Desert Habitat: Soil Microorganisms

By Garry Rogers

The Role of Soil Microorganisms in Desert Ecosystems

There would be no life on the land if there was no soil.

“When you thrust a shovel into the soil or tear off a piece of coral, you are, godlike, cutting through an entire world. You have crossed a hidden frontier known to very few. Immediately close at hand, around and beneath our feet, lies the least explored part of the planet’s surface. It is also the most vital place on Earth for human existence” (Wilson, 2010).

Biological Soil Crusts

1-Gt Basin Lower Valleys-003

Biological Soil Crust (Brown stipplescale) growing in a rocky area in the Great Basin Desert.

In sunny desert environments, various species of algae, cyanobacteria, microfungi, lichens, and bryophytes form thin crusts over the surface of the ground.  The crusts protect the soil from erosion, enrich its composition, and enhance plant growth.  The crusts are among the most important components of desert ecosystems.

Biological soil crusts (BSCs) are quite fragile.  If they are damaged, soils lose moisture and nutrients and become susceptible to erosion and invasion by alien plants.  BSCs are susceptible to considerable damage by livestock (e.g., Brotherson et al. 1983). Recovery of BSCs at some sites can occur within 20 years (Anderson et al. 1982), but most studies have concluded that longer periods are required (e.g., Jeffries and Klopatec 1987), and that full recovery can require centuries (Belnap 1993).

Following a disturbance that removes desert vegetation, there is a gradual recovery that takes place as seeds disperse back into the disturbed area.  In deserts, the recovery isn’t an orderly process.  Forrest Shreve, a leading authority on desert plant ecology, explained that desert recovery is a random process of seed dispersal and reoccupation of a disturbed site by the former occupants (Shreve 1964:  28).  Shreve mentioned the role of soil-surface conditions in determining the returning species’ seed germination, but he did not mention the critical role of biological soil crusts (BSCs) in the process [BSCs are also known as cryptogams, cryptobiota, and microbiota].

During the first half of the 20th Century, when Shreve studied desert plants, few scientists had given much thought to soil crusts.  Concern for the contribution of BSCs to natural ecosystems didn’t develop until the second half of the 20th Century (Belnap and Gardner 1993, Bond and Harris 1964, Chaudhary et al. 2009, Eldridge and Greene 1994).

2008. Cedar Mountains by Garry Rogers (color)

A barren Great Basin landscape where native vegetation was removed by fire and replaced by Cheatgrass.

On smooth soil surfaces, biological crusts can form continuous cover that blocks germination of the seeds of many invasive species.  Even in rocky areas such as those in the photographs above, partial cover by BSCs will benefit native plants and help them resist replacement by invaders.  Field and laboratory studies have demonstrated that healthy BSCs might have blocked the massive invasion of the Great Basin Desert by Cheatgrass (Bromus tectorum) (Larsen 1995; Kaltenecker et al. 1999a; Belnap et al. 2001:  33).

The haphazard treatment of soil microorganisms is evident in the way that land managers use herbicides.  Millions of gallons are sprayed along roads and transmission corridors.  This is despite uncertainty about the consequences.  “There are few studies addressing herbicide effects on biological soil crusts. Therefore, caution should be used when applying these chemicals to soils supporting biological soil crusts … or to areas where management goals include crust recovery (BLM 2008: BLM Final Programmatic EIS 2007: Section 4, Page 15).

Arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi (AMF) are another important group of soil microorganisms.  AMFs form sheaths around plant roots and they spread subterranean networks of filaments that connect the roots of plants across large areas.  AMFs are obligate symbionts whose carbon nutrition depends on the photosynthetic success of their host plant (Bloss 1995).  Their presence improves plant success by increasing nitrogen fixation and absorption of water and nutrients (Allen 2007).  Healthy AMF networks make soils more resistant to erosion (Chaudhary et al. 2009).  Like BSCs, AMFs are a critical component of desert ecosystems.  Their abundance and diversity contribute to plant and animal species diversity (Li et al. 2006, Rinaldi et al. 2008).

AMFs inhibit the growth of most invasive species, but some invasives can inhibit AMF growth and thereby reduce the competitive ability of native plants (Bethlenfalvay and Dakessian 1984, Eriksson 2001, Garrido et al. 2010, Guadarrama et al. 2008, Vogelsang and Bever 2009, Wang et al. 2003).

Invasive species often undergo rapid adaptive changes that enhance their success.  Seifert et al. (2009) found that mycorrhizal dependence in St. John’s wort (Hypericum perforatum) declined during the plant’s invasion of new habitats without familiar AMF.

AMF interaction with invasive plants is complex.  Belnap and Sherrod (2009) found that when they grew invasive Cheatgrass (Bromus tectorum) together with native Galleta Grass (Hilaria jamesii), the Cheatgrass grew much more rapidly than when they grew it alone.  The authors suggested that Cheatgrass was tapping into the mycorrhizal network connecting Galleta Grass.


A substantial body of research indicates that soil microorganisms are critical components of native desert vegetation.  BSCs and AMFs protect soil, improve native plant health, and block invasive species.  Land managers in charge of Human activities in North American deserts are familiar with the importance of soil microorganisms (e.g. Pellant et al. 2005:  32-33, BLM 2008), but their practices do not reflect this knowledge.  For instance, they often allow ranchers to return cattle to a burned area long before the microorganisms can recover. This can prevent BSC and AMF recovery, make the area more susceptible to invasive plants, reduce soil fertility, and increase erosion.

Protection and improvement of desert habitats requires public education and management leadership to limit burning, construction, recreation, livestock grazing, and herbicide treatments.  Land managers must not fail to satisfy either of these requirements.  If they do, they will be responsible for continuing and accelerating the current downward spiral of habitat productivity, stability, and biodiversity.

Challenge for All Desert Dwellers

Watch for BSCs.  If you visit an area with native vegetation, look closely at the soil surface.  If a crust is present, you will see it.  Take some pictures.


An extensive collection of information is available from the Mycorrhiza Literature Exchange (

Allen, M. F.  2007.  Mycorrhizal fungi: Highways for water and nutrients in arid soils.  Vadose Zone Journal 6:291-297.

Anderson, D. C., K. T. Harper, and S. R. Rushforth. 1982. Recovery of cryptogamic soil crusts from grazing on Utah winter ranges. Journal of Range Management 35:355-359.

Belnap, J. 1993. Recovery rates of cryptobiotic crusts: Inoculant use and assessment methods. Great Basin Naturalist 53:89-95.

Belnap, J., and J. S. Gardner.  1993.  Soil microstructure in soil of the Colorado Plateau: The role of the cyanobacterium Microcoleus vaginatus.  Great Basin Naturalist 53:40-47.

Belnap, J., J. H. Kaltenecker, R. Rosentreter, J. Williams, S. Leonard, and D. Eldridge.  2001.  Biological soil crusts:  Ecology and management.  USDI BLM Tech Ref 1730-2.  111 p.

Belnap, J., and S. Sherrod.  2009.  Soil amendment effects on the exotic annual grass Bromus tectorum L. and facilitation of its growth by the native perennial grass Hilaria jamesii (Torr.).  Plant Ecology 201:709-721.

Bethlenfalvay, G.J., and S. Dakessian. 1984. Grazing effects on mycorrhizal colonization and floristic composition of the vegetation on a semiarid range in northern Nevada. Journal of Range Management 37:312-316.

BLM. 2008.  Agua Fria National Monument and Bradshaw-Harquahala proposed resource management plans and final environmental impact statement—May 2007.  U. S. Department of the Interior, Bureau of Land Management, Phoenix District Office, Arizona.  1199 p.

Bloss, H. E.  1995.  Studies of symbiotic microflora and their role in the ecology of desert plants.  Desert Plants 7:119-127.

Bond, R.D., and J.R. Harris.  1964.  The influence of the mircoflora on the physical properties of soils.  I. Effects associated with filamentous algae and fungi.  Australian Journal of Soil Research 2:111–122.

Brotherson, J.D., S.R. Rushforth, and J.R. Johansen. 1983. Effects of long-term grazing on cryptogamic crust cover in Navajo National Monument, Arizona. Journal of Range Management 36:579-581.

Chaudhary, V., M. A. Bowker, T. E. O’Dell, J. B. Grace, A. E. Redman, M. C. Rillig, and N. C. Johnson.  2009.  Untangling the biological contributions to soil stability in semiarid shrublands.  Ecological Applications:  19:110-122.

Eriksson, A.  2001.  Arbuscular mycorrhizae in relation to management history, soil nutrients and plant diversity.  Plant Ecology 155:29–137.

Garrido, E., A. E. Bennett, J. Fornoni, and S. Y. Strauss.  2010.  Variation in arbuscular mycorrhizal fungi colonization modifies the expression of tolerance to above-ground defoliation.  Journal of Ecology 98:43-49.

Guadarrama, P., S. Castillo-Argüero, J. A. Ramos-Zapata, S. L. Camargo-Ricalde, and J. Άlvarez-Sánchez.  2008.  Propagules of arbuscular mycorrhizal fungi in a secondary dry forest of Oaxaca, Mexico.  International Journal of Tropical Biology 56:269-277.

Jeffries, D.L., and J.M. Klopatec. 1987. Effects of grazing in the vegetation of the blackbrush association. Journal of Range Management 40:390-392.

Kaltenecker, J.H., M. Wicklow-Howard, and M. Pellant. 1999a. Biological soil crusts: natural barriers to Bromus tectorum L. establishment in the northern Great Basin, U. S.A. In:  Eldridge, D., and D. Freudenberger, eds. Proceedings of the VI International Rangeland Congress, Aitkenvale, Queensland, Australia. Pages 109-111.

Kaltenecker, J.H., M. Wicklow-Howard, and R. Rosentreter. 1999b. Biological soil crusts in three sagebrush communities recovering from a century of livestock trampling. Pages 222-226 in  E. D. McArthur, W. K. Ostler, and C. L. Wambolt, Comps. Proceedings: Shrubland Ecotones. Proceedings RMRS-P-11. USDA Forest Service, Rocky Mountain Research Station. Pages 222-226.

Larsen, K.D. 1995. Effects of microbiotic crusts on the germination and establishment of three range grasses. Unpublished thesis, Boise State University, Boise, ID.  86 p.

Li, X. R., Y. W. Chen, Y. G. Su, and H. J. Tan.  2006.  Effects of biological soil crust on desert insect diversity:  Evidence from the Tengger Desert of northern China.  Arid Land Research and Management 20:263-280.

Pellant, M., P. Shaver, D.A. Pyke, and J.E. Herrick. 2005. Interpreting indicators of rangeland health, version 4.  Technical Reference 1734-6. U.S. Department of the Interior, Bureau of Land Management, National Science and Technology Center, Denver, CO. BLM/WO/ST-00/001+1734/REV05.  122 p.

Rinaldi, A. C., O. Comandini, and T. W. Kuyper.  2008.  Ectomycorrhizal fungal diversity:  Separating the wheat from the chaff.  Fungal Diversity 33:1-45.

Rogers, G. F.  1982.  Then and Now: A Photographic History of Vegetation Change in the Central Great Basin Desert.  Univer­sity of Utah Press, Salt Lake City, UT.  188 pp.

Seifert, E. K., J. D. Bever, and J. L. Maron.  2009.  Evidence for the evolution of reduced mycorrhizal dependence during plant invasion. Ecology 90:1055-1062.

Shreve, F.  1964.  Vegetation of the Sonoran Desert.  Pages 6-186 in F. Shreve and I. L. Wiggins, Vegetation and flora of the Sonoran Desert.  Stanford University Press, Stanford, CA.  1740 p. + 37 plates.

Vogelsang, K. M., and J. D. Bever.  2009.  Mycorrhizal densities decline in association with nonnative plants and contribute to plant invasion.  Ecology 90:399-407.

Wang, F.Y., R. J. Liu, X. G. Lin, J. M. Zhou.  2003.  Comparison of diversity of arbuscular mycorrhizal fungi in different ecological environments.  Acta Ecologica Sinica 23:2666–2671.

Wilson, E.O.  2010.  A cubic foot.  Online at:

18 thoughts on “Desert Habitat: Soil Microorganisms

  1. Honor the Microbes…there’d be no life anywhere without them.

    Great article, Garry–I’ve often wondered who made those crusty little spires in desert soil–I try not to step on them.


  2. Truly fascinating! It is difficult to appreciate how delicate is the balance that needs to be maintained if desert environments are to survive, and their importance to the rest of us. It is past time that soil erosion generally took a leading role on the world conservation stage, especially as some authorities are beginning to quote doomsday dates for the end of topsoil as we know it!


  3. Thank you Frederick. I guess soil conservation is even farther from the concerns of average people than wildlife conservation, and we know that’s not going well. One of us needs to have a brainstorm.


  4. Thank you Cindy. By the way, the Hawk Headed Parrot is fabulous. I have been working on a children’s story about a parrot and hadn’t settled on a species. I’ll do some research, but this may be my bird!


  5. It is amazing that there are so many things about this earth we take for granted. Truly
    Every little thing is so important to our welfare! Thanks for teaching us!


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