Investigation of microbial groups involved in the uptake of atmospheric trace gases in upland soils

Abstract

Atmospheric trace gases play a leading role in the changes occurring in the atmosphere at present, including climate change. A significant part of atmospheric trace gas fluxes occurs at the interface between atmosphere and upland soils. Unfortunately, the microorganisms in charge of these dynamics are not fully understood. This thesis therefore focuses on the investigation of microbial groups in terrestrial environments, responsible for or proposed to be involved in the uptake of atmospheric trace gases (CH4, CO2, H2), namely the potential atmospheric methane oxidizer upland soil cluster α (USCα), the autotrophic ammonia oxidizing archaea (AOA), and the hydrogen oxidizing streptomycetes. Several methods were tested to investigate the incorporation of labeled substrate and to monitor the expression of their functional marker genes, pmoA for the high-affinity particulate methane monooxygenase of USCα, amoA for the ammonia monooxygenase of AOA, and hydB for the high-affinity [NiFe]-hydrogenase of Streptomyces sp. PCB7. Although the upland soil cluster α (USCα) in forest soils is assumed to represent methanotrophic bacteria adapted to the trace level of atmospheric methane and to play an essential part in the removal of this greenhouse gas from the atmosphere, so far it is unclear whether these microorganisms are able to obtain all their energy and carbon solely from CH4 or use additional carbon compounds. Stable isotope probing was applied to investigate incorporation of labeled CH4 and acetate into nucleic acids of USCα. The results of this study indicate that USCα might only use atmospheric CH4 as an additional energy source or survival strategy, but utilizes additional carbon compounds, such as acetate, for growth suggesting the USCα represents rather facultative than obligate methanotrophs. Furthermore, CARD-FISH of pmoA transcripts visualized USCα in situ for the first time. These findings promote the knowledge and understanding of upland soils as a sink for atmospheric methane and the microorganisms proposed to be responsible for this process. While for a long time autotrophic bacteria were believed to be solely responsible for the process of ammonia oxidation, there is now increasing evidence that also Archaea are involved. But to date it remained elusive whether ammonia oxidizing archaea in soil can assimilate CO2 and to what extent they are functionally active. Stable isotope probing of nucleic acids using 13CO2 showed that ammonia oxidizing archaea were actively involved in microbial ammonia oxidation in an agricultural soil and did fix CO2 autotrophically, presumably via the hydroxypropionate-hydroxybutyrate cycle. CARD-FISH further demonstrated the numerical importance of the archaeal ammonia oxidizers to the overall archaeal community in this environment. These results give novel evidence that the contribution of nitrifying Archaea to ammonia oxidation and CO2 fixation in terrestrial environments might be substantial. Although hydrogen is considered to be one of the most important future energy carriers, little is known about the global biogeochemical cycle of this trace gas. Previous findings indicate that microorganisms rather than free soil enzymes are responsible for the uptake of atmospheric H2 in soils. In this thesis, CARD-FISH analyses demonstrated that streptomyces spores instead of the mycelia expressed the high-affinity H2 uptake activity. This suggests that H2-oxidizing streptomycetes, or actinobacteria in general, are essential for the uptake of atmospheric H2 in upland soils