methane and global change. Earth Science Reviews, 57, 177–210.

Ye, W. J. , Liu, X. L. , Lin, S. Q. , Tan, J. , Pan, J. L. , Li, D. T. , & Yang, H. (2009). The vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu. FEMS Microbiology Ecology, 70, 263–276. PubMed

Yu, Y. , Lee, C. , Kim, J. , & Hwang, S. (2005). Group‐specific primer and probe sets to detect methanogenic communities using quantitative real‐time polymerase chain reaction. Biotechnology and Bioengineering, 89, 670–679. PubMed

Zeikus, J. G. (1983). Metabolism of one‐carbon compounds by chemotropic anaerobes. Advances in Microbial Physiology, 24, 215–299. PubMed

Zeleke, J. , Lu, S. L. , Wang, J. G. , Huang, J. X. , Li, B. , Ogram, A. V. , & Quan, Z. X. (2013). Methyl coenzyme M reductase A (mcrA) gene‐based investigation of methanogens in the mudflat sediments of Yangtze River Estuary, China. Microbial Ecology, 66, 257–267. PubMed