Dr. Tiedje has 3,000 sq. ft. of laboratory space in a modern building (built in 1986) which is equipped with 3 laminar flow hoods, 6 fume hoods, 3 walk-in incubators, a 4 degree laboratory, a walk-in -20 degree C freezer, and 4 -80 degree C freezers. One of the laboratories is approved BSL 2. Adjacent space includes an autoclave room, instrument lab, isotope lab, and a microscope room. The laboratory is equipped with a full range of microbiological and molecular biological equipment including fluorescent microscopy with image processing, shakers, anaerobic glove box, Hungate-type anaerobic gassing apparatus, microfuges, centrifuges, 3 ultra-centrifuges, electrophoresis systems, spectophotometers, 3 Perkin-Elmer thermocyclers, Molecular Devices SpectraMax fluorimeter/spectrophotometer, and UV transilluminator with digital camera. The laboratory also has several GC's, HPLC's, and a capillary electrophoresis unit with laser-induced fluorescence detector.
The Center for Microbial Ecology (CME) has a collection of over 100 soil samples from unique sites around the world (under USDA permit) stored at 4C and some also at -80C. These include samples from very young Hawai'i soils (200 yrs since volcanic origin) to the oldest soils on Earth from central Australia (350 million years, before Pangea broke up). Soils devoid of human influence include those from pre-human contact (I,000 and 4,000 yrs ago) but isolated by burial under lava layers, and northeast Siberia permafrost soils buried and continuously frozen for 30,000 to 3 million years, depending geologic layer. Through a collaboration with a mastodont expert, we also have buried mastodont gut contents from animals dated 12,000 years ago. In addition to this we have soil samples from pristine (usually national preserves) from all continents and, except for Antarctica, taken along transects and in replicated vegetation areas. We also have soils taken from under different US agriculture practice, and will be getting in December soils from an area in Vietnam with high human and animal (pigs and aquaculture) use of antibiotics These soils will be the resource for attempts to capture the ABR gene cassettes. We will use a strategy of trying the most extreme soils first to see if there are different patterns in recovery, and based on this information, optimizing the strategy for obtaining the most interesting information.
CME genomics and informatics resources
CME has an arrayer and two Axion Instruments GenePix 4000A and B laser scanners. We have developed a custom laboratory information management system (MicrobeArrayDB) to track any information about 96 or 384 plates, which is especially useful for the development and quality control. This system uses the Oracle 8i RDBMS for data storage and Sun's Java Enterprise server for the user interfaces. The CME Computer Laboratory has 700 sq. ft. of office space with 100Mbit Ethernet connection to the University's fiber-optic backbone, 5 high-end PC workstations, 3 Macintosh G-4 workstations, two Sun UltraSparc workstations, a file server and printers. CME also manages the ribosomal database (RDP) which is housed in a separate 300 sq. ft. office with 6 Sun Ultra 10 workstations and a dual processor Sun Ultra 60 server. The RDP's current projects have licenses for the ObjectStore Enterprise ODBMS and Oracle RDBMS to support custom database development. The RDP staff also serves as a bioinformatics and database development resource for other projects as needed. For example, they are helping with an antibiotic resistance and virulence factor sequence database built on using Hidden Markov Models.
The MSU Genomic Technology and Support Facility is in the adjacent building and has 3 high throughput sequencers and associated robotics, both a 96 and 384 plate real time (quantitative) PCR unit, Affymetrix scanner, cDNA and oligo spotting robots, scanners, software and staff. Also next door are the Macromolecular Synthesis Facility (for primer synthesis, peptide sequencing), the NIH-supported Regional Mass Spectrometry Laboratory, and the MSU Center for Electron Optics with a range of electron microscopes and confocal laser scanning microscopes with 3-D image reconstruction.