Prepping for fieldwork
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To save time: Label collection bags with sampleID and date prior to going into the field
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Information required on labels includes: Site, Plot, Subplot, Timepoint, and any other specific descriptor of the area.
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Example:Site=CNF,Plot= 1, Subplot= N, Timepoint= T1 so bag was labeled as (CNF1NT1) 1.31.2022
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Bring extra collection bags (clean and sealed within a large zip lock bag), in case they are needed
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Gloves (carry enough clean gloves in a ziplock bag for the day)
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Ethanol spray and ethanol wipes
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Ethanol spray: easy to carry and useful if you run out of wipes
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Ethanol wipes can be made in the lab the day prior to going out. Cut paper towels in half, place them in large zip lock bags, add ethanol until the towels are saturated with ethanol and you see some ethanol pooling on the bottom of the bag and seal the bag. Wipes are ready!
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Soil corer or sampling tools
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Always carry an extra one or two, in case one of them breaks in the middle of the field)
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Flagging tape and stake flags
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Field tape
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Field bags to carry equipment and samples to and from the sites
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Sharpies and pens (if you have bright flagging tape, it is a good idea to flag your pens, you can easily locate them if dropped)
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Field notebook
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GPS and extra batteries
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Square plot (for measuring)
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A 1m2 square plot made w PVC pipe
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Yard stick or ruler (if measuring organic matter, litter etc)
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Shovel: required for emergencies such as getting stuck in mud
Safety tools
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Shovel (in case you get stuck)
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Snake guards
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Bear spray
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Gps, batteries & phone chargers
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Georeference maps (work offline and allow you to mark and make notes directly on them)
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Sunscreen, water, electrolytes, and food. sunglasses, sunhat, long sleeves, fieldboots, field pants, etc.
Fieldwork: experimental design and sampling
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Create maps using GIS (roads, vegetation, etc) and georeference them.
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Select potential sampling sites based on requirements for your study (i.e. dominated by Ponderosa pine, burned at high severity, south aspect, etc).
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Scout the site to ensure that they meet your requirements
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Set up plots: Single sampling event vs long-term monitoring plots (temporal sampling, multiple sampling events over time). In the latter case, ensure that you have material that will sustain weathering. See first book below
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Transect lines
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Circular plots
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Square plots
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Notes: take lots of notes of your plot/sites
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Don't forget to take a GPS reading from each plot or subplot
Recommended readings
Data Collection
Additional information on methods can be found in published articles (here)
In the field
Prevent contamination of samples:
1. Always wear gloves when collecting samples and ethanol/bleach
sterilize both the gloves and soil sampling tool after each
collection (per plot or subplot), etc.
2. Ensure that soil samples are collected in the same manner,
from all plots (treated and untreated).
3. Once collected, ensure soil samples are placed in a cooler
with ice packs or dry ice to transport to the lab.
In the Lab
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Always keep samples cool/frozen: If you are not processing the soil samples on the same day, make sure to put them in the fridge. If you have a walk-in fridge, put the cooler in the fridge but make sure the lid is not sealed on the cooler, so that the air can circulate into the cooler to keep your samples fresh.
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Process samples as soon as possible (sieve, separate, extract DNA, and store)
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Sieve soil samples 2mm sieve before storing
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Weight out soil samples to be stored for long-term storage (~30-50g, depending on your needs) in a sterile manner and store in -80C freezer (make sure bags are properly labeled.
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Weight samples for DNA extraction if extraction will be processed immediately (1-4 days)
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Additional analysis
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Mesure soil moisture (10g in weight boat)
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KCL analysis (Method here), weigh out soils into falcon tube, and process
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Air dry any other soil that will be used for geochem analysis in a sterile hood.
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If not doing any other analysis, soil samples can be sieved, and DNA samples separated (0.25g) into Qiagen tube or extraction kit tube, and the rest of the sieved soil can be stored in the freezer.
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When processing the samples make sure samples remain in a cooler with ice, and clean gloves and utensils with ethanol or bleach between samples to prevent cross-contamination.
Methods & Protocols
Note: protocols listed here have been used in published articles and have been used in the Glassman Lab (Ph.D. Lab). If you have additional questions, please feel free to email me.
Statistical
Analysis
One of the most important aspects of your project
Please see my GitHub account for R script of all statistical analysis used in my publications.
GitHub account here
Contact Information
Microbiology and Plant Pathology
University of California-Riverside
3401 Watkins Driver
Riverside CA 92521
Email: mpuli011@ucr.edu