Great Salt Lake nematodes

In this Dryad dataset, you'll find an excel file with 6 datasheets, each containing raw data from our manuscript on halophilic nematodes living in the Great Salt Lake, UT, published in Proceedings B in 2024. These datasheets include:

• Envi Analysis: Each row here is a soil sample from one of our 6 sampling sites. Most of the variables are self explanatory (data sampled, time, etc). Temp, ORP, and Salinity in situ are measurements from the conductivity meter that were taken at the time of sampling in the lake. Volume (ml) is the volume of sample from which we extracted nematodes. N worms is the number of worms we found in the indicated volume. Abundance is the number of nematodes per 100g of dry soil (calculated from N, wet weight, and dry weight). The salinity, ORP in columns R and S were extrapolated from the sample itself (see details in methods). The units from mass spec data are in mg per kg are ppm (1kg = 1 million mg). For Na for instance, the result would be 17.8 g of Na per kg of sediment (or 1.78%). Pb1, Pb2, and Pb3 were 3 independent measurements of lead via ICP-MS. Likewise, Cl and Cl_second (and SO4 and SO4_second) are independent mass spec measurements. Any NAs (here and across all these sheets) mean the data are not available. For instance, we only collected in-situ measurements of temperature, salinity, and ORP for each site during each collection date (not every sample); and we did not perform ICP-MS on samples collected after 2021; thus, the relevant cells are indicated as "NA".

• Survival Assay: Each row here is a survival assay trial. We tested nematodes (C. elegans or P. pacificus, Farmington Bay worms, or Gilbert Bay worms) under different conditions and noted their survival.

• GSL Worm Survival: Each row here is a plate of GSL worms in GSL water, each counted (N moving and N present) daily for 50 days.

• GSL Sanger Sequences: These GSL nematode sequences are from Sanger Sequencing at the University of Utah Core Facilities. Each row here is a single nematode, its sequence data, and the BLAST results (NCBI).

• Owens Lake Envi: Each row here is a soil sample from one of our 6 sampling sites from Owens Lake. Most of the variables are self explanatory (data sampled, time, etc). Temp, ORP, and Salinity in situ are measurements from the conductivity meter that were taken at the time of sampling in the lake. Volume (ml) is the volume of sample from which we extracted nematodes. N worms is the number of worms we found in the indicated volume. Abundance is the number of nematodes per 100g of dry soil (calculated from N, wet weight, and dry weight). The salinity, ORP in columns R and S were extrapolated from the sample itself (see details in methods).

• Owens Lake Sanger: These nematode sequences are from Sanger Sequencing at the University of Utah Core Facilities. Each row here is a single nematode, its sequence data, and the BLAST results (NCBI).

You'll also find two R Markdown files with extensive annotations enabling anyone who wants to recreate all the analyses from the manuscript.

• Rmd_for_Dryad.Rmd: This is my R script that I used to recreate the analyses in this paper.

• 16s_analysis_for_Dryad.Rmd: This is my R script that I used to to the 16s analysis. The 16s data analysis script requires you to download additional sequence data from SRA (you'll find that info in the data availablity section in the manuscript).