Microbial Adaptation to Arid Conditions

While the desert seems to be an inhospitable place, in reality it contains a multitude of diverse microorganisms. Many of these microorganisms live in the crust, the top several mm to cm of soil. In this environment, organisms survive high levels of UV irradiation with very little water. I am interested in ‘how microorganisms can live in such an environment?’.

Much of what is known about desiccation resistance comes from the Class Deinococci. Deinococcus radiodurans, the most famous member of the Class, was initially isolated from a can of spoiled meat that had been irradiated for sterilization. D. radiodurans has been shown to withstand 500,000 rads of radiation and still maintain the viability of some cells (Mattimore & Battista, 1996. J. Bacteriol. 178:633-637). PFGE was used to analyze the effect of irradiation on the genome – the results showed the breakdown of the full length genome, approximately 3 Mbp in length, into small fragments estimated to be 50 kbp. Over time, the wild-type irradiated organisms were shown to rebuild a full-length functional, stable, genome from these fragments (Harris et al., 2004. PLoS Biol. 2: e304:1629-1639). Our overriding question is: does the mechanism that allows D. radiodurans to survive irradiation occur in organisms present in the desert crust?


Interest in the generation of renewable fuels has gained momentum in the last decades in the face of global warming associated with the continued use of fossil fuels, and because of the finite nature of their reserves.

Biohydrogen production from photosynthetic organisms constitutes a conceptually promising avenue in renewable bioenergy, because it would couple directly solar radiant energy, essentially inexhaustible, to the generation of clean, carbon-neutral biofuels, particularly if water-splitting (oxygenic) phototrophs were used.

Cyanobacteria, the only group of oxygenic phototrophs among the bacteria, have been regarded as good models for research and eventual application in this area for several reasons: they are capable of growth with minimal nutritional requirements, they are demonstrable producers of hydrogen gas under certain physiological conditions, and some can be genetically modified with ease. Among cyanobacteria, three different enzymes participate in hydrogen metabolism nitrogenase, and two types of Ni-Fe hydrogenases (uptake and bidirectional).

Euendolithic Cyanobacteria

There are several classes of endolithic organisms: euendoliths actively carve out or bore into mineral material, chasmoendoliths live in the crevices and cracks of mineral material, cryptoendoliths live within structural cavities of porous rock including previously excavated now vacant euendolithic dwellings.

Our research focuses on euendolithic organisms which bore into calcium carbonate containing minerals. Carbonate minerals like calcite or dolomite, and other carbonates like dead coral, carbonate sand, marble sculptures, fountains or even concrete represent some of the preferred substrates for euendolithic microbes. The reasoning behind the evolution of this particular lifestyle is poorly understood but we believe that by choosing this niche they improve their chances of survival, and consequently play both friend and foe in the environment taking an important role in the rock cycle (via bioerosive forces), and sometimes accelerating the deterioration time of monuments made of carbonates.

Biological Soil Crusts

Biological soil crusts (BSCs) are also known as cryptogamic or cryptobiotic microbial communities. They are complex microbial communities dominated by cyanobacteria as primary producers that build crust on the top layer of arid lands soils.

Facts numbers:

  • 35% of the total Earth’s continental surface is covered by arid lands, BSC usually cover these areas
  • 30 to 350 kg C ha-1 is the annual range of carbon input in BSC
  • 1 to 100 kg N ha-1 is the annual range of nitrogen fixation in BSC
  • 4th is the position of Microcoleus vaginatus in the World ranking of the most abundant cyanobacteria
  • 54 x 1012 g of Carbon is the biomass of microbial primary producers in BSC

In spite of their geographic extent and ecological importance, many aspects of the biology of BSCs remain unknown; this is why we are studying them!

BSC formation, story of a very slow process

1) Crusting is initiated by growth of filamentous cyanobacteria (e.g. Microcoleus sp.) during episodic events of available moisture.
2) As they grow, these cyanobacteria produce a high amount of slime (extra-polymeric substances) that traps mineral particles.
3) This process result in the formation of a pioneer light-crust
4) Once the crust is stabilized other microbes colonize the crust. For instance other cyanobacteria (e.g. Nostoc sp.) forms black colonies on the top of the crust
5) Later on, other organisms, such as lichens, eukaryotic microalgae, and mosses, may be integrated as dwellers of the crust.

Greening deserts: the incredible ability of Microcoleus sp.

When BSC get wet they rapidly turn green.
This is due to Microcoleus sp. that moves to the surface of the crust once exposed to water. These bacteria are doing oxygenic photosynthesis and carry green-blue photosynthetic pigments; this is why the surface of the soil turns green when they move there.
The answer of Microcoleus sp to wetting event corresponds to a quick metabolic shift that allow the turn ON of metabolism pathways.
Once the crust get dry, Microcoleus sp go back inside the crust, a few millimeters below the surface. Microcoleus sp filament can survive for long periods in this hostile environment ( dry, with low light and low nutrients input) through days, months or years…until the next wetting event.
The behavior of Microcoleus sp. and more generally of the whole crust microbial communities through these wetting-drying cycles is studied in collaboration with research groups from LBL and JGI.

Objective :

We are interested in the description of how the community switch ON when the crust get wet and then switch OFF and get prepared to long periods of desiccation when the crust dry.


To describe this process we are using a combination of cultivation, direct DNA/RNA sequencing, metabolites identification, in silico modelling and imagery based techniques.
If you want to know more about this project, please contact us!
You can also visit the webpage of our collaborators in Laurence Berkeley laboratory.

References :

1) F Garcia-Pichel, J Belnap, S Neuer, F. Schanz – Algological Studies , vol. 109, 2003 Estimates of global cyanobacterial biomass and its distribution
2) F Garcia-Pichel, O Pringault – Nature, 2001 Microbiology: Cyanobacteria track water in desert soils

Destruction and recovery

Human disturbances in Biological Soil Crust (BSC) often create severe environmental problems. The dust storms or “Haboobs” that have been increasingly striking Phoenix area in the recent years are a good local example. Biological Soil Crusts are responsible for maintaining soil cohesion and stability in arid areas. They also improve the soil fertility and play an important role in the germination, growth and survival of native species of plants.
Our main research objective is to facilitate the recovery of degraded arid and semi-arid lands through the restoration of the biological soil crusts. This project is developing laboratory methodologies and establishing a nursery for testing the inoculation techniques and biocrust formation. The inoculation techniques will also be tested and monitored in the field, operating in a degraded biocrust from the Department of Defense Training Areas. Special attention will be paid on whether biocrust restoration may facilitate the function of native plant vs. colonization of exotic plants.


Garcia-Pichel, F., Lopez-Cores, A., and Nubel, U. (2001) Phylogenetic and morphological diversity of cyanobacteria in soil desert crusts from the Colorado Plateau. Applied and Environmental Microbiology 67: 1902-1920.

Belnap, J., and Lange, O.L. (2001) Biological soil crusts: Structure, function, and management. Springer-Verlag. Berlin, 479 p.

Zaady, E., Gutterman, Y., and Boeken, B. (1997) The germination of mucilaginous seed of Plantago coronopus, Reboudia pinnata, and Carrichtera annua on cyanobacterial soil crust from the Nagev Desert. Plant Soil 190: 247-252

Garcia-Pichel, F., and Belnap, J. (1996) Microenvironments and microscale productivity of cyanobacterial desert crust. Journal of Phycology 32: 774-782.


Solar ultra violet radiation or UVR (wavelengths shorter than 400 nm) is associated with biological deleterious effects in living organisms. Among these, some cyanobacteria must thrive in habitats exposed to high doses of UVR such as soil and rock surfaces, and thus have the ability to synthesize and accumulate UV-sunscreens. Sunscreens serve as passive preventative mechanisms that allow the organism to stop UVR before it reaches the cellular machinery, DNA, or produces reactive oxygen species.

The indole-alkaloid, scytonemin, found exclusively among cyanobacteria, is one such sunscreen. It is a brownish-yellow, lipid-soluble pigment located in the extracellular matrix of the cells. The production of scytonemin is induced by UV-A (315-400 nm) and the conjugated double-bond distribution allows for the molecule to absorb strongly in that range (with a maximum of ~384 nm). Scytonemin also has potential in biomedical applications because of its strong anti-proliferative and anti-inflammatory activity.

Another class of sunscreens found in cyanobacteria are the mycosporine-like amino acids (MAAs), water soluble, colorless products that absorb and are induced by UV-B (280-315 nm).

Our lab is currently focusing on the molecular genetics of scytonemin and MAAs biosynthesis.

Hypersaline Mats

As part of a large scale, multidisciplinary effort to understand the complex interactions between microbial community structure and emergent ecosystem properties we are studying hypersaline microbial mats from Guerrero Negro in Baja California (México) as models of microbial ecosystems.

These photosynthetic communities are benthic, laminated aquatic biofilms consisting of highly structured, and dynamic communities of microorganisms. Hypersaline microbial mats harbor a large variety of organisms able to tolerate and thrive under environmental extreme conditions such as high salinity, light exposure and gases such as hydrogen sulfide and hydrogen.

We are particularly interested in explaining the distribution and abundance of these microorganisms in time and space in terms of environmental gradients and interactions. These microbial mats represent the modern analogs for what must have been the major type of ecosystem on Earth for much of its early history. Understanding their functioning gives us the key to understanding the past features of Earth’s biogechemistry.

Microbial Biosignatures

Why ‘microbial’?

From all the life we know, prokaryotes (archea and bacteria) are the most widespread organisms, in time and space. They are the first organisms that populated the Earth, and would likely be the first dwellers on other planets where life may have developed. They have also the widest limits of environmental tolerance (temperature, pH, radiation, desiccation, etc.), the widest variability in metabolic strategies, and they occupy all the known ecological niches. Additionally, they have been the dominant form of life for about 70% of the geologic time. Thus, they should be the starting point for the search of ancient life on Earth and beyond.

Evidence of the existence and activity of microbes in the fossil record consists primarily on stromatolites, microfossils, and biomolecules, whose antiquity can go far back to the Archean (~3.5 Ga). These microbial signatures can be traced almost continually over time since their appearance on Earth, but the older they are, the hardest to prove them biogenic and the easiest to confuse them with abiogenic structures. Hence, because their biogenicity becomes less evident, not one, but many biosignatures should be retrieved from the study objects, and these biosignatures should converge into a unique conclusion supporting a life-originating process. Otherwise, the object could be discarded as life-related.

What kind of fossil biosignatures exist?

Life can be manifested in several ways, and thus traced using:

  • Biomarkers : chemical compounds produced inside cells
  • Biominerals : minerals produced by their influence on the environment
  • Bioisotopes : isotopes derived from metabolic activity
  • Ichnofossils, microbialites or biofabrics : sedimentary structures biologically originated
  • Microfossils : any cell remains


The Cuatro Ciénegas Basin (Coahuila, Mexico) is a complex karstic system in which the underlying Cretaceous limestone, dolomites and gypsum formations are actively dissolved by an aquifer of distant origin. This results in the formation of innumerable springs, surface and underwater streams, caves and sinkholes pozas, which are famous for their beauty and the biological diversity they harbor. Within the frame of a large multidisciplinary effort funded by NASA’s National Astrobiology Institute, scientist at ASU are looking at the food-web stocihiometry, biosignatures, grazer interactions, and microbial populations of these springs.

Cyanobacteria are often dominant primary producers in calcareous freshwater springs. In most cases, they occur as sessile, benthic or epiphytic dwellers, and are also typically associated with the precipitation of the microcrystalline calcite, that often results in the formation of macroscopic stromatolitic structures and rolling oncolites. These systems allow us to study the interactions between microbial metabolism and carbonate precipitation, in a manner that may help us understand present and past microbialites.

Soil microbial ecology

Soil archaea and bacteria are known to oxidize ammonia to nitrite in a key pathway of nitrification. The nitrogen (N) cycle may be affected by N inputs from natural (e.g. mineralization) or anthropogenic (e.g. atmospheric deposition) sources. Most research has shown that N enrichment alters ammonia-oxidizing microorganisms, increasing ammonia oxidation (AO) rates and abundance of ammonia-oxidizing putative enzymes. However, the archaea and bacteria, and subgroups within each microbial group, may respond uniquely to available NH4+ concentrations and to changes in the environment. We ask, what are the dynamics that control ammonia-oxidizing communities and their effects on ecosystem processes? We used soils from N fertilized (NH4NO3 added at 60 kg N ha-1 yr-1 since 2005) and unfertilized Sonoran Desert soils near Phoenix, Arizona, to measure AO using the nitrite-accumulation method. To test for effects of patch type in aridlands, soils were also collected away from plants and under the canopy of creosote shrubs. In the lab, we measured potential rates using shaken-slurries and actual net rates using static incubations. Rates were measured under a range of starting NH4+ concentrations to develop a response-curve of AO kinetics. Additionally, ammonia-oxidizers were quantified using real-time PCR and identified to the species level using clone libraries and pyrosequencing (data processed with Qiime).

Long-term N fertilization increased rates of potential and actual AO in soil away from and under plants. Based on molecular analyses, N fertilization increased diversity and absolute number of ammonia-oxidizers in the total community. Additionally, one archaeon population makes up 74-95% of all the ammonia-oxidizers across treatments and patch types in these desert soils. Interestingly, inspection at a fine level of resolution within the archaea and bacteria reveal that many individual populations either increase or decrease, exhibiting niche separation through a community shift. Furthermore, the rate of AO per copy number of ammonia-oxidizing cells (i.e. AO efficiency), increases with N fertilization. These results suggest that environmental N addition in aridland soils alters ammonia-oxidizing communities at the genetic level and elevates nutrient cycling rates at the ecosystem scale.