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» Astrobiology Web 
Microbes and other life forms in extreme environments. (Although the title of this site implies that it is about space, this is an excellent resource about microbial ecology in unusual environmental conditions here on Earth.)
http://www.reston.com/astro/extreme.html
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» Bacteriophage Ecology Group
Possibly the only site dealing with bacteriophage virus ecology. Includes a wealth of photos and drawings of these viruses as well as all you'd ever need to know about them.
http://www.phage.org/
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» Biodegradation Group - GBF AMICO project
About research on development of molecular and biochemical tools to retrieve information from environmental samples, microbial degradation of contaminants in BTEX, bacterial shifts and adaptation in changing conditions, and evolution of catabolic genes fa
http://espanol.geocities.com/gbfonamico/
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» Digital Learning Center for Microbial Ecology
Michigan State University website with extensive resources on microbes and the environments they live in, as well as links to other microbial ecology resources on the web. Includes the Microbe Zoo.
http://commtechlab.msu.edu/sites/dlc-me/
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» IMPACT Project Home Page
Interactions between microbial inoculants and resident populations in the rhizosphere of agronomically important crops in typical soils.
http://www.ucc.ie/impact
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» LTER Microbial Observatories
Describes the Long-Term Ecological Research (LTER) programs concerned with microorganisms at a wide variety of sites around the world.
http://www.lternet.edu/technology/microbial_ecology/
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» Microbial Ecology Group
Research documents, publications, programs, projects, staff. Technische Universitaet Muenchen, Germany.
http://www.microbial-ecology.de/
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» Microbial Ecology Working Group
Main areas are compost and soil microbiology, molecular ecology, microbial communities, anaerobic digestion, fertilizer development. Page includes list of projects and publications. Located at the University of Innsbruck.
http://www.microbial-ecology.at
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» The Center for Microbial Ecology (CME)
The intellectual focus of the Center for Microbial Ecology is to understand factors that influence the competitiveness, diversity and function of microorganisms in their natural and managed habitats.
http://www.cme.msu.edu/
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» The Nüsslein Lab
On-going research on microbial ecology carried out by the Nusslein Lab, University of Massachusetts, USA.
http://www.bio.umass.edu/micro/nusslein/
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