Background

(Micro-) organisms govern virtually all geochemical cycles at the earth’s surface and have major consequences for heat balance, water flow and sediment transport and stability, which in turn govern the dynamics of organisms and communities. An understanding of the transformation processes carried out by (micro-) organisms is consequently essential for a meaningful analysis and quantitative description of the biogeochemical dynamics of System Earth. Microbial life has colonized every habitat on the planet by using virtually every thermodynamically favorable redox couple. This accomplishment reflects a fundamental linkage between genome evolution and the geochemical environment. The evolution of life on Earth has not only been shaped by changing environmental conditions determined by geological forces, but life itself has played a decisive role in this process through its impact on the biogeochemical cycling of key elements (C, H, N, O, P, S, Fe, Si). This indicates that, for a full understanding of the evolution of life, we need to reconstruct the rise and, in some cases, decline of the key players in biogeochemical cycling.

Organisms are subject to changing environmental conditions, but in turn may also influence environmental conditions, both in the geological past and at present. Global warming may cause melting of permafrost, changes in plant communities and changes in methane and carbon-dioxide fluxes, which in turn may affect global climate. Similarly, climate changes may affect aquatic systems, with consequences for the production and exchange of climate-active gases such as carbon dioxide, methane, nitrous oxide and dimethylsulfide. Warming of oceans and lakes has consequences for dissolved oxygen inventories, while high atmospheric carbon dioxide induces ocean acidification, with consequences for marine organisms, in particular calcifiers, and global biogeochemical cycles. Both hypoxia and ocean acidification have occurred in the geological past and are of societal concern at present.

System Earth has experienced major environmental changes in the past, some of them abrupt due to external forces and some of them abrupt due to internal feedbacks, while others have been more gradual. Organisms and communities have shown differential sensitivity (in terms of loss) and differences in resilience (in terms of recovery from major environmental disturbances), both in the geological past and in the present time. The role of organisms in system recovery and the re-establishment of ecosystem functioning requires integration of studies on recent and past community dynamics.

Challenges

The application of molecular techniques will deepen our fundamental understanding of the coupling between (micro-) biology and biogeochemistry. Molecular biological approaches will allow us to identify the key players in biogeochemical cycles and to study the responses of microbial communities to environmental changes. Through the combination of activity measurement and molecular tools it may be possible to link microbial activity and biogeochemical fluxes with the identity of the organisms involved. Such knowledge is essential when developing the next generation of predictive models for global and regional biogeochemical cycling.

How do climate and environmental change (warming, changes in precipitation patterns, higher N and S deposition, elevated carbon-dioxide levels) affect ecosystems and their functioning and how do changes in ecosystems feed back (via, for example, emission of climate-active gases) on climate change? Although there is some information on individual components of climate change, we have little if any understanding of compensating mechanisms and synergetic effects. For instance, aquatic systems are subject to elevated atmospheric carbon dioxide and global warming and we have to collect knowledge on the combined effects on organisms and ecosystems. The two-way interactions between organisms and biogeochemical cycles operate on micro-, macro-, and mega-scales. Ecosystem engineers (i.e. organisms that substantially modify the physical structure or material flows of their habitat, and thus directly or indirectly change the availability of resources to other species) can have a major impact on the appearance (pattern formation) and functioning of ecosystems. Vegetation and animals, for instance, can modify water flow and in that way optimize their performance and influence other organisms and biogeochemical cycles. Bacteria, algae and metazoans can also influence sediment deposition and erosion and thus shape their local environment. Microbial mats may or may not induce calcification and we have little understanding of the governing factors.

Most environmental changes imposed on ecosystems are gradual (carbon-dioxide increase, global warming etc.); yet recent and historical observations and the geological record show that gradual changes in forcing can over time result in abrupt and major (and sometimes even catastrophic) changes in community structures. It is important to identify whether tipping points exist (a certain critical carbon-dioxide level, for example) and whether these tipping points may be deduced from the geological record or from experimental and modeling studies of the coupled dynamics of biosphere-geosphere interactions.