Ferran Garcia-Pichel - US grants

A grant has been awarded to Drs. Ferran Garcia-Pichel and Jean M. Schmidt at Arizona State University, in collaboration with Dr. Richard M. Keller at NASA Ames Research Center to conduct a survey of the microbial diversity present in biological soil crusts of North America. In arid lands, where plant cover is restricted, a half-inch thick live mantle of microbes develops in the topsoil that traps soil particles together and enriches the soils with organic carbon and nitrogen. Known as biological desert crusts, they cover spaces between plants, stabilizing the soil against wind erosion and preventing formation of blow-sands. There is presently a lack of knowledge regarding the microbial species inhabiting these important and widespread topsoil habitats. In a variety of sites of North American deserts and semi-deserts, the investigators will embark in an effort to detect and document local bacteria important in terms of abundance or novelty. For this, they will use modern DNA technology. They will also attempt to cultivate those microbes in the laboratory. Two repositories will be established. A DNA database will enable the future recognition of crust microbes by other investigators. Cultivated bacteria will be characterized with respect to their ecological role and properties, and will be deposited in public culture collections for the benefit of the scientific and biotechnology community at large.

It is expected that these documentation and repositories will constitute the base for improved knowledge of desert bacterial communities, complementing our understanding of desert ecology, facilitating sound rangeland management, and enabling bioremediation attempts in heavily impacted arid areas.

Among the many interactions between living organisms and the mineral world, the formation and destruction of carbonates stands as one of the most conspicuous and widespread, from microscale calcification in biofilms to the accretion of coralline atolls. 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. One can say that boring cyanobacteria are intriguing. 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 will use: 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 and secondary ion mass spectroscopy (SIMS). The project also entails significant educational and outreach activities. It calls for the development of geomicrobiology materials for High School and K-12 educators, a web page for the general public, and participation in yearly outreach activities.

Hartnett
0525569
Arid desert environments are home to a unique microbe-mineral system in which cyanobacteria and microalgae form biological soil crusts. These systems are important because they significantly impact the carbon cycle and nutrient budgets in arid regions, and because they may be representative of early terrestrial biota before the rise of land plants. Biological soil crusts exist in an environment profoundly limited by the lack of water and nutrients, especially bioessential trace metals. We hypothesize that biological soil crusts maximize their retention of water and nutrients through the production of organic compounds. The soil crust community's mediation of organic compounds and the bioessential metals in the soil provides a fundamental biogeochemical link between microbes and earth-materials. Our experimental studies focus on the interactions of soil crust microbes with mineral substrates, and the nature and effects of the organic compounds produced and/or lost to the soil porewater on metabolically relevant metals. Our specific objectives are: 1) To characterize desert soil crust and the underlying soil mineralogy and geochemistry; 2) To compare crusted and uncrusted soil systems with respect to carbon and trace element composition; 3) To simulate rain events and assess changes in biological soil crust organic carbon production and metal distributions before, during and after water exposure. Electrospray ionization tandem mass spectrometry will be used to identify specific organic compounds directly from water samples, and ICP-mass spectrometry will be used to determine trace metal concentrations and distributions. This integration of organic biogeochemistry, trace element biogeochemistry, and geomicrobiology is quite unusual and our graduate and undergraduate students will gain unique trans-disciplinary research experience.

Biological soil crusts are topsoil organo-sedimentary assemblages of microorganisms that are prevalent in arid lands, where the lack of water restricts the development of much higher plant cover. This study will build on a previous survey of microbial biodiversity in North American soil crusts by including the Mohave and Chihuahuan desert regions. With the addition of these data the hypothesis that there exists a great biogeographical divide in the distribution of microbes between hot and cold deserts can be tested. Research activities will include attempts to bring into culture a variety of microorganisms that have been detected but not yet studied. In all approaches, a combination of DNA-based methodologies and traditional microbiological and systematic techniques will be used.

A sustained effort in inventorying and describing microbial populations of soil crusts is crucial in order to understand the biogeochemical functions of deserts at large, and to safeguard them in the face of ever increasing anthropogenic disturbances. These efforts will likely enhance management and preservation of arid land ecosystems. Because the trial and error approach is not appropriate for ecosystems that are inherently slow-growing, such as soil crusts, explanatory and predictive abilities have to rely on a thorough mechanistic understanding of the environmental constraints and functional properties of these ecosystems, which hinges heavily on available inventories of the microbial diversity that sustains them.

Drs. J. Touchman (Arizona State Univ), R. Blankenship (Washinton State Univ) and M. Madigan (Southern Illinois Univ.) are carrying out the genome sequencing and metabolic analysis of five photosynthetic prokaryotes. Organisms for this project were chosen to provide significantly wider coverage of genomes of phototrophic taxa than is now available. The broad goals of the project are to use the genomic data to understand the origin and evolution of photosynthesis and to explore mechanisms of the anoxygenic to oxygenic transition. The organisms being sequenced include species that live at low temperature (psychrophilic), high temperature (thermophilic), high pH (alkaliphilic), in environments subject to periodic drying, and environments high in sulfide. The organisms chosen include two heliobacteria, Heliorestis convoluta and Heliophilum fasciatum; four proteobacteria, Rhodoferax antarcticus, Rhodopila globiformis, Blastochloris viridis, and Thermochromatium tepidum; and one cyanobacterium, Leptolyngbya (a.k.a. Oscillatoria) amphigranulata. The proteobacteria include members from the beta and gamma divisions and one that contains bacteriochlorophyll b as its principal photopigment. The finished, annotated genome sequences are being used to fill large gaps in the available genomic data for photosynthetic prokaryotes. The metabolic capabilities of these organisms are also being analyzed using pathway analysis software tools. Each organism has individual characteristics that justify its inclusion in a genome-sequencing project, including evolutionary relationships, agricultural applications and environmental aspects.
Dr. Touchman is involved in the Be a Biologist program at ASU. All of the investigators are involving undergraduate and high school students in sequence analysis and annotation activities in their labs.

Cyanobacteria are among the most common, widespread and environmentally significant agents of bio-erosion, boring microscopic galleries as they grow within carbonate substrates. The mechanisms by which they achieve this against chemical equilibrium are poorly known. Our work showed that boring is likely driven by the action of membrane-bound Ca2+ transporting ATPases, powered directly by photosynthetically derived ATP, acting to maintain the levels of free Ca2+ in the interstitial space of the distal borehole very low, a situation that promotes local calcite dissolution, with Ca2+ then travelling intra-cellularly down a concentration gradient in the filament to be released into the outside medium. We intend here to advance our understanding of the boring mechanism at the molecular, genetic and cellular level and to test its universality, by probing its variability in essence or detail with respect to microbial agents other than the models previously used, and for mineral substrates other than CaCO3. We will achieve this through genetic and cellular characterization of the Ca2+ transport systems, molecular biology techniques and micro-imaging techniques based on confocal microscopy of model microbes. We will also interrogate natural complex communities of boring microorganims from a variety of geographic and mineralogical settings (limestones, dolostones and biogenic carbonates) for their compliance with the Ca2+-transport mechanism. Finally, renewed efforts of cultivation will be used to address the mysterious excavation of phosphates, dolomite, and magnesite, a capacity that model microbes lacks, but is assumed to take place in nature.

Moving from descriptive to mechanistic models of understanding, as this work will attempt, remains one of the frontiers of geobiology. The research will attempt to ascertain the exact mechanisms by which microbes can use the energy from the sun to power dissolving minerals like limestone, when geochemistry would predict they should not dissolve at all. This knowledge would offer the potential to explain several biological and geological phenomena of widespread importance. For example, it will involve the study of physiology of calcium transport, the same phenomenon that drives muscle movement in humans, in a very different setting. It may also contribute to our ability to predict the consequences of global acidification of the oceans with respect to coastal limestone dissolution. It will contribute basic knowledge with potential applications in biomaterial science, potentially even providing a means for combating calcification in engineered systems, or for deterring the bio-deterioration of buildings and monuments. The research will be intricately embedded with activities in education, training, dissemination and outreach.

Intellectual Merit. Some microorganisms, notably cyanobacteria, are known to synthesize secondary metabolites that serve a sunscreen function to protect them from damaging effects of exposure to ultraviolet radiation (UV). In cyanobacteria, two main types of such compounds have been described: scytonemin, a unique alkaloid of interesting biological properties, and mycosporine-like amino acids (MAAs), a family of small water-soluble compounds derived from amino acids. In the past few years we have successfully developed the cyanobacterial strain, Nostoc punctiforme ATCC 29133, to study the genetic and molecular basis of such sunscreens. Great strides have been made during the past few years in this field of research. In this project we will be probing aspects of sunscreen biology that relate to the association of gene function with cell compartmentalization, to their regulation and their evolution. This work will provide links between existing knowledge at the molecular, physiological and environmental levels of organization, eventually enabling an integrated understanding of microbial sunscreens and setting the basis for their potential application.

Broader Impacts. Sunscreens are important factors in the ecological physiology of adaptation of many organisms in Nature, from plankton to corals at a time when increased UV-fluxes are of concern. Microbial sunscreens have attracted interest not only because they represent novel classes of secondary metabolites, but also because of their potential applicability for biotechnological purposes.
Additionally, this research will represent a very attractive opportunity to populate ongoing efforts in outreach to STEM underrepresented minority K-12 students and the general public in Arizona, where protection from UV exposure is a constant concern, and where, we think, microbial sunscreens may offer an enticement to get to know the world of science.

Carbon cycle models are used to assess how future carbon policy scenarios will influence atmospheric carbon pools and climate. The accuracy of those models depends on our understanding of major pathways in the carbon cycle. One such pathway, the decay of dead plant material (litter), is responsible for releasing more carbon into the atmosphere each year than the combustion of fossil fuel. Litter decay in forests is reasonably well understood, but both the rate and temporal pattern of litter decay are different in deserts. The effects of direct sunlight on litter may increase the rate of decay, while the lack of moisture may reduce microbial activity and decrease the decay rate. This project will test whether the optical properties of litter produced by desert plants contribute to the different pattern of litter decay. Laboratory and field experiments will be used to test the importance of sunlight as an agent of litter decay relative to other mechanisms such as microbial activity.

This research, which will be conducted in the Sonoran Desert, will contribute to our understanding of carbon cycling in deserts and in other ecosystems where litter is exposed to intense sunlight (e.g. grasslands and agricultural systems).The investigators will develop a website that contains a guide to litter decomposition for K12 students, a companion guide to aid teachers in conducting litter decomposition experiments, and they will solicit K12 teachers to take part in this experiment. This project will provide research experience for K12 students and teachers, and undergraduate and graduate students.

Biological soil crusts (or “biocrusts”) are communities of microorganisms that develop naturally on the surface of soil from arid and range lands based on the photosynthesis of tiny, plant-like organisms known as cyanobacteria. In unaltered settings biocrust can cover much of the landscape, providing several important benefits to the ecosystem. They can take up nutrients from the air, for example, increasing soil fertility. And, importantly, they build veritable surface crusts that protect the soil from erosion by wind and water and prevent the formation of fugitive dust. Their effects are measurable both locally and globally. Unfortunately, biocrusts are negatively impacted by several human activities, including cattle grazing, agriculture, urban sprawl, and global warming, among others. This often leads to the degradation of soil quality and increases in fugitive dust formation. During the last decade, the rehabilitation of biocrust has become a goal in ecological restoration efforts in many countries, including the US. However, less than optimal outcomes on this front made it patent that knowledge about the basic biology and ecology of these communities is insufficient. While we have learned much about the biology of the all-important photosynthetic microbes that build these crusts, the lack of success in producing new crusts pointed to some yet unknown factor or factors that are crucial for their growth and overall fitness. This research focuses on the non-photosynthetic microbes that establish specific biological relationships with the photosynthetic microbes. This project will provide training to graduate and community college students and will provide critical information necessary to advance biocrust restoration.

The project will address this knowledge gap experimentally by first rigorously identifying and characterizing the main non-photosynthetic microbial actors involved in such interactions using a combination of pedigreed cultivation and molecular approaches. Subsequently, the project will study the mechanistic nature of the interactions at play, by reconstructing the mutualistic interactions in culture and by experimentally disrupting the need for a mutualistic interaction in field samples. Finally, the project will assess the importance of these interactions as determinants of growth and fitness in natural biocrusts. Because of their particularly crucial role, the project will focus on microbial interactions with pioneer cyanobacteria and on early stage biocrusts. The plan calls for three discrete tasks, each driven by specific hypotheses based on preliminary evidence. These are: 1) that interactions are a staple of pioneer biocrust forming cyanobacteria, 2) that these are based on mutualisms that are specific with respect to purpose and partner, and 3) that predatory bacteria constitute a universal, ecologically significant loss factor in biocrusts. The project includes efforts to involve stakeholders in land management, to facilitate technological transfer, and contributes significantly to science workforce development at various levels.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.