Biogeochemistry and microbiology of methane cycling

1. Biotic and abiotic controls of methane oxidation

Most methanotrophs are drought resistant forming a microbial seed bank. Only a subset out from this seed bank is active, but we just begin to understand when and why the others are becoming active. We mixed X-ray sterilized with native soil simulating a die-off. While the functioning, i.e. methane oxidation, was even over-compensated after disturbance, the active community was different. Methanotrophs are gradient organisms living in counter-gradients of oxygen and methane. While such gradients form in any situation where methanotrophs are active, the flux of methane and, hence, the energy flow through a population may vary by orders of magnitude. Indeed, the active community varied depending energy flow. Further factors explored are rice genotypes, nitrogen fertilization, heat stress, and drought. In summary, the Italian paddy soil used as a model system contains all relevant groups of freshwater methanotrophs, but the active methanotroph population is dominated by type I, while type II became active only upon severe disturbance.

2. Diversity and biogeography of methanotrophs

Our focus was so far on the Mediterranean and on rice fields, but has now been expanded to the Subtropics, the Tropics and the Arctic, and to natural wetlands and landfills. We have combined a pmoA-specific microarray with classical Sanger- and pyrosequencing. We found a wide geographical distribution of pmoA genotypes that seem to be specifically adapted to paddy fields. On the smaller scale, we revealed different community patterns at three field located 10 to 20 kilometers apart. With the current agronomical practice being nearly identical, historical contingencies might be responsible for the site differences. Considering a large seed bank of viable yet inactive methanotrophs, past management practice may have shaped the communities. However, rice varieties planted to these fields may also have been important: we revealed a rice cultivar effect on the root associated methanotroph community that could be affiliated to the plant genotype.

Paddy fields in subtropical China revealed about two times as much operational taxonomic units as the fields in the Mediterranean. On the contrary, the Arctic hosts a very simple methanotrophic community dominated by a few phylotypes. Altogether, this suggests a latitudinal diversity gradient.

Current work aims on improving the pmoA-based phylogeny of methanotrophs, and on developing a software tool to classify pmoA-sequences obtained with next generating sequencing techniques. A prototype has been tested with excellent results and is available on request.

3. Evolution of microbial communities in paddy soils

We have worked on the development of the methanotrophic community along a chronosequence covering soils recently reclaimed from the sea, up to rice fields continuously planted to rice since 2000 years. Potential methanotrophic activity increased with age of soil. Overall community composition was relatively similar in all fields, but growth and activity of one particular subgroup of methanotrophs correlated to soil age suggesting that continuous rice agriculture did not only shape the microbial community, but also modified the micro-environment in a way enabling faster growth and higher activity of particular populations. Methanogens used preferably acetate ( ~ 80%) with the active community dominated by Methanosarcinales. Together with W. Amelung, University of Bonn, Germany, we are currently studying how rhizodeposits in a young (50 a) and an old (2000 a) paddy soil are passing through the microbial community becomming eventually stabilized in soil organic matter.

4. Arctic microbiology

Arctic phylotypes are closely related to Methylobacter tundripaludum dominating both the seed bank and the active population. In-situ methane oxidation seems to be controlled by temperature and methane availability limiting activity to a few weeks per year (work in progress together with M. Svenning, University of Tromsø, Norway). Ongoing experiments are focused on methanogenesis and methanogens in thawing permafrost (Alaska, together with K. Walter-Anthony, University of Fairbanks, USA), and on fermentation, methanogenesis and transcriptomics in an Arctic wetland (Svalbard, together with M. Svenning, University of Tromsø, Norway, and T. Urich, University of Vienna, Austria).