Please feel free to try out our lab’s protocols. The links below will redirect to Google Docs with the relevant protocol.
If you use our methods, please cite our specified publications and any earlier work they build upon. And please don’t create scientific ‘scavenger hunts’ in your Materials and Methods section—describe everything thoroughly so that it can be reproduced!
SOPs 1-9: Sampling and initial sample processing
SOP1: DNA extraction from filter samples (filtered seawater or freshwater)
SOP2: DNA extraction from sediment samples
SOPs 10-19: Molecular techniques
10. QPCR
11. DNA quantification via PicoGreen
12. ARISA
SOPs 20-29: Biogeochemical measurements
20. Dissolved nitrite concentrations
21. Dissolved ammonium concentrations
SOPs 30-39: Biogeochemical rate measurements
30. Ammonia/nitrite oxidation rates
31. Respiration rates using dissolved oxygen
SOPs 40-49: Data analysis, statistics, and bioinformatics
40. 16S sequence processing [OLD]
41. 16S sequence processing
42. Metagenomic analyses
43. R code and analyses
Lab/Field Safety
In addition to doing things properly and precisely in the lab and field, it is most important to do it safely. We encourage a culture of safety in the lab; there is no valid reason to compromise one’s physical and/or mental health and/or safety for a few datapoints. Below please find important lab safety information:
UC Merced Laboratory Safety Plan
Beman Lab Safety Plan Supplement (LSPS)
University of California Field Safety Manual
Field Safety Planner – fill this out every time you go into the field!!
UC Merced Injury and Illness Prevention Program (IIPP)
Annual acknowledgement that you have read all safety documentation
Beman Lab, University of California, Merced 