Lab Protocols and Safety

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


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 Plannerfill 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