Microbial ecology has been a late developing field in science, compared to its counterparts in animal and plant ecology. An understanding of the presence and the functional role of a particular organism in its environment requires techniques for the rapid identification of an organism in situ and an analysis of its activities there. Both identification and analysis are comparatively easy with a squirrel or an alder tree, for example, but difficult with a microbe.

Microbes are hard to recognize in their natural habitat. Conventional identification systems require the isolation of pure cultures together with a complex series of morphological and physiological tests, and microbial activities have mainly been assessed in broth cultures rather than on a small scale in a structured microhabitat. For many decades, isolation of pure cultures and analysis of their metabolic capacities in the context of their putative natural habitats provided the most reliable basis for microbial ecology. This approach, which has its roots in the schools of microbiology at Breslau and Delft, has been extremely valuable and has laid the basis for general microbiology and microbial diversity. The metabolic capacities of microbes laid the foundation also for an understanding of the cycling of elements in nature, connecting microbial physiology with environmental chemistry. Nevertheless, experiments on direct staining of bacteria in natural samples revealed that only a small fraction of the microbial community there could be cultivated by conventional techniques. Shortcomings in the existing cultivation methods were recognized early on: “It must, however, be recognized that in nature the conditions are seldom simple. Hence we must learn to study more carefully the effects of complicating circumstances.… This will require much imaginative work, and correlation of many kinds of observations.” (van Niel, 1955).

Through the 1970s, microelectrode techniques were adapted to the study of microbial mats and sediments allowing an analysis of the distribution and fluxes of metabolites in structured environments at a microscale. More refined cultivation techniques, e.g. the use of opposing diffusion gradients of different substrates in semi-solid media, allowed the nurturing of bacteria that depend on such conditions for growth. Another discovery of the 1970s, the application of sequence similarities of conserved cellular polymers, such as the ribosomal small subunit RNAs, to the elucidation of evolutionary relationships within the microbial world, developed through the 1980s and 1990s into a highly refined system for the fast identification of microbes. Combined with the development of molecular probes linked to optical tracers and the invention of the laser scanning microscope, microbial communities can be analyzed with respect to their composition and their spatial organization. Today these techniques allow a fascinating resolution of microbial communities, identifying single members of such communities in their natural surroundings, sometimes down to the genus or species level. The combination of molecular probing techniques with high-resolution chemical analysis has opened our eyes to a better understanding of micro-ecosystems as dynamic metabolic entities. The cooperation of various types of microorganisms in transformation processes is still far from being understood in detail, but in several instances at least a glimpse of their intrinsic logic could be caught. In addition, the cooperation of microbes with higher organisms, such as higher plants or the digestive systems of invertebrates, has developed a new level of understanding, away from the static view of ‘what is there?’ to ‘how do the microbes contribute to the function of the system?’.

We have seen an exciting time of development in this fast evolving scientific field, and part of this development is documented in this issue. I thank all the authors for their dedicated work and for sharing their views on the present and the future of this field with the scientific community.

Bernhard Schink

Guest Editor