Remote Sensing of
Biological Soil Crusts
Jonathan A. Key
M.S. Environmental Science
University of Colorado Denver
Small patches of vascular plant growth
Morphology and Structure
Cyanobacterial microfilamentsBiological soil crust macrostructure
Arches NPS Arches NPS
Also known as cryptogamic, microbiotic, and microphytic soils.
Consist of photosynthetic cyanobacteria, lichens, green algae, fungi,
nonvascular plants, and various bacteria.
• Occupy a wide range of
• Species composition of
alpine tundra is similar
to that of cool desert
• Constitute up to 75
percent of the living
Selection of Data Sets
Landsat 5 Thematic Mapper
• Multispectral imagery using 7
• Large enough temporal range
to do an analysis spanning
more than ten years
• Decent spatial resolution
• Data acquired was from May
18, 1996 and May 6, 2009
Image Acquisition User Analysis
• NDVI, Tasseled
• Contrast Adjust
• Band layer
• Training sites
• Max likelihood
• Determination of
# of classes
• 2nd set of
Repeat for Later
Biological Soil Crust Index
• Analysis of this technique with ground truth data suggests
that BSCs can be detected as long as they cover
approximately one third of the pixel (10 m for Landsat)
(Chen et al. 2005)
Class Change Analysis
• Pixel-based class change analysis indicates that there
was a 124 percent increase in microbiotic soil coverage
from May 1996 to 2009
Class Change Analysis (Percentage)
Clouds Desert Veg Water Rural Dev Crops
0.079 72.318 3.981 24.878 0.607 21.889 3.2 0.492 0.362
Desert Veg 8.562 1.248 2.136 3.684 1.097 40.586 0.146 37.235 4.206
Alpine Veg 45.824 0.075 15.212 0.049 2.75 1.305 2.993 1.712 6.347
Water 0.031 0 0.588 0.001 0 0.001 70.224 0 0
Clouds 2.038 1.295 42.073 1.917 73.967 0.893 10.2 2.558 1.285
Snowcap 4.359 0 13.788 0.05 0.468 0.023 0.093 0.01 1.332
Bedrock/Dry Soil 11.967 21.803 16.786 66.11 17.694 18.23 10.259 9.769 3.098
Rural Dev 25.711 2.776 5.104 3.122 3.254 14.351 2.751 41.048 14.082
Class Changes 54.176 27.682 86.212 33.89 26.033 59.414 29.776 58.952 30.712
Image Difference -45.058 124.896 -24.829 20.702 -20.19 -40.162 -27.59 205.334 704.3
Error Matrix (Percent)
Class Alpine Veg
Snowcap Clouds Desert Veg Water Crops
Alpine Veg 96.58 0 7.35 0.01 5.45 0.11 13.06 0.03 18.28 21.3
0.04 88.88 0 0 0.11 0 0 5.78 0.94 14.67
Snowcap 0.36 0 89.32 12.37 0.02 0.43 0 0 0 3.84
Clouds 0.19 0.01 3.27 87.62 0.23 0.03 0 0.41 0.57 6.61
Desert Veg 1.23 4.24 0.04 0 93.69 0 0.71 0.32 5.71 17.23
Water 0 0 0 0 0 99.36 0 0 0 3.67
Crops 0.34 0 0 0 0.03 0 65.17 0 3.66 0.37
Bedrock/Dry Soil 0 6.83 0.02 0 0.47 0.07 0 93.46 2.97 28.91
1.26 0.04 0 0 0.01 0 21.06 0 67.86 3.39
Error Report and Uncertainties
Potential sources of error
• BSCI was developed while studying Gobi Desert with ETM+
• Landsat 5 has relatively low radiometric resolution
• Overlap of desert vegetation and microbiotic soils and season
• Training site selection not based on ground truth data
• Soil stability reduces wind-blown dust
• Dust deposited on snowcapped mountains will decrease
the albedo of the surface
Painter et al. 2007
• Ground truth data is required for this study to mean
• Based on this analysis there has been a substantial
increase in biological soil crust coverage from 1996 to
2006 in the Colorado Plateau region.
• This technique provides a cost-effective method for
continued monitoring of microbiotic soils
Any thoughts or questions?
Belnap, J., & Gardner, J. S. (1993). Soil microstructure in soils of the Colorado Plateau: the role of the cyanobacterium Microcoleus vaginatus.
Great Basin Naturalist, 53(1), 40-47.
Belnap, J., & Eldridge, D. (2003). Disturbance and recovery of biological soil crusts. In Biological soil crusts: structure, function, and
management (pp. 363-383). Springer Berlin Heidelberg.
Chen, J., Yuan Zhang, M., Wang, L., Shimazaki, H., & Tamura, M. (2005). A new index for mapping lichen-dominated biological soil crusts in
desert areas. Remote Sensing of Environment, 96(2), 165-175.
Harper, K. T., & Belnap, J. (2001). The influence of biological soil crusts on mineral uptake by associated vascular plants. Journal of Arid
Environments, 47(3), 347-357.
Karnieli, A., Kidron, G. J., Glaesser, C., & Ben-Dor, E. (1999). Spectral characteristics of cyanobacteria soil crust in semiarid environments.
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Painter, T. H., Barrett, A. P., Landry, C. C., Neff, J. C., Cassidy, M. P., Lawrence, C. R., & Farmer, G. L. (2007). Impact of disturbed desert soils
on duration of mountain snow cover. Geophysical Research Letters, 34(12).
Peterson, P. (Ed.). (2001). Biological soil crusts: ecology and management. US Department of the Interior, Bureau of Land Management,
National Science and Technology Center, Information and Communications Group.
Van der Meer, F. D., van der Werff, H., van Ruitenbeek, F. J., Hecker, C. A., Bakker, W. H., Noomen, M. F., ... & Woldai, T. (2012). Multi-and
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Weber, B., Olehowski, C., Knerr, T., Hill, J., Deutschewitz, K., Wessels, D. C. J., & Büdel, B. (2008). A new approach for mapping of biological
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(Presentation 10-15 mins) Hi everyone, my name is Alex, I’m in the environmental science masters program and I’m going to talk to you about the importance of biological soil crusts and techniques for their conservation.
I took this picture last summer on a mountain biking trip I was on and it was really the first time I had heard of biological soil crusts. There are a few signs here and there urging visitors to stay on designated trail areas so as not to disturb them. Some of you may have seen signs like this before. If you notice, even in this seemingly barren landscape there are small patches of vascular plants dotted about the area. Shown here. Biological soil crusts play a significant role in allowing the establishment of these plants through a variety of mechanisms which I will explain.
You may have heard biological soil crusts being referred to by various names such as cryptogamic coils, microbiotic soils, and microphytic soils. There is no right or wrong name to call them by, and I think because there is so little known about them and real research on them has only started in past decade or so. The image on the left here shows what the crusts look like up close. They have a very definite structure about them that takes many years to build. On the right is a scanning electron microscope image of the microfilaments that makes the complex soil structure possible. Cyanobacteria are responsible for the physical microstructure but soils crusts consist of various forms of life such as lichens, green algae, fungi, nonvascular plants such as mosses, and an array of bacteria.
Another interesting article I came across when reviewing literature was by Painter et al in 2007 and they claimed that the stability of soil in arid and semi-arid environments could have an impact on the surrounding alpine snowpack. This particular picture was taken from the Colorado Plateau of the La Sal Mountains in Utah. One wouldn’t normally think of arid environment impacting snow but there are many regions in the world where these two local climate are in pretty close proximity to each other. The implication of this is that if soil stability is reduced then wind erosion will increase and deposit sediment on the snow surface. This graph shows the potential reduction in albedo, or reflectivity, on the snow fields. Warmer snow leads to faster melting and more solar insolation. The point here is that microbiotic soils have an influence that extends beyond the ecosystem in which they reside.