A REU Site grant was funded at Biosphere 2 – and B2 is doing an abbreviated recruitment so
that we can run with a 2010 summer program. Our focus is on environmental and Earth system
sciences. We can bring 10 students here – they will be housed on the Biosphere 2 campus and
work in B2 and UA labs, potentially some southern Arizona field sites too. The program is 10
weeks, looking like first weekend in June through mid Aug. We provide travel costs to Tucson
(up to $500), the room costs, a $5000 stipend, and a food allowance. There is also money to
send them to a conference to present their findings as appropriate.
Our program is unique in many respects – we‟re thematically working with a very
interdisciplinary approach to environmental and Earth systems science that links ecology,
biology, geology, chemistry, atmospheric sciences, hydrology, etc. One of our themes is
questions of scale: (a) each individual project is a smaller part of an integrated whole, and (b) the
B2 structure itself and the questions associated with research here look at the ability to use tight
control across large spatial scales. Additionally, students will be part of B2‟s outreach activities
– a unique training opportunity, as they will work within our models for improving science
communication. The program will function as 3 parallel tracks: (1) their individual research
project, (2) their research in the broader context of Earth systems science, and (3) their research
in the context of society and the culture of science.
We‟re working on an online application form now, but we will require:
1) A completed online Application Form.
2) An unofficial copy of your Academic Transcript. If accepted into the REU program,
applicants will be required to provide an official copy before arriving in Tucson to start the
3) Letters of recommendation from two persons. Individuals that are able to comment on
the applicant‟s academic ability are preferred, and should be faculty advisors at the student‟s
home institution, or mentors from previous research activities. Please provide each of your
respondents with the Applicant Recommendation form that is available in the links to the left or
4) A two-page essay that describes your background and interest in the B2 REU program.
You may want to include: (a) your general career and science interests and goals within
environmental and Earth systems sciences, (b) what experiences you have had that qualify you
for this research program, (c) previous research experiences and what you got out of them, (d)
what you hope to achieve by spending your summer conducting research with Biosphere 2, how
the program will contribute to your degree program, (e) anything else that you think would be
helpful in evaluating your application. Please be as specific as possible, the essay helps us make
placement decisions among many highly qualified applications. We recommend a clear focus on
the goals, features, and faculty mentors associated with this REU program. Try to emphasize
your recent professional and educational experiences and avoid describing events during
childhood. Essays should be 2 pages max in length with single-spacing and a blank line between
consecutive paragraphs, a legible font (11-12 point), and 1 inch margin – they are pasted into the
application form you will fill out. We‟re looking for a min 3.0 GPA. Students have to be US
citizens or permanent residents – we will only be able to take students who will be incoming
sophomore, junior, or seniors in the Fall following the program.
Below are attached descriptions of available projects. Please pass around to students you think
might be interested.
REU Site: Environmental and Earth Systems Research at Biosphere 2
PI: Mitchell Pavao-Zuckerman Co-PI: Katerina Dontsova
Project Summary: The University of Arizona (UA) is proposing a new 10-week summer
Research Experiences for Undergraduates site: the Environmental and Earth Systems Research at
Biosphere 2 (B2-EESR REU) program that will take advantage of the unique nature of the UA
Biosphere 2 (B2). B2 provides everything needed for an outstanding REU experience, including
housing at its “Student Village,” and opportunities to participate in a cutting-edge university-run
suite of experimental projects. B2 facilities are open and accessible to the public, providing the
students additional opportunities to interact with a broad spectrum of stakeholders. The specific
objectives for an individual student in this summer REU program are to: (1) develop research
skills in laboratories, observations and/or computer modeling; (2) achieve a broad understanding
of Earth system science; (3) experience the cross-disciplinary collaborations that characterize
work in Earth system science; (4) network within the scientific field that will aid in their further
education and research; and (5) develop an understanding of practical aspects of pursuing a
career in science, including the nature of graduate school. Research projects conducted through
this program will contribute to an interdisciplinary understanding of the Earth system with
particular focus on the critical zone, and how ecosystems respond to variation and changes in
climate. Projects will draw from research conducted „under the glass‟ at B2 as well as from local
CZO sites, allowing the students to learn first-hand how model and real world systems are used
to generate scientific understanding.
The targeted students are undergraduates majoring in biological and physical sciences relevant to
Earth systems science at institutions without significant research opportunities. Location in AZ
and partnership with local community colleges enhances our ability to reach Hispanic and Native
American students. Partnerships with the UA Graduate College Summer Research Opportunities
Program (SROP) will facilitate broad recruitment for this REU and also leverage many
successful summer workshops and seminars in professional development for our students. The
B2-EESR REU is designed to provide parallel „tracks‟ to give students experience in an
individual research project, the context for how their part fits into a broader understanding of the
Earth system, understanding of the responsibilities and skills required for translation of science,
and their own professional development as young researchers. A supplemental workshop will
focus on the ethical implications and considerations involved in doing environmental and Earth
systems research. This pilot REU program will make important steps in training the next
generation of diverse and interdisciplinary scientists for environmental and Earth system
Potential Research Experiences
At UA, we are building a program to bridge the gap between laboratory- and field-scale studies
by utilizing the unique infrastructure of Biosphere 2. Biosphere 2 offers unique opportunities for
the exploration of complex questions in Earth Sciences because of its ability to combine varying
scales, precise manipulation and fine monitoring in controlled experiments. First, it allows the
control of environmental variables at a considerable spatial scale, such as in the different
wilderness biomes represented under the glass. Second, it also permits the utilization of novel
techniques and instruments that are not amenable to field studies. This ability for high resolution
measurements and fine environmental
manipulation is crucial for the development of experiments of more mechanistic nature.
Biosphere 2 has the potential to provide unique contributions to science in the understanding of
how earth systems respond to environmental change. In the past, research at Biosphere 2 resulted
in significant contributions in aspects such as ecosystem responses to elevated carbon dioxide
concentrations. Under the new administration by the UA, we intend to extend this approach to
the study of water and temperature. By building upon the academic excellence of the UA and its
large external scientific network in hydrology, geology, geochemistry, ecology, biology, physics,
engineering and atmospheric sciences, we are developing a strong multidisciplinary team of
researchers who are undertaking the design and deployment of top-notch science to address
complex questions in environmental sciences. Here we offer sample projects from faculty
mentors who are affiliated with B2, the Critical Zone Observatory (CZO), or both.
Project A. Coupling subsurface ecohydrology and biogeochemistry.
Mentor: Dr. Jon Chorover, Soil Water and Environmental Sciences.
Students working in the Chorover lab would have the opportunity to be involved in a
collaborative and multi-disciplinary Critical Zone Observatory (CZO). The "Critical Zone" is
defined as that portion of the Earth's terrestrial surface that extends from the outer periphery of
the vegetation canopy to the lower limit of ground water penetration (National Research Council,
2001 "Basic Research Opportunities in Earth Sciences"). REU students would have an
opportunity to work at one of two sites within the UA CZO, including the Santa Catalina
Mountains (AZ) and the Jemez River Basin (NM). Projects in the Chorover lab would focus on
coupling field work and laboratory studies to understand subsurface biogeochemical processes at
these sites, and the interaction of biogeochemistry with ecohydrology and landform evolution.
Project B. Using environmental gradients to link soil biology and ecosystem functions.
Mentor: Dr. Mitchell Pavao-Zuckerman, B2 Earthscience.
Understanding the contribution of organisms to biogeochemical cycling is one of key points in
linking across scales in ecosystems. Additionally, the response of organisms to their local
environment reflects one way in which ecosystems directly respond to environmental variation
and changes in climate. Pavao-Zuckerman‟s lab focuses on the connections between
environmental variability, the structure of soil food webs, and biogeochemical cycling. The
biomes of B2 represent excellent macrocosms for such studies due to the range of environmental
variation between biomes and the degree of control within them. He has been studying microbial
and microfaunal diversity, litter decomposition, and nitrogen transformations in B2 and wild and
urbanized environments in southwestern Arizona. Research projects for REUs would focus on
microcosm studies and observational studies in the B2 biomes that use climatic differences and
resource availability gradients in the biomes to look at the interaction of soil food webs and C
and N transformations.
Project C. The role of root-mycorrhizae-bacterial associations on the extent of total
weathering vs. chemical denudation.
Mentor: Dr. Katerina Dontsova, B2 Earthscience.
Establishing the role of rootmycorrhizae- bacterial associations on the extent of total weathering
versus chemical denudation represents an important grand challenge within the broader
bioweathering realm. Specifically, to what extent do biota (plants and microbes, differentially)
contribute to weathering rock to form high surface area secondary solids while also diminishing
the loss of weathering products in solution. Biota can contribute to weathering, while still
diminishing system losses of lithogenic nutrients, in several ways, for example by lithogenic
nutrient uptake into biomass, the nucleation and precipitation of colloids in association with
biomolecular matrices, etc. We would like to quantify and predict biotic weathering based on
parameters that can be readily measured or ones that we have tools to predict/model. The
challenge of quantification is that it is difficult to separate weathering by plants from microbial
and fungal weathering because they are both driven by carbon derived from plant biomass.
Experimental designs that involve studying plant effects with treatments to kill microbes, or
studying fungal and bacterial weathering without plant hosts present does not replicate
conditions present in field soils, because plant growth is suppressed without mycorrhizal fungi
that improve mineral nutrition, while bacterial and fungal growth is greatly diminished in the
absence of a direct supply of plant-derived carbon. Thus plant and microbial/fungal effects are
not simply additive, but rather synergistic. Mesocosm studies with and without plants will be
conducted and soil weathering denudation, and biotic uptake of weathering products will be
quantified to establish contribution of biota to weathering and denudation. Since soil microbial
biomass is much smaller than the total biomass in plant tissues, its ability to serve as a sink for
weathering products is likewise much smaller. This ability of plants to uptake and retain
lithogenic elements increases total weathering and decreases denudation. Balogh & Brunstad et
al. (2008) have shown that in plots that contain non-vascular biomass only (lichens) weathering
is lower and denudation is higher than in plots with vascular plants. Modeling by Godderis et al.
(2009) also indicates that removal of plants results in marked increases in denudation.
Project D. Abiotic effects of woody plant cover.
Mentor: Dr. David Breshears, School of Natural Resources and Environment.
The overall theme of the research for this project will be related to gradients of woody plant
cover, which can span from grassland to forest. More specifically, key questions focus on abiotic
effects of woody plants and their responses to changes in climate and land use. Specifically
projects could include assessments of changes in near ground microclimate conditions associated
with different densities of woody plant cover, spatial variation in dust production as a function of
woody plant cover, and or plant water stress preceding tree mortality along vegetation gradients.
Approaches would include hemispherical photography and computational assessments of solar
radiation regimes, measurements of dust production using a variety of instruments, and/or
measurements of plant water stress and related physiological metrics.
Project E. Native versus exotic desert grass mortality.
Mentor: Dr. Travis Huxman, B2 Earthscience.
The susceptibility of native and exotic grasses to drought and temperature, and potential
competitive interactions will be evaluated by growing different species in pots across the
environmental gradients at B2. We are designing manipulative experiments in B2 to investigate
the impact of droughts, rising temperatures on native and invasive grass communities and how
these communities partition resources (soil moisture, nutrients) in these changing environmental
conditions. Modeling studies will address the impact of rapid vegetation changes and
implications on ecohydrological processes and desertification. These studies will provide
suitable cases to link across scales and to link data with modeling exercises.
Project F. Climate and coupled C&N cycles.
Mentor: Dr. Kathleen Lohse, School of Natural Resources and Environment.
We are examining how increased variability in precipitation will alter coupled soil carbon and
nitrogen cycles and losses and how these interactions will feedback on net primary productivity
(NPP). Specifically, we will asking 1) How does variability in precipitation (intensity, frequency,
duration) influence soil C and N cycling and partitioning of loss pathways? and 2) how do these
processes feedback on productivity? I will address these questions through a set of lab and field
experiments with variable rainfall exclosures along an elevation gradient (climate) in the
Catalina Mountains of Arizona. Possible REU projects associated with this project include
estimating plant cover, aboveground productivity, belowground biomass, trace gas loss
associated with different intensities or frequencies, and changes in nutrient availability with
Project G. Integrating multiple scale measures of carbon and water flux.
Mentor: Dr. Greg Barron-Gafford, B2 Earthscience.
Research within this project will focus on integrating measures of soil, leaf, plot, and ecosystem
scale carbon and/or water flux. Research projects could be carried out in one of two venues.
Potential sites include a space-for-time substitution of sites representing a woody plant
encroachment (WPE) gradient or a mixed conifer forest. WPE refers to the large-scale
vegetative change of an ecosystem from a grassland to a shrubland or woodland. This transition
in vegetative cover has the potential to alter local and regional carbon and water flux, as the
grasses and trees differ in their rates of CO 2 uptake, sensitivity to temperature, responsiveness to
precipitation, and amount of water use. Previous work within the WPE sites has characterized
the temperature sensitivities of leaf, soil, and ecosystem fluxes. However, a further
quantification of how temperature varies within in a canopy, how efficiently these two growth
forms utilize light, and how they respond to variations in atmospheric CO 2 concentrations are
needed. Within the mixed conifer forest, we will estimate the component fluxes within the sub-
canopy and canopy of various coniferous species. Potential projects include quantifying
measures of carbon and water flux in transects radiating from the tower to capture variation due
to slope, aspect, and degree of canopy cover. Methods within either setting will include
measures of carbon flux using a variety of scale-specific techniques, measures of plant water
status, and hemispherical photography for quantification of incoming solar radiation (a driver of
sub-canopy biological activity and soil water loss).
Project H. Volatile organic compounds in semi-arid ecosystems.
Mentor: Dr. Kolby Jardine, B2 Earthscience
During photosynthesis, plants fix atmospheric carbon dioxide into organic material but release a
fraction of it back into the atmosphere in the form of volatile organic compounds (VOCs). By
participating in photochemical reactions resulting in the production of secondary organic
aerosols and toxic compounds like ozone, VOCs have a strong influence on air quality and
climate. Initial research indicates that natural biogenic VOC emissions greatly exceed human
caused sources by a factor of 10. A preliminary study during April 1999 demonstrated that
significant emissions of terpenoids (isoprene and monoterpenes) and oxygenated VOCs are
released by plants in the Sonoran Desert (Geron et al., 2006). Due to the water availability, high
temperatures and solar insolation, and productivity of this ecosystem during the Monsoon, we
suggest that during this season the Sonoran Desert emits large amounts of VOCs into the
atmosphere which impact air quality and climate and may represent a significant fraction of the
net exchange of CO_2. These conditions may not only result in large emission rates of the VOCs
typically observed from forests, but may also include the emissions of VOCs not previously
detected in the atmosphere. This is in part because of the high diversity of plant species, many of
which are unique to the Sonoran Desert, and the sudden availability of water into a dry system.
While cooler than the previous summer months, the high temperatures during the monsoon will
favor the volatilization of compounds that are not gasses at lower temperatures. We propose to
conduct a long term field study where ecosystem scale fluxes of CO_2 and VOCs are monitored
at a field site near Tucson, AZ before, during, and after the desert monsoon. Our hypothesis is
that the high heat and water availability during the monsoon will lead to large emissions of
biogenic VOCs that will strongly alter the regional air quality and climate of the southwest. In
addition, we suggest that the water limited ecosystem of the Sonoran desert suddenly becomes
carbon limited during the monsoon as a large fraction of the assimilated carbon is lost as VOCs.
To test these ideas, we will set up a field site with a meteorology and chemistry tower at a
Sonoran Desert field location to be determined. Instruments such a proton transfer reaction mass
spectrometer (PTR-MS) and two infrared gas analyzers (for carbon dioxide and water vapor
concentrations and for stable isotope analysis of water vapor) will be housed in a small mobile
laboratory. Measurements will consist of branch enclosure flux studies, ambient concentration
monitoring, and ecosystem flux measurements using eddy covariance (PTR-MS), and relaxed
eddy accumulation (REA). VOC samples collected on tubes packed with solid sorbent will be
analyzed by gas chromatography-mass spectrometry (GC-MS) at Biosphere 2.
Project I. Solute fluxes in surface water.
Mentor: Dr. Jennifer McIntosh, Hydrology and Water Resources.
McIntosh is a Co-PI on the University of Arizona‟s recently funded NSF Critical Zone
Observatory (CZO) project, and lead for the Surface Water Dynamics subtheme. She proposes to
involve NSF REU students in CZO research in the Santa Catalina Mountains and Jemez River
Basin. Potential student research questions include: How do solute fluxes in surface waters vary
as a function of bedrock lithology and age? How do weathering rates vary as a function of
hillslope aspect and water transit times? What are the dominant sources of organic carbon to
surface streams, and how do these inputs vary across the landscape? Student research would
involve field sample collection, laboratory analyses, and interpretation of data.
Project J. Modeling of soil water dynamics.
Mentor: Dr. Marcel Schaap, Soil Water and Environmental Sciences
A: students would participating in _modeling_ (computer simulation of ) of soil-water dynamics
in selected soils in the CZO project or the B2 hillslope project. In particular, they would study
the relation between soil (geo)morphology and drainage and vegetation dynamics. The students
would obtain knowledge on how to implement dynamic eco-hydrological systems in computer
models and interpret simulation results.
B: students would participate in _measurement_ of water dynamics in B2 hillslope soils. In
particular students would use an existing 1-Dimensional representation of the B2 hillslope soils
to determine soil water dynamics, but also soil chemical weathering rates. The students would
obtain experience with complex measurement and control systems.
Project K. Using digital images to link the hydrologic cycle and ecosystem phenology.
Mentor: Dr. Shirley Kurc, School of Natural Resources and Environment.
For water-limited ecosystems worldwide, global climate models predict (1) changes in the intra-
annual variability of precipitation and (2) a decrease in average annual precipitation. These
changes in the timing, frequency and magnitude of precipitation will alter the pulses of soil
moisture that drive basic phenological activity in water-limited ecosystems, such as flowering
and green up. One interest of the Kurc Lab is to understand phenological triggers in water-
limited ecosystems caused by precipitation induced variability in soil moisture. As a means to
get at this, we collect daily digital images within the footprint of an eddy covariance tower.
These images serve as a robust digital archive of phenological changes within the ecosystem at a
daily scale. Using MATLAB® image-processing tools, we can develop a quantitative measure
of phenology from these images which can be directly linked to meteorological and flux data
collected at the tower. Consisting of a team of scientist, MS student, and undergraduate student,
the Kurc lab has investigated one measure of digital image-derived greenness and one measure
of digital image derived flowering in a single plant species using these images with success.
However, each of these images has multiple species that can be investigated, and multiple
methods of analyzing the images need to be explored.
Because most everyone can connect phenological activity (e.g. spring bloom and fall color are
tourist attractions), phenology is an easy topic for engaging students in environmental science.
An REU student would select a plant species within a camera image and using the literature,
develop hypotheses about the phenological triggers (e.g. temperature, rainfall) for their species.
Then, the student can inspect the images by eye to determine the timing of phenological events.
Next, using learning modules developed by Dr. Kurc, a student with computer programming
experience can quickly learn to process the images in MATLAB®; this has already been
confirmed with the current undergraduate working in the Kurc Lab. The student can then explore
various methods and develop an index within MATLAB® to automatically detect their
phenological phases, and compare their index to results from their visual inspection. Lastly, the
student will use meteorological data and flux data from the tower to explain the timing of their
phenological events to determine if their hypotheses were correct. Project Objectives: (1)
understand phenology and the triggers of phenological events; (2) write and test hypotheses; (3)
develop computer programming skills through image processing; (4) make projections about
how climate change might impact the timing of phenological events; (5) create a scientific
presentation of their work in poster, talk, or paper form.
Project L. Interaction of landscapes, pedogenesis and mass fluxes.
Mentor: Dr. Craig Rasmussen, Soil Water and Environmental Sciences.
The proposed REU project would include quantifying the interaction among landscape position,
soil formation and elemental mass flux. Landscape scale variation in chemical and physical
weathering has emerged as a key component modulating terrestrial biogeochemistry. In
particular, CO2 consumption associated with mineral weathering and the interaction of this
process with pedogenesis and erosion appear to be significant factors controlling long-term
patterns in atmospheric CO2 concentration. The REU project would specifically focus on the
hypothesis that weathering and mass flux vary predictably with landscape position and climate
forcing. Testing of this hypothesis will be accomplished by quantifying the mass flux of
elements such as Na and Si from soil profiles located at various landscape positions on north
facing slopes embedded within various ecosystems along the environmental gradient
encompassed by the Santa Catalina Mountains. The project would include a combination of field
sampling, physical and chemical laboratory analyses, and data synthesis with the goal of
generating a dataset suitable for publication and/or the pursuit of further funding to address
broader scale biogeochemical processes.