Microbes make up most of the biodiversity on Earth, and several of the processes which microorganisms perform are of critical importance for the cycling of nutrients, the degradation of various compounds, and the global climate. Knowledge of microbes in the environment helps mankind to develop ecosystem services and to find strategies to utilise our agricultural natural resources in a long term sustainable manner.
A driving factor for deeper understanding has been the technological revolution which environmental microbiology has undergone over the past 10 year period, with new methods to identify and count microorganisms in the environment opening up an entirely new world. Discoveries of new groups of organisms with previously unknown properties have rapidly increased. We are however only just beginning to understand how microbial communities can be linked to various functions in ecosystems, and new interdisciplinary approaches are important in advancing research in environmental microbiology.
Strong research environment
A number of research groups at Swedish University of Agricultural Sciences (SLU) at Ultuna and Uppsala University (UU) recognised the need to develop methods and theories to understand the dynamics, composition and function of microbial communities in land and water. The ideas found support at Formas, and Uppsala Microbiomics Center was allocated support as a "strong research environment".
UMC is coordinated by Professor Janet Jansson at the Department of Microbiology, SLU, now at Lawrence Berkely National Laboratory in California, and since this year by the deputy coordinator Sara Hallin at SLU.
The strength of UMC is that the network unites researchers, who are working with microorganisms from all three domains of life, i.e. Bacteria, Archaea and Eukarya, both in terrestrial and aquatic environments, with groups who are specialised in protein chemistry and micromechanics (see the box). The main objective of UMC is to develop and apply new methods to analyse and characterise entire microbial communities and individual species, in order to understand their ecology and significance for agriculture, forestry and the environment.
Carbon and nitrogen cycling
Technical development is driven on several fronts. The researchers chiefly focus on developing advanced biomarkers to study active proteins in the environment, as well as new tools at microscale, e.g. cell sorting directly in the field. The latter is based on microfluidic techniques and may be used to separate single cells or specific organisms from a complex system. Experiments have also been made for the rapid diagnosis of the composition of bacteria in complex samples using chip based methods. The new techniques are now being integrated into ongoing research in which the researchers are focusing on a number of key issues in the cycling of carbon and nitrogen, with the aim to describe what microbes are involved and who does what.
The groups are engaged on a joint project in which the microorganisms involved in the degradation of chitin are studied. Chitin is the second most common biopolymer in the biosphere and is an important source of carbon and nitrogen in nature. Degradation is thus important, inter alia for the growth of conifers in nitrogen-deficient forest soils. Chitinases, which are the active component in degradation, exist in a large number of variants, and it is not clear which of these are active in different ecosystems and how they can be linked to specific groups of microorganisms. The researchers have recently finished work on mapping the relationships among different chitinases and developing biomarkers for studying them in the environment. Plans are now being made for a major study of chitinases in different ecosystems.
The climate is affected
Other areas in which the research groups are interested are the significance of microorganisms for the inflow of carbon dioxide into environments poor in carbon, as well as new organisms and enzymes involved in nitrogen cycling between ecosystems and the atmosphere. Research on carbon sequestration and nitrogen turnover helps us answer fundamental ecological questions of great interest, and can also provide new information that is of critical importance for the global climate. Intensive research is in progress to investigate the role of Archaea for these processes. It is commonly assumed that Archaea are primarily found in extreme environments such as hydrothermal vents or seas of extreme salinity, but research shows that they are likely to be of major importance in the cycling of both carbon and nitrogen in non-extreme ecosystems.
National competence centre
After its inception, UMC has generated further grants and resources, and attracted visiting researchers and post-docs from different parts of the world. International courses are regularly arranged, as well as conferences and seminars. UMC is now building up a national resource and competence centre for a broad spectrum of issues concerning microbiology and microbial ecology, in order to enhance readiness and prospects for the climatic, energy related, agricultural and environmental issues of the future. The centre is continually developing as new methods and knowledge become available, and UMC invites both researchers and the public to contact the network members for collaborations or to pose questions related to this fascinating and rapidly expanding field.
Department of Microbiology, SLU. Address: Box 7025, 750 07 Uppsala; Tel +46 18-673209; Fax: +46 18-673392.
Department of Evolution, Genomics and Systematics, Evolutionary Biology Centre, Uppsala University. Address: Norbyvägen 18C, 752 36 Uppsala; Tel +46 18-4716129; Fax: +46 18-4716404.