Structural and Functional Links between Denitrifiers, Fermenters and Methanogens: Impact on Greenhouse Gases
Final Report Abstract
Peatlands including fens are major reservoirs of carbon and nitrogen, and emit the greenhouse gases CH4 and N2O. The activity of methanogens and denitrifiers regulates the production and eventually consumption of such greenhouse gases. Methanogenic Archeae are highly specialized microbes that rely on fermenters to fuel them with C1- to C2-substrates and reductant. Thus it is of major interest how fermenters, methanogens, and denitrifiers are trophically linked and might react to environmental changes projected to be induced by climate change. Potential activities of fermenters, methanogens and denitrifiers decreased with increasing depth, although cell numbers were essentially the same over depth. Temperature optima for methanogenesis and denitrification were 30-40 °C, indicating mesophilic organisms. Major fermentation products from biopolymers and sugars were H2/CO2 , acetate, propionate and butyrate; formate was detected occasionally. The analysis of hydrogenase genes as gene marker for H2-producing fermenters indicated that those organisms were new and diverse. 16S rRNA stable isotope probing (SIP) and cultivation indicated that diverse, acid-tolerant, and novel facultative aerobic and obligate anaerobic taxa form trophic links to methanogens. Indeed, H2/CO2 and formate were identified as important substrates for fen methanogens, and diverse and novel CO2 and formate assimilating fen methanogens were identified by SIP. Bacterial and Archaeal community composition was spatially highly variable, which was reflected in the variability of methanogenic potentials. However, putative hydrogenorather than acetotrophic taxa always pre-dominated gene libraries from fen soil, suggesting that hydrogenotrophic methanogens are important in the fen. Denitrifiers in the fen were novel, highly diverse, acid-tolerant, and capable of complete denitrification and consumption of atmospheric N2O at in situ pH. Such findings are in line with the temporary sink function of the fen for N2O. The community composition of bacteria (including fermenters), methanogens, and denitrifiers appeared to be rather stable. Neither drying/rewetting nor flooding significantly changed the detected community structures. Potential fermentation activities were rather insensitive to experimental drying. However, drying and rewetting impaired methanogenic activities as indicated by microcosm incubations. qPCR and gene expression studies suggested that methanogens were less abundant and less active after drying, corroborating microcosm results. Gene copy numbers of denitrification associated genes were higher post-than predrying, indicating that drying favored. Indeed, denitrifiers are facultative aerobes and N2O emissions from drying plots were higher than from control plots. Flooding did not change the potential of the microbial community to ferment but stimulated formate dependent methanogenic potentials. Methanogenesis associated gene copy numbers were increased in flooding plots, indicating an increase in population size of methanogens during flooding. Denitrification including N2O consumption potentials appeared to be stimulated in flooding plots. The ratio of genes encoding enzymes catalyzing nitrous oxide reduction and nitrate reduction suggested that flooding stimulated N2O consuming denitrifiers relative to nitrate reducers, and thus might mitigate N2O emissions. Although many new results on fermenters, methanonges, and denitrifiers in a fen were obtained in the current project, the complexity of trophically linked taxa that finally yield CH4 are still poorly understood and warrant further research.
Publications
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2008. Anaerobic consumers of monosaccharides in a moderately acidic fen. Appl. Environ. Microbiol. 74: 3112-3120
Hamberger, A., M.A. Horn, M.G. Dumont, J.C. Murrell, and H.L. Drake
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2009. Genome derived criteria for assigning environmental narG and nosZ sequences to operational taxonomic units of nitrate reducers. Appl. Environ. Microbiol. 75: 5170-5174
Palmer, K., H.L. Drake, and M.A. Horn
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2009. Intermediary ecosystem metabolism as a main driver of methanogenesis in acidic wetland soil. Environ. Microbiol. Reports 1: 307-318
Drake, H.L., M.A. Horn, and P.K. Wüst
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2009. Trophic links between fermenters and methanogens in a moderately acidic fen soil. Environ. Microbiol. 11: 1395-1409
Wüst, P.K., M.A. Horn, and H.L. Drake
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2010. Association of novel and highly diverse acid-tolerant denitrifiers with N2O fluxes of an acidic fen. Appl. Environ. Microbiol. 76: 1125-1134
Palmer, K., H.L. Drake, and M.A. Horn
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2010. Hitherto unknown [Fe-Fe]-hydrogenase gene diversity in anaerobes and anoxic enrichments from a moderately acidic fen. Appl. Environ. Microbiol. 76: 2027- 2031
Schmidt, O., H.L. Drake, and M.A. Horn
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2011. Competing formate- and carbon dioxide-utilizing prokaryotes in an anoxic methane-emitting fen soil. Appl. Environ. Microbiol. 77: 3773-3785
Hunger, S., O. Schmidt, M. Hilgarth, M.A. Horn, S. Kolb, R. Conrad, and H.L. Drake
