Impact of changes in environmental parameters (pH and elevated CO2) on soil microbial communities involved in N-cycling

Microorganisms involved in the nitrogen (N)-cycle in soils are the major drivers of N-transformation changes and the main source of the potent greenhouse gas nitrous oxide (N2O) from soil, which has a global warming potential of 298 times that of carbon dioxide (CO2). Accordingly, it is of great int...

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Bibliographic Details
Main Author: Brenzinger, Kristof
Contributors: Braker, Gesche (PD Dr.) (Thesis advisor)
Format: Doctoral Thesis
Published: Philipps-Universität Marburg 2015
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Summary:Microorganisms involved in the nitrogen (N)-cycle in soils are the major drivers of N-transformation changes and the main source of the potent greenhouse gas nitrous oxide (N2O) from soil, which has a global warming potential of 298 times that of carbon dioxide (CO2). Accordingly, it is of great interest to explore shifts in the rates, balances and reactions of the N-cycle impacted by climate changes, in order to offer more accurate predictions. Particularly, since increases in CO2 concentrations or changes in the pH of agricultural fields due to anthropogenic influences often lead to changes in the N-transformation rates, along with an increase of N2O emissions. However, the N-cycle and its corresponding pathways are very complex and the response to different environmental changes is difficult to predict. Many of the interactions between microorganisms and their contribution to N-transformation rates as well as N2O emission are not well understood, controversially discussed and plenty of important interactions remain puzzling. Therefore, the main objective of this thesis was to shed light on the interaction of the overall and active microbial communities involved in the N-cycle in response to pH shifts or elevated atmospheric CO2 concentrations in soils, two variables known to influence N2O fluxes from soils. In the first part we studied the influence of an acidic pH on a denitrifier community from an initial neutral pH. We followed the abundance and composition of an overall and active denitrifier community extracted from soil (pH = 7.1) when exposed to pH 5.4 and drifting back to pH 6.6. When exposed to pH 5.4, the denitrifier community was able to actively grow, but only reduced N2O to N2 after a near neutral pH was reestablished by the alkalizing metabolic activity of an acid-tolerant part of the community. The genotypes proliferating under these conditions differed from those dominant at neutral pH. Denitrifiers of the nirS-type appeared to be severely suppressed by low pH whereas nirK-type and nosZ-containing denitrifiers showed strongly reduced transcriptional activity and growth, even after restoration of neutral pH. Our study suggests that low pH episodes alter transcriptionally active populations which shape denitrifier communities and determine their gas kinetics. The second part of this thesis analyses the effect of elevated CO2 (eCO2) on the N-cycle to reveal the underlying microbial mechanisms and process inside the N-cycle causing the enhanced emission of N2O. To gain a better understanding of the impact of eCO2 on soil microbial communities, we applied a molecular approach targeting several microbial groups involved in soil N-cycling (N-fixers, denitrifiers, archaeal and bacterial ammonia oxidizers, and dissimilatory nitrate reducers to ammonia) at the Gießen Free Air Carbon dioxide Enrichment (GiFACE) site. Remarkably, soil parameters, overall microbial community abundance and composition in the top soil under eCO2 differed only slightly from soil under ambient CO2. We concluded that +20% eCO2 had little to no effect on the overall microbial community involved in N-cycling. Based on these findings, in a third part we conducted a comprehensive study monitoring N-transformation rates, nutrient fluxes, and gaseous emission, while analyzing the dynamics in microbial communities involved in N-cycling under eCO2 accompanied with simultaneous addition of N-fertilizer. We could show that long-term fumigation with eCO2 influences the response of the soil microbial communities to N inputs via fertilization. Compared to aCO2 distinct parts of the community were transcriptionally activated. Here, nirS-type denitrifiers showed the greatest positive feedback to eCO2, which correlated with increasing N2O emissions. This stimulation may be an effect of higher labile C input in the rhizosphere by increased photosynthesis. However, the input of N by fertilization rather seems to exert short term effects on the expression of functional marker genes with consequences for N-transformations which do not translate into the development of distinct communities under eCO2 in the long-term. In conclusion this thesis provides evidence that already small changes in abundance and composition of the microbial community involved in N-cycling are sufficient to strongly influence emission of N2O from soil under changing environmental parameters such as pH and elevated CO2.