Hyperspectral reflectance values and biophysicochemical properties of biocrusts and soils in the Fryxell Basin, McMurdo Dry Valleys, Antarctica (2019)


This data package includes ecological parameters of biocrust and soil from samples collected in-situ within the Lake Fryxell Basin of the McMurdo Dry Valleys, Antarctica during December of 2019. Parameters include biological (ash-free dry mass, pigment concentration, and counts of soil invertebrates), physical (water content, electrical conductivity, and pH), and chemical properties (inorganic nitrogen, inorganic phosphorous, total nitrogen, and total organic carbon) of the surface soil, biocrust, and underlying soil. This data package also contains reflectance measurements of biocrust, soil, and granite samples acquired in a laboratory using a hyperspectral spectrometer. Included are hyperspectral reflectance measurements of a laboratory study using a variety of mixtures of soil and biocrust (0 – 100% biocrust), as well as reflectance measurements of individual grab samples collected from each of the field plots. These data aid our understanding of the ecological structure and functioning of biocrust microhabitats as well as the location of these communities throughout the Lake Fryxell Basin. This work also aims to assist in understanding the carbon budget of the basin and highlight the importance of these snowpack-fed biocrust communities, which are understudied but likely an important piece of the overall carbon budget in this region.

LTER Core Areas: 

Dataset ID: 


Associated Personnel: 


Short name: 


Data sources: 

field hyperspectra
lab hyperspectra


In-situ Environmental Sampling & Analyses

At 30 locations throughout the Fryxell basin, we documented surface type present (biocrust, soil, or oxidized granite) and collected a surface layer sample of soil or biocrust (if present) and rock from all sites for subsequent hyperspectral analysis in the laboratory. At 12 of these sites, we established 5 m x 5 m intensive sampling plots. We collected 5 surface layer soil or biocrust samples (128 cm2) from each corner and center of the plots for subsequent pigment analysis and organic matter content via ash-free dry mass (AFDM). We also collected underlying soil down to 10 cm below the surface for gravimetric water content (GWC), electrical conductivity (EC), pH, inorganic nitrogen (N) concentration in the form of ammonium (NH4+) and nitrate (NO3-), inorganic phosphorus (P) concentration in the form of phosphate (PO43-), total organic carbon (TOC), total nitrogen (TN), and invertebrate abundance (nematodes, tardigrades, and rotifers).

Ash-free dry mass (AFDM): The surface layer soil and biocrust samples were measured for AFDM by weighing a known area of sample, combusting at 550 °C for 24 hr using a muffle furnace, gently stirring samples halfway through combustion, and reweighing after cooling in a desiccator. The rehydration of clays was assumed negligible, so we did not rewet samples.

Pigments: We estimated pigment concentration on the surface ~1 cm layer soil and biocrust samples using a trichromatic spectrophotometric method for chlorophyll-a, carotenoids, and scytonemin at 663, 490, and 384 nm, respectively (Garcia‐Pichel and Castenholz, 1991). Throughout the process, care was taken to avoid exposing the samples to light. The samples were dried at 105 °C for 24 hr, sieved through a 4 mm sieve, and extracted for 24 hr at ambient temperature in 90% unbuffered acetone using a 3.75:10 soil to solvent ratio, based on protocols from Couradeau et al. (2016) and the McMurdo Dry Valleys Long Term Ecological Research Program (MCM LTER) standard methods. After centrifugation, the extracts were analyzed on a spectrophotometer using 10 mL cuvettes. The absorbances contributed by each pigment were calculated using the trichromatic equations outlined in Garcia‐Pichel and Castenholz (1991), and the pigment concentrations were calculated using the Beer-Lambert Law with the extinction coefficients of 89.7 L g-1 cm-1 for chlorophyll-a (Couradeau et al., 2016), 112.6 L g-1 cm-1 for scytonemin (Brenowitz and Castenholz, 1997), and 262 L g-1 cm-1 for carotenoids (Thrane et al., 2015).

Invertebrate counts: The number of soil organisms (nematodes, rotifers and tardigrades), divided by species, sex and maturity was determined at each of the 12 plots. Invertebrate abundance was enumerated using inverted light microscopy on soil solutions using a modified sugar-centrifugation extraction procedure described by Freckman and Virginia (1993).

Gravimetric water content: Water content was determined as the mass of water per mass of dry soil. This was conducted by weighing field moist soil, drying in an oven at 105 °C for 24 hr, and reweighing the soil after.

Electrical conductivity: Using the underlying 1-10 cm soil, we measured electrical conductivity using a 1:5 soil to DI H2O slurry.

pH: Using the underlying 1-10 cm soil, we measured pH using a 1:2 soil to DI H2O slurry.

Inorganic N and P: We extracted inorganic N (NH4+ and NO3-) in 2 M potassium chloride and inorganic P (PO43-) in 0.5 M sodium bicarbonate; inorganic N and P were measured on extracts using a Lachat flow injection analyzer. 

Total N and organic C: We measured TOC and TN using an Elementar Vario Cube TOC/TN analyzer after fumigating samples with concentrated hydrochloric acid to remove the influence of carbonates on TOC values.

Remote Sensing Analyses

Hyperspectral reflectance of field samples: Spectra were acquired of samples from each of the 30 plots using an Analytical Spectral Devices (ASD) FieldSpec4 high-resolution hyperspectral reflectance spectrometer set up for use in a stable lab environment. Data were collected between 400 and 2500 nm at a 1 nm sampling interval. A halogen lamp was used to illuminate the samples at 30° off-nadir, while reflectance was measured at nadir using the ASD’s bare fiber optic cable roughly 3 cm above the sample surface. To minimize instrument noise, particularly at the longest and shortest wavelengths where the output of the halogen bulb is lowest, we averaged 50 individual spectra for each sample.

Hyperspectral reflectance of laboratory mixtures: Sample mixtures of varying percent biocrust and soil (not containing biocrust) were created by mixing a known amount of soil with a known amount of biocrust. The soil was collected from the Fryxell basin, Antarctica, and the biocrust was collected from Arizona, USA, and each were separately ground into a homogenous fine particle size. Hyperspectral reflectance data were gathered for dry samples with the same methods above. Samples were also moistened with DI water for damp readings as well. The targeted water content for the damp samples was approximately 0.25 GWC (g H2O/g dry soil and biocrust material). These data were used to determine the nature of the observed spectral mixing relationship between soil and biocrust, validating our ability to confidently translate spectral unmixing to orbital data.

Additional information: 

Funding for this work was provided by the National Science Foundation (NSF) grants #OPP-1637708 and #OPP-2224760 to the MCM LTER, NSF #OPP-1745053 to Mark Salvatore, and a Virginia Space Grant Consortium award to Sarah Power.


Subscribe to RSS - LTER