Lasse Bergmark:
Soil bacterial community responses to global changes

Date: 15-04-2013    Supervisor: Søren J. Sørensen & Professor Anders Priemé

Soil bacteria and archaea are essential for ecosystem functioning and plant growth through their degradation of organic matter and turnover of nutrients. But since the majority of soil bacteria and archaea are unclassified and “nonculturable” the functionality of the microbial community and its overall importance for ecosystem function in soil is poorly understood. Global change factors may affect the diversity and functioning of soil prokaryotes and thereby ecosystem functioning. To gain a better understanding of the effects of global changes it is of fundamental importance to classify the bacterial soil population.

The thesis addresses the effects of different global change manipulations on the soil microbial community composition (climate change in Manuscript 1-4 and unconventional urban fertilizers in Manuscript 5-6). A special emphasis was put on combining molecular techniques like 454-pyrosequencing and qPCR with a range of soil measurements and analyses to provide a better understanding of the drivers in soil microbial communities. The thesis contains a brief introduction where the most important concepts of global change, soil as a habitat, the nitrogen cycle and nitrification are being introduced. Followed by a description of the scientific relevance and the experimental setup of the sites to where my experimental work can be related. Then the enclosed manuscripts followed by a short discussion of the major findings, future perspective.

Manuscript 1 describes the impact of five years’ of climate change manipulations on soil microorganisms and nutrient availability in a Danish heathland, where the samples were taken shortly after a prolonged pre-summer drought. The major findings in the study are that warming increased measures of fungi and bacteria and drought might shift/change the microbial community towards a higher fungal dominance. That could lead to a change in the carbon and nutrient flow in soil.

In Manuscript 2 the impact of climate change manipulations and the seasonal dynamics of soil fungi and bacterial communities are investigated. Our results show that the soil fungal and bacterial communities respond differently to the manipulation and the seasonal variation. The bacterial community composition remained stable across both seasons and treatments without any major shift in the bacterial phyla.

At the experimental site where the climate manipulations were conducted, two competing and very contrasting plant types (Calluna and Deschampsia) dominated the vegetation. This led to Manuscript 3 where the impact and responses of the climate change manipulations on the microbial community composition was investigated under the contrasting vegetation types. Our results show a high stability of the overall bacterial community where the vegetation is influencing the microbiological composition more than the few changes related to/caused by the climate manipulations.

By using the same soil samples as in Manuscript 3 we were able to relate the impact of climate changes to the nitrification process (Manuscript 4). In the manuscript, the relative abundance and community structure of the archaeal and bacterial amoA genes are related to the potential nitrification rate and relevant soil measurements. The major findings of the study include an increased nitrification rate due to elevated temperature. It is furthermore showed that the nitrification process is being driven by different factors under the two vegetation types.

In Manuscript 5 + 6 the impact of different unconventional urban fertilizers on the bacterial community composition is investigated. Manuscript 5 is largely a method paper where the specificity of two newly designed primer sets are being tested on the fertilized soils. One of the primer sets is then applied in Manuscript 6 where the impact of fertilizers on the bacterial community composition in soil is being analysed. No major changes in the community composition due to different fertilizer treatments were found, demonstrating a high robustness of the soil microbiota.