Soil microbial ecology

Niche differentiation of ammonia-oxidizing microbial communities and their function in soil

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.

Link to 2013 CAP-LTER Symposium Poster by Yevgeniy Marusenko, Ferran Garcia-Pichel, and Sharon J. Hall

Litter decomposition in arid systems

Litter decomposition is a key pathway in the global carbon (C) cycle, releasing more C into the atmosphere annually than fossil fuel combustion. While litter decay in mesic systems is reasonably well predicted by empirical models based on climatic and litter chemistry factors, this is not the case in arid systems. Specifically, mass loss in arid systems is faster than predicted and decay patterns are near linear rather than exponential. Recent research has revealed that breakdown of litter by solar radiation (photodegradation) can be a significant driver of mass loss in arid systems, although the relative strength of this driver appears quite variable. The UV component of sunlight appears to be the most effective waveband in driving mass loss, and lignin appears to be the main target. We propose that the optical properties of leaf litter vary substantially among different plant growth forms, and that this has a large influence on the effectiveness of photodegradation. We suspect that the surface UV-screening of leaf litter is greatest in evergreens, intermediate in grasses, and least in forbs. Screening effectiveness is important because it dictates radiation fluxes inside litter, such as in vascular tissue where the majority of lignin resides. We also suspect that effective surface screening persists much longer in evergreen litter than in grasses or forbs, because of the high concentrations of wall-bound screening compounds in evergreens that are not be readily lost during decay. Hence, photodegradation may become a stronger driver of decay much earlier in the decomposition of forb and grass litter than evergreen litter. We contend that these changes in the potential effectiveness of photodegradation during decomposition may explain the relatively linear litter decay patterns, as well as the variable effectiveness of photodegradation, found in arid systems.



Stromatolites and Oncolites from Desert Springs

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 multidisplinary 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 precipiation, in a manner that may help us understand present and past microbialites.

Jet-Suspended, Calcite Ballasted Waterwarts

While studying the Cuatro Ciénegas microbialites, we noted planktonic populations of marble-sized colonies of blue-green algae developing at Escobedo’s Warm Spring, a sheltered, small, fast-flowing spring. There, cm-sized waterwarts were kept in suspension by the upwelling waters of a central 6-m deep well. Waterwarts were built by an Aphanothecelike unicellular cyanobacterium and supported a community of epiphytes that included filamentous cyanobacteria and diatoms, but were free of heterotrophic bacteria on the inside. Waterwarts contained orderly arrangements of mineral crystallites, made up of microcrystalline low-magnesium calcite, with high levels of Strontium and Sulfur. An analysis of the hydrological properties of the spring well and the waterwarts demonstrated that both, large colony size and the presence of controlled amounts of mineral ballast, are required to prevent the population from being washed out of the well. The mechanisms by which controlled nucleation of extracellular calcite is achieved remain to be explored.


Mircrobial Biosignatures

Microbial Biosignatures

What are biosignatures?

Any evidence of life

Why are they useful for?

Look for past life, look for life on other planets, to understand life.

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 countinually 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 fact is:

  • We need to understand life to understand biosignatures
  • Biosignatures must prove biogenicity or non abiogenic origin
  • Lots of biotic and abiotic processes, their products and effects are still unknown
  • Morphology may be valid, but more independent biosignatures confirming biogenicity are encouraged
  • As technology, knowledge and interdisciplinarity advance, more biosignatures will be able to detect, and more things known about them.

Biosignatues of terrestrial microorganisms

Biological Soil Crusts(BSCs) are organo-sedimentary structures formed by microbes(mainly dyanobacteria, but also fungi, byrophytes, and algae) that cement topsoil sediments forming a crust.

crusts diagram

Modern BSC are important because they:

  • increase/decrease runoff of rain water
  • hydrate topsoil for a longer time
  • water from below escape at lower rates
  • prevent/decrease soil erosion
  • contribute to C, N and other nutrients in soils
  • enhance seed anchoring and germination
  • are distributed all over the world(principally in arid to semiarid areas


Because cyanobacteria, the main builders of biological soil crusts, are a very old taxa (~3,500 Ma), very well adapted to UV-light and desiccation conditions, they were probably dwellers on the early Earth’s land. They likely colonized and formed crusts in incipient soils as they do today. But yet, there is no evidence for that. To prove that they existed in the Precambrian would have deep evolutionary and ecological implications.

How to distinguish BSC in rocks?

Many other structures that resemble BSCs are found in the rock record (varves, mud cracks, cohesive sand layers, etc.). Thus, unique features of modern BSCs must be recognized in the rocks.

crusts poster

We study sedimentological, chemical and biological features of a variety of BSCs and other structures. The architecture of modern BSCs, its variability within depositional settings, and the morphological changes under diagenetic processes may provide useful elements to distinguish crust-like structures from the rock record.

We found that the crust tends to be enriched in metals as compared to the soil underneath the crust and the uncrusted soils. Minerals are slightly different also, and characteristic sedimentary structures develop only when microbes are present. So, microbes are leaving behind their signature in many of the aspects we study. The metabolic diversity should be further studied so to understand more on the interactions between microbes and particles.

So far, we can say that soil type, water regime, local temperature and wind may influence the interaction between microbes and sediments, which together determine the structure and constitution of BSCs. Differences among BSCs from different sedimentary environments comprise crust thickness, topology, porosity, and layering. Layers of fine sediment, formed by microbial action, can be preserved and recognized after compaction. These features may be useful as indicators of microbially-produced crusts and may be identifiable in the rock record.

Given the great diversity of abiotic sedimentary structures found in nature, individual features alone cannot be counted as biosignatures. Several biosignatures (biominerals, bioisotopes, biomarkers, microfossils, etc.) must be considered when looking for BSC in the rock record. Finally, a definition of BSCs should encompass an array of characteristics that distinguish them from other crust-like structures. This work is a preliminary approach to that goal.

Hypersaline Mats

Hypersaline Communities from Baja California

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.




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.

The model organism that we use to study sunscreen biosynthesis is the filamentous heterocystous cyanobacterium Nostoc punctiforme ATCC 29133/PCC 73102 (from the order Nostocales).
N. punctiforme was originally isolated from the symbiotic association with the gymnosperm cycad Macrozamia sp. and it is one of the few cyanobacteria that can grow heterotrophically. In addition, the fact that N. punctiforme is amenable to genetic manipulation (by electroporation or conjugation) and its genome is fully sequenced (US Department of Energy’s Joint Genome Institute (JGI) database), make it a good model for our work.

Using N. punctiforme, we have been able to obtain a scytonemin-deficient mutant by random transposon insertion into a putative gene. The genomic region of mutation has been identified and is currently being studied for its significance in the biosynthesis of scytonemin, as well as its presence in other scytonemin-producing cyanobacteria.

Biological Soil Crusts

Definition: Surface-bound assemblages of microorganisms consolidate soils into mm to cm-thick crusts that occur on arid lands wherever the lack of water restricts the settlement and development of plant cover. To know more about Biological Soil Crusts, please explore the further sub-sections.

Introduction :

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 dessication 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. Spirnger-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.

Image gallery

Euendolithic Cyanobacteria

Insights into the world of 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 inluding 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.

Autofluorescence test

Cyanobacteria are photoautotrophs which utilize the sun’s radiant energy to ultimately produce glucose which is then respired to produce ATP. The stars of our research are the true endoliths or “euendoliths” that actually dissolve the rock matrix, boring into the substrate and making a tunnel where the cells spend their life. This biogenic destruction of carbonates contributes to erosion and the transformation of the mineral matrix into microcrystalline carbonate or micrite. The process is not always negative; in some microbial communities like in the case of stromatolites the micritization actually contributes to the growth of these structures by cementing sediments together, providing support. This micrite layer often encases the organism which can lead to microfossil formation. The fascinating thing about these boring microbes is that we do not really know how they do it.

test BD-TH

Some researchers have suggested various mechanisms including mechanical destruction, symbiosis with heterotrophs, dissolution by acid secretion, and active transport of metal ions by ATP driven pumps, the later being our proposed mechanism of action.
Our current model organism, Mastigocoleus testarum strain BC008, is a marine cyanobacteria isolated from the coast of Cabo Rojo, a coastal town on the island of Puerto Rico. This particular microbe dissolves calcium carbonate by a mechanism that is not well understood and is the topic of our groups research. We hypothesize boring is mediated by a series of ATP-driven calcium pumps as well as calcium channels (García-Pichel, 2006). Our experimental approach includes using calcium-sensitive fluorescent dyes like Calcium Green 5N and confocal microscopy to try to image the dissolution of calcite (crystalline calcium carbonate) in situ. Other techniques include the use of calcium pump blockers to evaluate the effect on the boring activity, as well as measuring boring activity in minerals other than calcite. We are also interested in the genetics behind carbonate boring and will be utilizing high throughput RNA-seq in an attempt to identify transcripts putatively involved in carbonate boring.

Mechanisms of Carbonate Dissolution by Cyanobacteria.

Among the many interactions between biology and geology, the formation and subsequent destruction of carbonates stands as one of the most conspicuous and widespread. At the microscale one can go from calcification in biofilms to the accretion of coralline atolls. Historically biogenic carbonate precipitation has received the most attention, but its dissolution can also be mediated by organisms, and by microorganisms in particular. Fungi, microalgae and cyanobacteria that actively bore into calcareous substrates have been known for more than a century, and have been leaving fossils and trace fossils since the Precambrian. These organisms are fairly ubiquitious in both marine and fresh water ecosystems as well as in many terrestrial envronments. The mechanisms by which many of these euendolithic organisms bore into carbonate substrates has been studied predominately in fungi and microalgae. The boring mechanistics of euendolithic cyanobacteria are largely unknown but our lab has recently developed a model system to study cyanobacterial euendolithic carbonate boring in the laboratory.

Colonies of Hyella sp. growing on marine carbonates.

Colonies of Hyella sp. growing on marine carbonates.

Biogenic carbonate precipitation has received the most attention, but its dissolution can also be mediated by organisms, and by microorganisms in particular. Fungi, microalgae and cyanobacteria that actively bore into calcareous substrates have been known for more than a century, and have been leaving fossils and trace fossils since the Precambrian. These boring microorganisms are centrally implicated in a variety of geological phenomena, ranging from the erosive morphogenesis of coastal limestones, the destruction of coral reefs, the reworking of carbonaceous sands and the cementation of stromatolites. But for all their significance, the mechanism by which they can excavate carbonates in a controlled manner remains to be studied. The most common hypothesis as to their action mechanisms has been that they dissolve limestone by excretion of acids. However, we contend that, in the case of photosynthetic organisms like cyanobacteria, their activity constitutes an apparent paradox, since the dissolution of carbonates runs contrary to the well-known geomicrobial effects of oxygenic photosynthetic metabolism, which will tend to make the surrounding medium alkaline and therefore promote calcification, not carbonate dissolution. We will test three alternative models than can explain cyanobacterial boring and still be consistent with thermodynamic, physiological and mineralogical constraints. Two models are based on the separation of photosynthetic and respiratory activities (either temporally or spatially). The third model is based on localized and directed cellular calcium transport. We will undertake a three-tiered experimental approach using cultivated microorganisms and well characterized mineral substrates that should offer evidence regarding the validity of each of these models.

We are currently using: a) long-term monitoring of the rates of growth and boring with manipulations of various environmental parameters, b) short- term studies of microscale mass transfer in actively boring systems, including the effects of specific inhibitors, using microsensors, and c) advance microscopy studies of active mineral /microbe systems that offer both visual and micro-chemical information: laser scanning confocal microscopy using extracellular and intracellular calcium fluorophores, fluorescent localization, and secondary ion mass spectroscopy (SIMS).


García-Pichel, F. Ramirez-Reinat, E. Gao, Q., 2010. Microbial excavation of solid carbonates powered by P-type ATPase-mediated transcellular Ca2+ transport. Proc. Natl. Acad. Sci. U.S.A. 107:21749-21754.

García-Pichel, F., 2006. Plausible mechanisms for the boring on carbonates by microbial phototrophs. Sedimentary Geology 185 (2006) 205-213

See also an example of past microborers.


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).



In principle, production of biohydrogen based on nitrogenase systems requires significant modifications of the enzyme or cumbersome growth conditions in order to promote proton reduction and prevent N2 reduction. The hydrogen produced by nitrogenase is often recycled back into metabolic reducing equivalents by means of the uptake hydrogenase. Under physiological conditions, and as the name suggests, the latter enzyme can only consume, rather than produce H2, and so does not constitute a viable platform for biohydrogen production; in fact, it needs to be inactivated to improve yields of nitrogenase-based hydrogen production. Certain cyanobacteria, however, host a bidirectional hydrogenase that can catalyze both the production and the uptake of hydrogen under physiological conditions. One of the major disadvantages for sustained H2 production via the bidirectional hydrogenase is the easy reversal of the reaction direction.

Therefore, our lab focuses on surveying newly isolated cultures from diverse environments for the presence of the bidirectional hydrogenase gene and a concurrent quantitative comparison of their hydrogenase activities under non nitrogen-fixing conditions. We target cyanobacteria from terrestrial environments, since no bidirectional hydrogenase genes originating in these environments were known from public databases, suggesting that they may have been differentially under-sampled. Marine microbial intertidal mats were also of special interest since a high flux of hydrogen had been reported from these cyanobacterial mats. To this we add a survey of freshwater plankton, a habitat well known to harbor cyanobacteria with bidirectional hydrogenases and hydrogen producing capabilities.


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?