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In 1995 the Center for Environmental Biotechnology (CEB) was set up as a multidivisonal center under the direction of Dr. Jennie Hunter-Cevera. In 1998, the Ecology Department was created within the Earth Sciences Division to provide personnel resource management for scientists and engineers within ESD whose expertise was in the general area of ecology, including population ecology, community ecology, systems ecology and environmental engineering. This was a new department, and the personnel were originally scattered among the other ESD departments, though most were originally organized under the CEB. In 1999, the name of the Ecology Department was changed to the Microbial Ecology and Environmental Engineering Department, because it was felt that this more closely reflected the expertise of the small group of scientists and engineers that were within that department. Hydroecological engineering advanced decision support (HEADS) was organized as a new group within the Department in the spring of 2002. This group focused on water and wastewater research, with an initial special emphasis on California water resource issues. The department name was changed back to the Ecology Department in 2004. Today, personnel in the Ecology Department still serve as the primary support staff for the CEB, which houses all of their offices and laboratory facilities.
The expertise that exists within the Ecology Department and the unique facilities provided by the CEB allow the department to provide biogeochemistry, microbial ecology, and environmental engineering support within ESD and Berkeley Lab. Currently, personnel are primarily supported by the three Programs under the Environmental & Biological Systems Sciences Program Area, which are the Environmental Remediation & Water Resources; Ecosystems Biology, and Bioenergy. Additionally, Ecology personnel are supported by various Programs within Energy Resources Program Area and the Climate and Carbon Sciences Program Area.
The current Ecology Department Head is Gary Andersen.