Microbial population and community ecology
Microbial ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life Eukaryota, Archaea, and Bacteria as well as viruses. Microbial ecology is the study of the interactions of microorganisms with their environment, each other, and plant and animal species. It includes the study of symbioses, biogeochemical cycles and the interaction of microbes with anthropogenic effects such as pollution and climate change. Microbial population biology also encompasses the evolution and ecology of community interactions (community ecology) between microorganisms, including microbial coevolution and predator-prey interactions.
Microbial population biology can include aspects of molecular evolution or phylogenetics. The concept of community ecology arose in plant and animal ecology. Communities are defined as multi-species assemblages, in which organisms live together in a contiguous environment and interact with each other. This discipline seeks to analyze how biological assemblages are structured, what are their functional interactions and how community structure changes in space and time. Recent developments in community ecology have begun to recognize that the biological assemblage cannot be defined without reference to its abiotic environment. An appreciation for the tight interrelationship between microbes and their microscale physical and chemical environments is particularly important for delineation of microbial communities. A weakness of most current applications of community metagenomics or metaproteomics to complex communities is that gene sequences and proteins are disassociated from the intact organism that possessed them. A measure of functional redundancy could be derived from cataloging genes or proteins with annotated functions and correlated to ecosystem resiliency to experimentally imposed perturbations (such as Hg stress).
However, a mechanistic understanding will require analysis of the co-occurrence of those functional genes or gene products with stress resistance determinants in discrete organisms, either by bioinformatic analysis of single genomes or physiological analyses of cultivated organisms. For complex microbial communities, we may have to wait for the advent of technologies, whereby several hundred bacterial cells could be individually plucked from a habitat, and their genomes amplified (if necessary) and sequenced in a high-throughput and inexpensive manner. In this way, the community metagenome would comprise a list of functional genes in the complete context of the other genetic determinants within the organism.
Microbiology: Current Research