Dynamics of microbial communities involved in carbon and nitrogen turnover during paddy soil evolution in relation to different soil types
Final Report Abstract
During paddy soil evolution different chemical and physical soil properties may influence soil microbial communities involved in carbon and nitrogen turnover. Directly after conversion of tidal wetlands into paddy soils microbial communities might mainly respond to the leaching of marine salts by rainfall and the beginning agricultural management. With ongoing agricultural management and continuous input of carbon and nitrogen to the soil system, microbes may adapt to the new conditions and functional groups of the rare biosphere from tidal wetlands may become key players for certain functional traits. Long term cultivation of rice with repeated tillage management fertilization and pesticide application as well as effects by the plants (rhizosphere and litter) may strongly influence soil microbial communities and lead to a general increase in abundance and activity due to accumulation effects. Thus, we postulate to find differences in microbial community structure and function along a chronosequence with different histories in paddy soil management (phase 1 of the research unit). For phase 2 of the research unit we wanted to understand if the observed differences along a chronsequence are depending on the soil type or if unifying principles can be deviated. Together with the data obtained by P1, P2, and P7 it was possible to link this data to soil development along the chronosequence. Overall changes in abundance and diversity of the functional groups could be observed reflecting the different chemical and physical properties of the soils, which changed in terms of soil development. The tidal wetland was characterized by a low microbial biomass and relatively high abundances of ammonia oxidizing microbes. Conversion of the tidal wetlands into paddy soils was followed by a significant increase in microbial biomass. 50 years of paddy management showed a higher abundance of nitrogen fixing microbes compared to the tidal wetland, whereas dominant genes of nitrification and denitrification showed no differences. With ongoing rice cultivation copy numbers of archaeal ammonia oxidizers did not change, while that of their bacterial counterparts declined. The gene coding for the nitrite reduction nirK, which was dominating over its functional redundant counterpart nirS at all sites, increased with rice cultivation time in all soils. Relative species richness showed significant differences between all soils with the exception of archaeal ammonia oxidizers in the paddy soils cultivated for 100 respectively 300 years. In general, changes in diversity pattern were more pronounced than in abundance pattern. A metagenomic analysis revealed also pronounced differences in microbial communities related to carbon turnover. A closer look at the genes of the most dominant process - the central carbohydrate metabolism - analyzing level 3 SEED subclasses showed significant differences in functions of the pyruvate, alanine and serine interconventions. In addition, significant influence of cultivation time was determined for pyruvate metabolism I (anaplerotic reactions PEP) and pyruvate metabolism II (Acetly CoA acetogenesis from pyruvate). By analysing soils with different soil properties used for paddy soil cultivation, a unique core microbiome for paddy soils could be identified. Thus our results could clearly prove that i) microbial communities between tidal wetlands and paddy soil differ significantly, which results in different functional pattern and turnover rates and ii) that during ongoing paddy cultivation microbial communities adapt to the changes in soil structure and organic matter quality and specific phylotypes of selected functional groups become dominant, which are found to typically for paddy soils independent from the parental soil type.
Publications
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(See online at https://doi.org/10.1111/j.1365-2486.2011.02500.x) - 2011. Ageing well: methane oxidation and methane oxidizing bacteria along a chronosequence of 2000 years. Environmental Microbiology Reports, 3: 738-743
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(See online at https://doi.org/10.1111/j.1758-2229.2011.00292.x) - 2011. Changes in diversity and functional gene abundances of microbial communities involved in nitrogen fixation, nitrification and denitrification comparing a tidal wetland to paddy soils cultivated for different time periods. Applied Environmental Microbiology 77, 6109 – 6116
Bannert, A., Kleineidam, K., Wissing, L., Müller-Niggemann, C., Vogelsang, V., Welzl, G., Cao, Z.-H., Schloter, M.
(See online at https://doi.org/10.1128/AEM.01751-10) - 2011. Comparison of lipid biomarker and gene abundance characterizing the archaeal ammonia-oxidizing community in flooded soils. Biology and Fertility of Soils, 1-5
Bannert, A., Mueller-Niggemann, C., Kleineidam, K., Wissing, L., Cao, Z.-H., Schwark, L., Schloter, M.
(See online at https://doi.org/10.1007/s00374-011-0552-6) - 2011. Improved protocol for the simultaneous extraction and column-based separation of DNA and RNA from different soils. Journal of Microbiological Methods 84, 406-412
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(See online at https://doi.org/10.1016/j.mimet.2010.12.028) - 2011. Nitrogen turnover in soil and global change. FEMS Microbiology Ecology 78, 3-16
Ollivier J., Töwe, S., Bannert, A., Hai, B., Kastl, E.M., Meyer, A., Su, M., Kleineidam, K., Schloter, M.
(See online at https://doi.org/10.1111/j.1574-6941.2011.01165.x) - 2011. Recovery of methanotrophs from disturbance: population dynamics, evenness, and functioning. ISME J 5, 750-758
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(See online at https://doi.org/10.1038/ismej.2010.163) - 2012. Heat stress and methane-oxidizing bacteria: effects on activity and population dynamics. Soil Biology and Biochemistry 50, 22-25
Ho, A., Frenzel, P.
(See online at https://doi.org/10.1016/j.soilbio.2012.02.023) - 2013. Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies. Environmental Microbiology Reports 5, 335-345
Ho, A., Kerckhof, F.M., Lüke, C., Reim, A., Krause, S., Boon, N., Bodelier, P.L.E.
(See online at https://doi.org/10.1111/j.1758-2229.2012.00370.x) - 2013. Selective stimulation in a natural community of methaneoxidizing bacteria: effects of copper on pmoA transcription and activity. Soil Biology and Biochemistry 65, 211-216
Ho, A., Lüke, C., Reim, A., Frenzel, P.
(See online at https://doi.org/10.1016/j.soilbio.2013.05.027) - 2014. Accelerated soil formation due to paddy management on marshlands (Zhejiang Province), China. Geoderma 228, 67 – 89
Kölbl, A., Schad, P., Jahn, R., Amelung, W., Bannert, A., Cao, Z., Fiedler, S., Kalbitz, K., Lehndorff, E., Niggemann, C., Schloter, M., Vogelsang, V., Wissing, L., Kögel-Knaber, I.
(See online at https://doi.org/10.1016/j.geoderma.2013.09.005) - 2014. Macroecology of methane-oxidizing bacteria: The alpha-diversity of pmoA genotypes in tropical and subtropical rice fields. Environmental Microbiology 16, 72-83
Lüke, C., Frenzel, P., Ho, A., Fiantis, D., Schad, P., Schneider, B., Schwark, L., Utami, S.
(See online at https://doi.org/10.1111/1462-2920.12190) - 2015. Recovery of paddy soil methanotrophs from long term drought. Soil Biology and Biochemistry 88, 69-72
Collet, S., Reim, A., Ho, A., Frenzel, P.
(See online at https://doi.org/10.1016/j.soilbio.2015.04.016)
