The Environmental Microbiology Laboratory is designed as a versatile platform supporting a broad range of tasks related to the study of microorganisms in the environment. The major tools of this facility are designed to be implemented as modules applicable to almost any sample type, with a current emphasis on deep aquifers and the continental subsurface, freshwater lake sediment, and desert springs. A major capability of the laboratory is the culture-free determination of microbial community structure in water, sediment, rock and air samples. A variety of molecular life-detection protocols are available, either directly through the laboratory or partially supported by allied facilities, such as the Nevada Genomics Center. Our major molecular tools (Terminal Restriction Fragment Length Polymorphism (T-TFLP), and clone library construction) utilize the small subunit of the ribosomal RNA gene (SSU rRNA/ 16S rRNA). In collaboration with Lawrence Berkeley National Laboratory, our facility is working to apply high-density 16S rRNA microarrays (containing 500,000 probes capable of detecting 9,381 prokaryotic OTUs) for the exploration of microbial community structure in much greater detail than has previously been possible.
The laboratory also employs a variety of cultivation-and functional gene-based techniques for the enrichment and tracking of microorganisms which influence the fate and transport of environmental contaminants including polyacrylamide, nitrate, and possibly radionuclides and endocrine disruptors.
Available equipment includes a full spectrum of tools enabling the collection, processing, and storage of quality samples for the detection and cultivation of environmental microorganisms. These include: peristaltic pumps and pressure filtration assemblies for surface- and well-water sampling, as well as sediment core processing and porewater squeezing equipment. The laboratory maintains an RBD3000 automated flow cytometer (Trace Analytical) for the accurate determination of planktonic cell density, live vs dead analysis, and FISH flow cytometry. For the cultivation of aerobic and anaerobic microorganisms, a Coy type B anaerobic chamber, Tuttnauer autoclave, Harvey sterilizer, Hungate equipment, BBL Gas Pac system, several lab-line orbital shakers, and high- and low-temperature incubators are available. Molecular facilities include a Labconco Purifier Class II laminar flow hood, Thermo PXE thermocycler, a variety of Owl submarine electrophoresis chambers with EC-105 power supplies, a Fotodyne FOTO/Analyst Express gel documentation system, UV 2400 Stratalinker, Savant Speed Fuge, a selection of Isotemp waterbaths and Lab-line heating blocks, a BioSpec mini-beater 8, and several complete sets of Pipetman micropipettors. The lab also has an Eppendorf 5810R refrigerated centrifuge (with a selection of rotors), an Eppendorf 5415D microcentrifuge, Thermo chest-type ultradeep freezer, -20 and 4oC refrigeration, a Labconco glassware washer, Accumet pH meter, balances, and MilliQ water.