10. Microbial Ecology and Applied Microbiology
10.1 Microbial Ecology and Metagenomics
Learning Objectives
- Define primary producer, consumer & saprophyte
- Explain the relevance of the microbes to soil and the marine environments
- Describe a Winogradsky column and its relevance to microbial ecology
- Understand the challenges of characterizing microbial communities and the various culture-independent methods that are part of the microbial ecology toolkit
- Explain why microbial ecology studies, in particular of the marine environment, are so important
- Define microbial dark matter
Microbes are vital to every ecosystem on Earth. Each species in an ecosystem is thought to occupy a separate, unique niche. The ecological niche of a microorganism describes how it responds to the distribution of resources and competing species, as well as the ways in which it alters those same factors in turn. In essence, the niche is a complex description of the ways in which a microbial species uses its environment.
The precise ecological niche of a microbe is primarily determined by the specific metabolic properties of that organism. For example, microbial organisms that can obtain energy from the oxidation of inorganic compounds (such as FeS, H2S, NH3 ) will likely occupy a different niche from the phototrophs (such as cyanobacteria). Within the euphotic zone or water column, the distribution of phototrophic bacterial and algal species are stratified according to the absorption spectra of their photosynthetic pigments and their tolerance of oxygen and H2S. Therefore, even microbes with similar metabolic properties may inhabit unique niches.
Organization of Ecosystems
Although ecologists tend to regard ecosystems as basic structural units, it can be difficult (if not impossible) to formally define the boundaries of a given ecosystem. As such, ecosystems are better thought of as conceptual rather than actual geographical locations. Rarely are ecosystems isolated from one another; rather, they should be considered parts of a larger functioning whole that together comprise the biosphere. In addition, given their microscopic sizes, within an ecosystem, conditions for the microorganisms can vary dramatically over the space of a few microns, as well as over time.
Despite the fact that clear boundaries between ecosystems may be difficult to identify, the myriad interactions that take place within an ecological community can often be observed and defined. These interactions may be best described by detailing trophic connections (what eats what) among biota in an ecosystem, thereby linking the ecosystem into a unified system of exchange.
All life forms in an ecosystem can be broadly grouped into one of two trophic levels:
- The autotrophs fix CO2, converting it into biomass. These are the producers and form the base of food chains. In terrestrial environments, the producers are the plants. In the marine environment however, the microbes are almost entirely responsible fo