It’s alive! The hidden microbial communities below our feet

Easily missed, biocrusts are ecosystem engineers in the soil. Here’s why we need to watch where we step.

Mojave Desert Land Trust
8 min readMar 16, 2020
Placidum lichen growing around quartz with some patches of cyanobacteria. Photo: Brianne Palmer

By guest writer, Brianne Palmer

California’s deserts are harbors of biodiversity — filled with blossoming wildflowers, charismatic animals, and imperceptible microorganisms. Walk through a desert and you might see a vast vista of protruding peaks speckled with desert scrub. Look a little closer and you might see pops of color, fragrant forbs scattered across the soil.

Look a little closer still and you might see something strange — a splash of green slime, a thin black blanket on the ground, multi-colored lichens carpeting the gaps between the plants, diverse communities of biocrusts covertly changing the surrounding soil properties and altering communities.

“Green slime” cyanobacteria dominated biocrust. This type of biocrust can be hard to see except when the conditions are right, cloud cover after a large moisture event. The moisture causes the cyanobacteria to move to the surface and we can see the photosynthetic pigments. Photo: Brianne Palmer

These elusive and cryptic biocrust communities are found on every continent and cover about 12% of the earth’s terrestrial surfaces (Elbert et al. 2012). Biocrust communities are diverse and variable across the landscape, composed of bacteria, lichens, fungi, and moss with each community providing a unique set of ecosystem functions. And we, as desert enthusiasts, should pay more attention to these ecosystem engineers.

In the desert, biocrusts grow in the interspaces between plants where there is enough exposed soil surface to establish. They may be patchy across the landscape or form seas of crusty surfaces.

Biocrusts are connected to the above-ground (plants, animals, UV radiation, etc.) and below-ground (soil microbes, micro-invertebrates, soil aggregation, etc.) ecosystems.

Mosses are also present in Mojave Desert biocrusts and contribute to the amazing biodiversity of the desert. The are highly desiccation tolerant and survive the harshness of the desert by only being metabolically active when there is enough moisture. Photo: Brianne Palmer

Individual organisms within each crust interact with each other and have an indirect impact on plants, shifting nutrient cycles, increasing water content, and improving soil stabilization.

Their connection to the soil and the flora, has spurred much research on the interactions of biocrusts with above-ground organisms, primarily vascular plants, and below-ground processes like nutrient cycling.

Biocrusts are vitally important in the soil carbon cycle and fix more carbon than they respire, thus increasing carbon sequestration (Castillo-Monoroy et al. 2011 [1] , Li et al. 2012). Additionally, due to their global presence, researchers determined biocrust communities account for 3–4% of global nitrogen fixation rates, acting as a natural fertilizer for the surrounding plants (Belnap 2002[2]).

Mixed biocrust community in the Mojave Desert composted of Placidium and Collema lichens with cyanobacteria and specks of moss. It is common to find very diverse communities if you stare at the soil surface long enough. Photo: Brianne Palmer

Although it is known that biocrusts increase available nitrogen in ecosystems, in grasslands we are uncertain how biocrust nitrogen fluxes differentially affect native and nonnative plant species. These shifts in nutrient availability influence the surrounding plant communities, and consequently, ecosystem processes on a landscape scale (Langhans et al. 2009, Garcia et al. 2015, Ghiloufi et al. 2016).

In some cases, biocrusts enhance plant growth (Garcia et al. 2015) and promote plant uptake of essential micronutrients (Harper and Belnap 2001).

Underneath the biocrust there are filaments, which indicate the presence of cyanobacteria holding the soil aggregates together. Photo: Brianne Palmer

However, biocrusts may also inhibit plant growth by creating a barrier on the soil surface, thus creating heterogeneity across the landscape (Song et al. 2017). These interactions are not fully understood, though some hypothesize that biocrusts may deter plant invasion and maintain community stability (Deines et al. 2007).

For example, in the California sage scrub, biocrusts that had been experimentally trampled increased the abundance of exotic annual plants, indicating disturbance of biocrusts may detract from native plant communities, because the seedlings that are able to germinate and establish benefit from increased available nutrients (Langhans et al. 2009, Hernandez and Sandquist 2011). The relationship between biocrusts and vascular plants are complex, and we don’t fully understand how biocrusts are shaping our grassland plant communities.

A restoration tool

Given the global importance of these microbial communities, there has been a push for more research and more concern for the status of biocrusts in conservation and restoration practices as both a community to be restored and a tool for restoration (Bowker 2007, Bowker et al. 2011[3]). Establishing a strong biocrust community may improve the biogeochemical cycling and relieve stress from the native plant species. In areas where biocrusts have been restored, there is improved soil moisture, reduced erosion, and improved soil fertility (Li et al. 2010, Zhao et al. 2016, Gomez et al. 2012).

Cyanobacteria biocrust growing beneath quartz. This is an example of a hypolithic biocrust. Photo: Brianne Palmer

The natural recovery time for biocrusts is slow and inconsistent, ranging from two to hundreds of years depending on the disturbance and the habitat (Belnap and Lange 2003). For example, after a fire in South Africa it took 8 months for biocrusts to reach a pre-disturbance community composition (Dojani et al. 2011) but in the Great Basin, it took up to 15 years to achieve the same result (Root et al. 2017).

There are currently researchers addressing biocrust recovery in the California deserts and there have been successful attempts to rehabilitate biocrust communities in the lab and the field.

A small field sample was grown in a nursery to re-establish 6000-m2 of dryland soil in the southwestern U.S. at 1–5% of the historical concentration (Ayuso et al. 2017). Additionally, the restoration of biocrusts improved soil fertility and the micro-environment of the top soil in Chinese semi-arid ecosystems (Wu et al. 2013).

The restoration of biocrusts in deserts may markedly improve the ecosystem function and enhance productivity.

What can we do to help?

Becoming a crust-odian, a caretaker of crusts, is as simple as being aware of their existence and minimizing damage to them when found. Often, biocrusts are nestled between bunch grasses, or smashed below our shoes, and we aren’t aware of the community we are impacting. Due to the high disturbance in our grasslands from human recreation, grazing, and fire, it is likely that the biocrust communities are remnants of what they once were. However, since biocrusts were largely absent from the literature until the late 20th century, we lack the perspective to restore biocrusts to their historical state (Bowker 2007). Given their influence on ecosystem functioning and growing support of biocrust research around the world, biocrusts should be considered in restoration plans and could potentially be used as a restoration tool, to assist the recovery of degraded ecosystems. We can do our part in conserving them by simply acknowledging their existence, watching where we step, and sharing the importance of these organisms with others.

Brianne Palmer is a PhD Candidate in the joint ecology program with San Diego State and University of California, Davis. The majority of her work is in the grasslands on San Clemente Island studying the recovery and functional shifts of biocrusts after fire. Follow her on Twitter or visit her website.


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Mojave Desert Land Trust

The Mojave Desert Land Trust is a 501(c)(3) non-profit organization protecting lands with natural, scenic, and cultural value within the Mojave Desert.