Biogeochemistry Lab Resource Page
How to Use This Site
- Find an SOP: Use the sidebar navigation or the search bar (top right).
- Download a PDF: Each SOP page has a “View as PDF” link at the top.
- Suggest a change: Click the “Edit this page” link on any SOP, or open an issue.
- Create a new SOP: Copy
lab_sops/SOP-TEMPLATE.qmd, fill it in, and submit a Pull Request.
SOP Numbering Scheme
SOPs are numbered by topic. Field SOPs use an F prefix and Lab SOPs use an L prefix, but both share the same numeric ranges:
| Category | Field SOPs | Lab SOPs |
|---|---|---|
| Safety and administration | F001–F099 | L001–L099 |
| Equipment and instrumentation | F100–F299 | L100–L299 |
| Water and aquatic methods | F300–F399 | L300–L399 |
| Soil methods | F400–F499 | L400–L499 |
| Air and atmospheric methods | F500–F599 | L500–L599 |
| Biology, ecology, and molecular biology | F600–F799 | L600–L799 |
| Data management and analysis | F800–F899 | L800–L899 |
SOPs (pdf)
SOP Subsets by Topic
Safety and Administration (001–099)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| F001 | Field Safety | 1.1 | |
| F002 | Field Equipment Checklist | 0.1 | |
| F003 | Field Notebook Protocols | 0.1 | |
| F004 | Site Access and Permits | 0.1 | |
| F005 | Random Sampling Design | 1.0 | FW |
| F006 | GPS and Site Navigation | 0.1 | |
| F007 | Field Decontamination Protocols | 0.1 | |
| F008 | Sample Labeling, Chain of Custody, and Transport | 0.1 | |
| L001 | Lab Orientation and Training Checklist | 0.1 | TBD |
| L002 | Laboratory Safety | 1.04 | |
| L003 | Hazardous Materials Handling | 1.04 | |
| L004 | Chemical Spill Response | 0.1 | |
| L005 | Chemical Inventory Management | 0.1 | |
| L006 | Waste Disposal and Hazardous Waste Pickup | 0.1 | |
| L007 | Equipment and Instrument Inventory | 1.0 | |
| L010 | Lab Notebook Recording | 0.1 | |
| L015 | Foreign Soil Handling (Import Permits) | 0.3 | |
| L020 | Reagent and Standard Preparation | 0.1 |
Equipment and Instrumentation (100–299)
Field Equipment (F100–F199)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| F100 | EA Program Vehicle Use | 0.1 | |
| F101 | Electrical Power in the Field | 0.2 | |
| F102 | Waders/Wetsuit | – | TBD |
| F103 | Canoe / Kayak / Small Watercraft | – | TBD |
| F104 | Field Laptop and Tablet Use | – | TBD |
Field Instrumentation (F200–F299)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| F200 | Eureka Manta2 Multiprobe | 0.7 | |
| F201 | Pygmy and Type A Velocity Meters | 0.1 | |
| F202 | SonTek Acoustic Velocity Meters | 0.1 | |
| F203 | HOBO Water Level Pressure Transducers | 0.1 | |
| F204 | HOBO Weather Station Deployment | 0.1 | |
| F205 | Handheld Turbidity Meter | 0.1 | |
| F207 | Secchi Disk and Secchi Disk Tube | 0.1 | |
| F208 | Portable Spectrophotometer / Colorimeter (Field) | 0.1 | |
| F209 | Dissolved Oxygen Meter (Field) | 0.1 |
Lab Equipment (L100–L199)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| L100 | Milli-Q Water System | 0.2 | Broken |
| L101 | Glassware Cleaning and Preparation | 0.1 | |
| L102 | Using Balances | 0.2 | |
| L103 | Micropipettes | 0.3 | |
| L104 | Using a Vortex Mixer | 0.1 | |
| L105 | Drying Ovens | 0.1 | |
| L106 | Refrigerators and Freezers | 0.1 | |
| L107 | Hot Plates and Dry Bath | 0.12 | |
| L108 | Clinical Centrifuge | 0.1 | |
| L109 | Sorvall ST8R Centrifuge | 0.1 | |
| L110 | Ozone Generator Operation | 0.1 | |
| L111 | Muffle Furnace | 0.1 | |
| L112 | Autoclave / Sterilization | 0.1 | |
| L113 | Laminar Flow Cabinet | 0.1 | |
| L114 | Vacuum Filtration Apparatus | 0.1 | |
| L115 | Sonicator | 0.1 | |
| L116 | Sample Grinding and Homogenization (Ball Mill, Mortar and Pestle) | 0.1 |
Lab Instrumentation (L200–L299)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| L200 | Analytical Balance Calibration | 1.0 | |
| L201 | Spectrophotometer Operation | – | |
| L202 | Accumet pH Meter | 0.4 | |
| L203 | Trilogy Laboratory Fluorometer | 0.4 | |
| L204 | Shimadzu TOC/TON Analyzer | 1.0 | |
| L205 | XRF (X-Ray Fluorescence) | 0.1 | |
| L206 | ICP-MS | 0.1 | |
| L207 | LA-ICP-MS (Laser Ablation) | 0.1 | |
| L208 | ThermoFisher Delta V IRMS | 0.2 | |
| L209 | Radiometric Dating | NA | TBD |
| L210 | Ion Chromatograph Operation | NA | TBD |
| L211 | Echo Labs Revolve Microscope | 0.1 | |
| L212 | NanoDrop Spectrophotometer | 0.1 | |
| L213 | Qubit Fluorometer | 0.1 | |
| L214 | QX200 Droplet Digital PCR System – Instrument Familiarization | 0.1 | |
| L215 | Hach DR3900 Benchtop Spectrophotometer | – | TBD |
| L216 | Dissecting and Compound Microscope | 0.1 |
Water and Aquatic Methods (300–399)
Field – Water / Aquatic Systems (F300–F399)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| F300 | Surface Water Sampling | 0.9 | |
| F301 | Stream Discharge Measurement | 0.1 | |
| F302 | Stormwater Sampling | 0.1 | |
| F303 | Groundwater Sampling | 0.1 | |
| F304 | Stream Physical Habitat Analysis | 0.1 | |
| F305 | Sediment Sampling (Streams and Lakes) | 0.1 | |
| F306 | Wetland Hydrology Monitoring | 0.1 | |
| F306 | Wetland Delineation | 0.1 | |
| F307 | Lake and Reservoir Profiling* | 0.1 | |
| F308 | eDNA Water Sample Collection | 0.1 | |
| F309 | Periphyton / Algae Sampling | – | TBD |
Lab – Water Analysis (L300–L399)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| L300 | pH and Conductivity (Bench) | 1.0 | |
| L301 | Alkalinity Titration | 0.1 | |
| L302 | Turbidity Measurement | – | TBD |
| L303 | Hach Colorimetric Analysis | 1.0 | |
| L304 | Nutrient Analysis (Water Samples) | – | TBD |
| L305 | Bacteria Screening (Colilert Quanti-Tray) | 4.3 | |
| L306 | BOD5 (Biochemical Oxygen Demand) | 0.3 | |
| L307 | ELISA: BPA, BPB, Pesticides | 0.3 | |
| L308 | Microplastics in Water | 0.2 | |
| L309 | Pesticide Analysis – Gas Chromatography | – | |
| L310 | Chlorophyll Extraction and Analysis | 0.1 | |
| L311 | Dissolved (NPOC) Organic Carbon (Water) | 0.1 | |
| L312 | Total Suspended Solids / Total Dissolved Solids | 0.1 | |
| L313 | Metals in Water (ICP-MS Prep and Acidification) | 0.1 | |
| L314 | Anion Analysis (Ion Chromatography) | – | NA |
| L315 | eDNA Lab Processing (Filtration, Extraction, Inhibition Testing) | 0.1 |
Soil Methods (400–499)
Field – Soil (F400–F499)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| F400 | Soil Sampling and Processing | 1.0 | |
| F401 | Texture by Feel | 0.1 | DLF |
| F402 | Soil Bulk Density (Core Method) | 0.1 | AC |
| F403 | Soil Infiltration Rate | 0.1 | |
| F404 | Soil Temperature Profiles | 0.1 | |
| F405 | Soil Color (Munsell) | 0.1 | |
| F406 | Soil Respiration Chambers (Field) | 0.1 | |
| F407 | Soil Profile Description | 0.1 |
Lab – Soil and Carbon Analysis (L400–L499)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| L400 | Soil Moisture – Gravimetric Method | 0.2 | |
| L401 | Soil Texture (Hydrometer Method) | 0.1 | DLF |
| L402 | Soil pH and Salinity | 0.1 | |
| L403 | Nitrate and Ammonium – KCl Extraction | 0.4 | MLH |
| L404 | Nitrate Quick Test | 0.1 | FW |
| L405 | Extractable Phosphorus | 0.1 | |
| L406 | Loss on Ignition (SOM) | 1.0 | |
| L407 | Total Carbon – Soil | 1.0 | DLF |
| L408 | Solvita CO2 Burst | 1.1 | |
| L409 | Microbial Biomass Carbon (CFE) | 1.0 | AC |
| L410 | Hot-Plate Acid Digestion of Soils for Trace Metal Analysis | 0.2 | |
| L411 | Soil Lead Analysis (MARS Microwave) | 0.2 | |
| L412 | Nitrification Potential | 0.1 | |
| L413 | Solvita Compost Maturity | 0.1 | |
| L414 | Flash EA Soil dN15 and dC13 Combustion | 0.1 | |
| L415 | Carbonate Isotope Analysis by GasBench II-IRMS | 0.1 | |
| L416 | Cation Exchange Capacity (CEC) | 0.1 | |
| L417 | Soil Aggregate Stability (Wet Sieving) | 0.1 | |
| L418 | Water-Extractable Dissolved Organic Carbon (Soil) | 0.1 | |
| L419 | Soil Color (Munsell – Lab Confirmation) | 0.1 | |
| L420 | Soil Labile Amino-Nitrogen – Solvita SLAN Test | 0.1 |
Air and Atmospheric Methods (500–599)
Field – Air / Atmospheric (F500–F599)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| F501 | Air Temperature Monitoring (Sensors) | 0.1 | |
| F502 | Air Quality Monitoring (Portable Sensors) | 0.1 | |
| F503 | Particulate Matter Sampling* | 0.1 | |
| F504 | Picarro GHG Analyzer (Field Deployment) | 1.0 | AC |
| F505 | Passive Air Samplers (Diffusion Tubes) | 0.1 | |
| F506 | Noise Level Monitoring | 0.1 | |
| F510 | Weather Monitoring and Field Meteorology | 0.1 |
Lab – Air / Atmospheric (L500–L599)
No lab air SOPs exist yet. Range is reserved.
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| L500 | Gravimetric PM Filter Analysis | – | TBD |
| L501 | Passive Sampler Extraction and Analysis | – | TBD |
Biology, Ecology, and Molecular Biology (600–799)
Field – Microbes, Plants, and Animals (F600–F699)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| F602 | iNaturalist for Biodiversity Documentation | 0.3 | |
| F603 | Vegetation Transect Surveys | 0.1 | |
| F604 | Tree DBH and Forest Inventory | 0.1 | |
| F605 | Leaf Area Index Measurement | 0.1 | |
| F606 | Canopy Cover (Densiometer & Hemispherical Photography) | 0.1 | |
| F607 | Tree Tagging for Restoration Monitoring | 0.1 | |
| F608 | Plant Tissue Sampling | 0.1 | |
| F610 | Macroinvertebrate Sampling | 0.1 | |
| F611 | Pollinator Observation Surveys | 0.1 | |
| F615 | Bird Point Count Surveys | 0.1 | |
| F620 | Camera Trap (CamPark T20) | 0.1 | |
| F621 | Acoustic Monitoring (Bioacoustics) | – | TBD |
| F622 | Small Mammal Trapping (Sherman Traps) | – | TBD |
| F630 | Drone Operations (DJI Matrice/Mavic) | 0.1 | |
| F631 | 360 Camera | – |
Field – Molecular Biology and DNA (F700–F799)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| F700 | eDNA Field Sampling and Preservation | 0.1 | |
| F701 | Soil Microbial Field Sampling for Molecular Analysis | 0.1 |
Lab – Microbes, Plants, and Animals (L600–L699)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| L600 | TBD | – | |
| L601 | Wet Mount for Microscopy | 0.1 | |
| L602 | Macroinvertebrate Sorting, Subsampling, and Identification | 0.1 | |
| L603 | Plant Tissue Drying, Grinding, and Preparation for Analysis | 0.1 | |
| L604 | Algae / Periphyton Identification and Enumeration | 0.1 | |
| L605 | Soil Enzyme Assays (Fluorometric) | 0.1 |
Lab – Molecular Biology and DNA (L700–L799)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| L700 | DNA Extraction | 0.1 | AC |
| L701 | Primer Selection and Design for Nitrogen Cycle Genes | 0.1 | |
| L702 | ddPCR Applications Guide – Absolute Quantification of Soil Nitrogen-Cycle Functional Genes | 0.1 | |
| L703 | PCR Amplification and Gel Electrophoresis | 0.1 | |
| L704 | Amplicon Library Preparation for Sequencing | 0.1 | |
| L705 | Bioinformatics Pipeline (QIIME2 / DADA2) | 0.1 | |
| L706 | eDNA Metabarcoding Lab Workflow | 0.1 |
Data Management and Analysis (800–899)
| SOP | Title | Current Rev. | Notes |
|---|---|---|---|
| L801 | RStudio Server and GitHub | 1.5 | |
| L802 | Quality Control and Quality Assurance | 1.0 | |
| L803 | Data Entry and Database Management | 0.1 | |
| L804 | GIS | 0.1 | |
| L805 | Drone Image Processing (Photogrammetry) | 0.1 | |
| L806 | Statistical Analysis Templates (R) | 0.1 | |
| L807 | Instrument Data Export and File Management | 0.1 |
Note
This table is maintained manually. Italicized entries marked TBD are planned SOPs that have not yet been written. Entries marked TBD are suggested additions identified during the 2026 renumbering review. The sidebar navigation reflects every .qmd file in the repository automatically.