daime is a scientific image analysis and visualization program for microbiology and microbial ecology. It contains numerous tools for analyzing 2D and 3D microscopy datasets of microorganisms that were labelled by fluorescence in situ hybridization or other fluorescence staining techniques. daime analyzes single planktonic cells as well as cell aggregates in many kinds of samples, including biofilms.
daime has already been used in hundreds of studies in microbial ecology, medical microbiology, microbiome research, and environmental engineering. Its 3D visualization features were used to render the cover illustrations of "Brock - Biology of Microorganisms" (12th edition) and of PNAS vol. 103(7).
The main research theme in my laboratory is the isolation and characterization of new anoxygenic phototrophic bacteria from extreme environments, in particular thermal, permanently cold, or extremely alkaline and hypersaline habitats. The long term objective is to better understand the physiochemical limits to and evolution of photosynthesis. We are interested in the physiology, phylogeny, pigments and other basic biological properties of extremophilic phototrophic bacteria that combine to allow these organisms to grow optimally under one or more physical or chemical extreme. Our work also contributes to an understanding of the evolution of phototrophic microorganisms since extreme environments are models of early earth conditions. Some of our work involves collaborations with biophysicists, biochemists, and geneticists interested in particular aspects of the biology of extremophilic phototrophs.
I - Soil microbiology. The microbiology of the biogeochemical cycles of carbon and nitrogen. Importance of microorganisms in the decomposition of organic matter in the soil. Rhizosphere and rhizoplane microbiology (e.g. mycorrhizae, endophytic fungi). The actinomycetes.
IV - Microbiology of extreme environments. Halophilic and xerophilic microorganisms. Psychrophilic and thermophilic microorganisms. Habitats and physiological and structural adaptations.
The microbiology of extreme environments and the foundations of astrobiology. Analysis of the soils of the Moon and Mars. Panspermia Theory? Aerospace microbiology: microbiological experiments in space.
Brock biology of microorganisms. 12th edition, 2009. San Francisco: Pearson/Benjamin Cummings, cop. 2009. Rev. ed. of: Brock biology of microorganisms / Michael T. Madigan. 11th ed. 2006. ISBN 978-0-321-53615-0
582128177f