Microbial ecology explores the diversity, distribution, and abundance of microorganisms, their abiotic and biotic interactions, and the effect that they have on ecosystems. Microorganisms exist as single cells or as clusters of cells and in a number of cases form intimate symbiotic associations with complex multicellular life-forms. Microbial cells typically, though not always, have an independent existence and range in size from the submicron up to the millimeter scale. Viruses which are noncellular range from the submicron to the micron scale. Although microorganisms encompass the vast majority of the genetic and physiological diversity on the planet and define the limits of the biosphere, microbial ecology has not been seen traditionally as a central theme in general ecology. Despite some notable exceptions this is reflected in the research literature and textbooks. Since the first observation of microorganisms by Antonie van Leeuwenhoek and Robert Hooke in the seventeenth century, microbiologists have been hampered by difficulties in identification, isolation, and in situ study. Accordingly, microbial ecology developed in different directions to, and, to some extent, in isolation from, the wider ecological disciplines. Despite these limitations, simple well-defined microbial systems (with short generation times and ease of ecosystem manipulation) have provided extremely powerful approaches for testing the predictions of fundamental ecological theories relating to evolutionary adaptation, competition, and demographic tradeoffs in biological populations and communities. With new measurement technologies, microbial ecology is entering an exciting phase of its development where approaches developed in classical ecology can now be applied directly to complex microbial ecosystems. This is critical because the size and complexity of these systems can only be properly understood and managed if there is a close interplay between theoretical understanding and empirical measurement.

The vital importance of understanding microbial ecosystems becomes evident when it is recognized that microbial communities drive most of the critical ecosystem processes responsible for the recycling of matter and energy and that microorganisms represent a significant resource for agriculture, food processing, industrial production, environmental cleanup, biotechnology, and medicine. Microorganisms in all their forms can literally be described as the 'unseen majority'. There are somewhere around 109 prokaryotic cells in a gram of soil or sediment and approximately 106 cells in every milliliter of sea or lakewater. It is estimated that there are around 1030 prokaryotic cells inhabiting Earth (6-8 orders of magnitude greater than the number of stars estimated to populate the known universe). Microbial eukaryotes are also massively abundant; in the euphotic zones of the world's oceans alone, there are 102-104 protist cells per milliliter. An upper estimate of global, prokaryote biomass suggests that prokaryotes may account for as much fixed carbon in the biosphere as plants.

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