Research and Teaching

Overview | Subsurface Biogeochemistry | Other Biogeochemistry Projects| Fe Biomineralization | Paleo/Astrobiology: Fe-based microbial life systems | Aquatic Ecosystem Science | Molecular Microbial Ecology | Biogeochemical Modeling | Teaching | References

Overview

I have a broad range of research and teaching interests in the biogeochemistry and geomicrobiology of soil and sedimentary environments. These interests are interdisciplinary in nature, integrating the fields of low-temperature aqueous geochemistry, microbial ecology and physiology, sediment chemical diagenesis, and ecosystem science. My specific area of expertise is microbial processes in hydromorphic soils and surface/subsurface sediments, and the influence of these processes on the fate of various types of inorganic and organic materials (both natural and contaminant) in sedimentary environments. Much of my work in recent years has been focused on process-level, experimental studies (including the use of pure culture model systems) of the kinetics and mechanistic controls on biogeochemical and geomicrobiological processes in soils and sediments. However, I have a long standing interest in field research dating back to my doctoral work on sulfur biogeochemistry in Chesapeake Bay sediments, and I am currently involved in several major field projects, including a NSF/EPA project on Hg biogeochemistry in Alabama rivers, and two DOE-funded projects pertaining to bacterial metal reduction and biomineralization in shallow subsurface sediments. I also have considerable experience and a burgeoning interest in numerical modeling of biogeochemical processes in surface and subsurface sediments.

Subsurface Biogeochemistry

An important theme of my current research revolves around several DOE (EMSP and NABIR programs) sponsored projects (see the research funding history attached to my list of publications, and the description of these research projects on my web-site) focused on process-level studies of bacterial Fe(III) oxide reduction and Fe redox cycling in relation to trace/contaminant metal biogeochemistry in subsurface sediments. These projects include studies of fundamental geochemical and microbiological controls on Fe(III) oxide reduction; the potential for immobilization of trace metals in carbonate minerals formed during bacterial Fe(III) oxide reduction; the interaction between nitrate and Fe(III) oxide reduction in anaerobic sediments, with specific focus on nitrate-dependent oxidation of solid-phase biogenic Fe(II) compounds; and the dynamics of uranium(VI) in Fe(III) oxide-reducing subsurface sediments. Most of these projects are laboratory-based and directed toward evaluating the potential controls on natural (intrinsic) and accelerated subsurface metal-radionuclide bioremediation. One field-based project is examining the heterogeneity of microbial Fe(III) oxide reduction potential in shallow subsurface sediments in relation to geochemical and geophysical properties. I am also a co-PI on a new DOE-NABIR Field Research Center project examining the potential for in situ immobilization of uranium in fractured subsurface sediments at Oak Ridge National Laboratory in Tennessee. This project provides a vehicle for applying the results of our ongoing mechanistic laboratory research to understanding the dynamics of Fe(III) oxide reduction and associated biogeochemical processes in a real subsurface sedimentary environment.

Other Biogeochemistry Projects

I have conducted (in collaboration with R.G. Wetzel, now at UNC Chapel Hill) a NSF project on organic carbon metabolism in freshwater wetland sediments, and the role of microbial Fe(III) oxide reduction in regulation of methane production and emission to the atmosphere. This is an ongoing project (now funded indirectly through research overhead) which has recently led to the discovery that dissimilatory metal-reducing bacteria (DMRB) can transfer electrons to solid-phase humic substances in soils and sediments. Although the ability of DMRB to reduce soluble humic substances and thereby promote (via electron shuttling mechanisms) the reduction of oxidized metals is well-recognized, our findings represent the first demonstration that solid-phase humics can be enzymatically reduced by bacteria. These findings have important implications for sediment biogeochemistry because solid-phase humics are generally 100 to 1000-fold more abundant (on a bulk sediment basis) than dissolved humics in sediment pore fluids. Our findings indicate that reduction of solid-phase humics has the potential to both accelerate the reduction of oxidized metals (e.g. Fe(III) oxides) as well as influence overall electron balance in organic-rich sediments.

I was a co-PI on a recently completed (June 2003) interdisciplinary NSF/EPA Water and Watersheds project examining the biogeochemistry of mercury in riverine ecosystems in Alabama, for which my laboratory was in charge of sediment biogeochemical characterization and microbial mercury transformation measurements. This work on sediment Hg biogeochemistry has led to participation (as Co-PI) in NSF Biocomplexity (Coupled Biogeochemical Cycles) and Ecosystem Studies proposals, both headed-up by Cindy Gilmour of the Philadelphia Academy of Natural Sciences, to examine mechanisms of net microbial methyl-mercury production in the Experimental Lakes Area in northwest Ontario. These projects are designed to complement the joint U.S./Canadian METAALICUS project, whose goal is explore the connection between atmospheric Hg loading and Hg biogeochemistry and trophodynamics in northern lake ecosystems. Finally, I have conducted studies of the controls on phosphorus mobility in anaerobic sediments, and more recently of aerobic bacterial Fe(II) oxidation and the potential for microscale microbial Fe cycling at redox interfaces (see further descriptions below), both with support from The School of Mines and Energy Development at The University of Alabama.

Fe Biomineralization

I am currently collaborating with several interfacial geochemistry colleagues (e.g. at the Environmental Molecular Sciences Laboratory at PNNL; note collaboration with Y. Gorby on DOE-EMSP U(VI) reductive immobilization project) on developing a more detailed understanding of how dissimilatory metal oxide-reducing microorganisms influence the mineralogy and surface chemical properties of Fe(III) oxide-bearing soils and sedimentary materials, through application of high resolution TEM with lattice-fringe imaging, Mössbauer spectroscopy, and X-ray spectroscopy/microscopy. Of particular interest is the physical and chemical nature of Fe(II)-bearing surface phases formed during bacterial Fe(III) oxide reduction, their metal sorption properties relative to unreduced oxide surfaces, and the potential for such phases to incorporate and immobilize contaminant metals. This is currently a subject of intense interest within the subsurface biogeochemistry community given the profound influence such modifications may have on the fate and transport of metals and radionuclides in the subsurface. I am working with Ravi Kukkadapu and John Zachara at PNNL/EMSL on analysis of Fe(III) oxide mineralogy and bacterial reduction end-products in the coastal plain aquifer sediments which we have been studying through the DOE-NABIR project on the heterogeneity of bacterial Fe(III) oxide reduction potential in subsurface sediments, and such collaborations will be extended through the new NABIR FRC project on which Zachara is a co-PI. In addition, I anticipate development of collaborations with Ken Kemner at Argonne National Laboratory on XAS analysis of Fe, S, and U-bearing minerals generated during experimental studies of the interaction between bacterial Fe(III) oxide reduction, bacterial sulfate reduction, and biotic/abiotic U(VI) reduction in subsurface sediments.

Paleo/Astrobiology: Fe-based microbial life systems

A new area of research, which evolved out of our recent studies on bacterial Fe(II) oxidation and microbial Fe cycling, involves studies of microbially-catalyzed Fe redox cycling in layered microbial communities, with specific goal of studying of natural and experimental systems as analogs to possible Fe-based microbial life on ancient Earth and Mars (note current participation in NASA Astrobiology project led by Jill Banfield at U.C. Berkeley). Such studies include the application of molecular techniques (fluorescence in situ hybridization with 16S rRNA probes) for tracking Fe(III)-reducing and Fe(II)-oxidizing bacteria in mixed culture, utilization of novel voltammetric microsensors for determination of dissolved Fe(II) concentrations at submillimeter resolution (collaboration with G. Luther at the University of Delaware), and determination of Fe stable isotope fractionation during bacterial Fe redox transformations. I participated this spring in the submission of major proposal to the NASA Astrobiology Institute program to develop a virtual research institute focused on Fe- and S-based microbial systems, and we recently received word that this project (entitled Biospheres of Mars: Ancient and Recent Studies) has been selected for funding. In addition, I was a co-PI (with B. Beard and C. Johnson at University of Wisconsin, and S. Benner at Desert Research Institute) on a recent (December 2002) NSF Biogeosciences proposal submission entitled “Biotic and Abiotic Controls on Iron Isotopic Geobiological Signatures in Authigenic Magnetite and Siderite”, which seeks a comprehensive analysis of Fe isotope fractionation during bacterial Fe(III) oxide reductive dissolution and associated Fe biomineralization. This project involves extensive experimental studies, which will be extended through measurement of the Fe isotopic composition of Fe(II)-bearing minerals and (when possible) dissolved Fe(II) in sediment pore fluids in natural Fe(III) oxide-reducing environments, including modern sediments and materials from the rock record in which reductive transformations have produced reduced Fe mineral phases. The fundamental goal of the proposed research is to advance the use of Fe isotopes as a biosignature and as a paleoenvironmental indicator of ancient environments.

Aquatic Ecosystem Science

I recently led a major collaborative effort (with scientists at UA, University of New Mexico, University of Florida, University of Vermont, and the South Florida Water Management District) to develop a project in the new NSF Frontiers in Integrative Biological Research program, which would examine the role of biogeochemical cycling and microbial-detrital food web function in the restoration of the Kissimmee River ecosystem in Florida. The Kissimmee River Restoration represents the largest river ecosystem restoration effort ever attempted, and provides a compelling venue for studying how hydro-biogeochemical processes and their linkage with detrital organic matter and nutrient processing influence aquatic ecosystem restoration. The interdisciplinary research would include monitoring and modeling of hydrological fluxes and their impact on biogeochemical processes in restored vs. impacted zones; molecular genetic analysis of microbial community structure/diversity across spatial and temporal gradients in relation to biogeochemical fluxes and the function of the microbial/detrital food web; and linked hydrological and spatially-explicit systems dynamics modeling of ecosystem function. Although the planning proposal submitted in November 2002 was not selected for funding, my engagement in this project was significant in that it stimulated my long-standing interest in ecosystem science, specifically in relation to the often-neglected role of biogeochemical processes in ecological restoration.

Molecular Microbial Ecology

Embedded in all of the studies described above is the goal of relating the spatial-temporal distribution of key functional groups of microorganisms to observed physiochemical properties and patterns of biogeochemical flux. Recently introduced molecular biological approaches for analysis of microbial communities in natural (and engineered) environments will be applied to achieve this goal. These techniques offer an unprecedented opportunity for rapid and accurate assessment of bacterial communities in virtually all types of environmental (as well as clinical) materials, and for testing hypotheses related to the role which microorganisms (e.g. ones with highly specialized metabolic capabilities) may play in controlling biogeochemical fluxes at environmental interfaces. Such studies initially revolve around the use of 16S rRNA/rDNA, but will eventually include analysis of the expression of specific genes involved in relevant microbial metabolic processes. We have recently used 16S rDNA techniques for analysis of aerobic bacterial diversity and community succession in freshwater wetland biofilms (Jackson et al., 1998; Jackson et al., 2000a; Jackson et al., 2000b), and are currently employing this approach for analysis of sediments undergoing redox shifts between nitrate-reducing, Fe(III)-reducing, and nitrate-dependent Fe(II)-oxidizing conditions (Weber et al., 2002). During a sabbatical leave last spring at Pacific Northwest National Laboratory, I pursued the development of microarray techniques for examination of the diversity and abundance metal-reducing bacterial communities in soil and sedimentary environments. The expertise gained during this sabbatical leave will be expanded through the new field-based subsurface metal reduction project described above. These and other molecular techniques (as well as traditional culture-based methods) will be used in all aspects of my ongoing research program in aquatic biogeochemistry.

Biogeochemical Modeling

Mathematical models provide an important quantitative (and ultimately, predictive) link between field and laboratory studies of chemical cycling and mass flux in aquatic systems. Beginning with my dissertation work on estuarine sediment biogeochemistry, I have directed substantial energy toward development of transport-reaction models of biogeochemical processes in sedimentary environments. I have worked extensively with one-dimensional transport-reaction modeling of aquatic sediments, and am well-accustomed to thinking about how physical transport and microbial metabolic processes interact to control the fate of various kinds of materials in environmental systems. Thus, I am capable of speaking the language of modeling professionals in the geosciences and engineering, and I consider this to be one of my strongest interdisciplinary talents.

Examples of my research which combine modeling with laboratory and/or field studies include: dissolved sulfide diagenesis in estuarine sediments (Roden and Tuttle, 1992); sulfate reduction and S recycling in low-salinity estuarine sediments (Roden and Tuttle, 1993); seasonal patterns of organic carbon metabolism in estuarine sediments, and particulate/dissolved organic carbon diagenesis in relation to decay kinetics and particle/solute transport (Roden and Tuttle, 1996); Fe diagenesis (redox cycling) in freshwater wetland sediments (Roden, 2002); nitrate-dependent ferrous iron oxidation (Weber et al., 2001); and kinetic and equilibrium speciation modeling of controls on microbial Fe(III) oxide reduction (Roden and Urrutia, 1999; Urrutia et al., 1999). I have also developed provisional simulations of parallel Fe(III) oxide and U(VI) reduction in subsurface sediments; subsurface microbial redox zonation and arsenic fate and transport, and sediment organic matter diagenesis/redox zonation and Hg speciation. Each of the latter models were created as contributions to federal (DOE and NSF) research proposals. A listing of VBA code as applied to simulation of parallel Fe(III) oxide and U(VI) reduction in a single Representative Elementary Volume (REV) of subsurface sediment is available on my web site.

I am currently working with a computer science graduate student on development of a biogeochemical modeling software package which employs Excel for data storage and graphical analysis, VBA for graphical user interfacing, and library of compiled Fortran programs for numerical computation. Once completed, the software will be supplemented with a user’s manual and made available to a variety of microbiological, geochemical, biogeochemical, and environmental engineering colleagues. In addition, the package will eventually be partnered with a textbook on biogeochemical modeling which I plan to produce within the next 3-5 years. I anticipate that these products will be of substantial use to biogeoscience researchers and students in need of a convenient, easy-to-use, and inexpensive simulation modeling environment.

Through collaboration with William Burgos at Penn State University and Carl Steefel at Lawrence Livermore National Laboratory, I have recently become involved in the use of more sophisticated reactive transport models (e.g. George Yeh’s HYDROBIOGEOCHEM; Steefel’s OS3D/GIRMT/CRUNCH) of geochemical and microbiological processes associated with metal-radionuclide contaminant fate and transport in subsurface environments. For example, I recently participated a DOE-NABIR sponsored workshop on the use of the BIOGEOCHEM module of Yeh’s HYDROBIOGEOCHEM code, and have interacted several times with Steefel en route to setting-up provisional simulations of subsurface microbial redox zonation. The next step in application of these advanced codes will be toward simulation of laboratory studies of coupled microbial-geochemical processes in anaerobic sediments, including reactive transport studies with experimental columns for which we are currently funded, as well as future experimental manipulation studies with intact subsurface core segments. Ultimately, one or more of these codes will be used in conjunction with field-scale remediation projects, e.g. the new NABIR FRC project on coupled Fe/U reductive biomineralization at ORNL.

Teaching

The focus of my teaching at The University of Alabama has been on the role of microbial processes in biogeochemical cycling and material flux at various levels of organization, including cell-molecular, population-community, and ecosystem-global scales. I have developed an interdisciplinary instructional program consisting of the following four courses: (1) an upper division/graduate lecture course in microbial ecology; (2) an upper division/graduate microbial ecology-biogeochemistry laboratory course, which includes use of molecular techniques for bacterial detection/quantification and community analysis; (3) an upper division/graduate lecture plus computer laboratory course in environmental modeling; and (4) a graduate lecture course in aquatic biogeochemistry. This curriculum is designed to support my research program in microbial ecology and biogeochemistry, and is thus reflective of my general philosophy that an effective advanced undergraduate/graduate-level teaching program should interface as directly as possible with (and be supported intellectually by) an effective research program. I have also coordinated (in collaboration with W.B. Lyons, formerly in the Department of Geology at UA) a graduate seminar course in trace metal biogeochemistry, and participated in a team-taught graduate course in Geomicrobiology offered through a current NSF-IGERT project collaboration with the University of New Mexico. In addition, I have on two occasions taught a 2-week minicourse on ecological modeling in an advanced ecology course offered at UA. Finally, I have recently participated in the development of interdisciplinary, inquiry-based undergraduate course entitled Introduction to Inquiry, which has been supported through grants from the NSF-ILI program, and the Howard Hughes Medical Institute. The goal of the course is to train students in hypothesis-driven research approaches, and to provide them with hand-on experience in state-of-the art molecular biological and experimental ecological techniques.

The advanced undergraduate/graduate curriculum described above could be readily adapted to fit the needs of an environmental science/engineering or geoscience program. For example, various components of the above courses could be folded into a one-semester advanced undergraduate/graduate course in biogeochemical cycling, which would be followed-up by graduate-level courses in geomicrobiology and biogeochemical modeling. The biogeochemical modeling course would emphasize fundamental concepts required to simulate coupled microbial-geochemical processes in natural environments. The Visual Basic, Matlab, and/or Fortran programs which I have developed for research applications are of substantial value for this purpose; other problems taken from texts on environmental [e.g. Brezonik (1994), Schnoor (1996)] and geochemical [e.g. Walker (1991)] and modeling have also been implemented. A salient aspect of my teaching philosophy is that all environmental science/engineering and geoscience students who intend to work on biogeochemical cycling problems need to receive specific training in how to incorporate microbially-catalyzed processes into standard (kinetic plus equilibrium) reaction frameworks for holistic simulation of biogeochemical processes in natural environments.

References

Brezonik, P.L. 1994. Chemical kinetics and process dynamics in aquatic systems, Lewis Publishers.
Jackson, C.R., E.E. Roden, and P.F. Churchill. 1998. Changes in bacterial species composition in enrichment cultures with varying inoculum dilution as monitored by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 98:5046-5048.
Jackson, C.R., P.F. Churchill, and E.E. Roden. 2000a. Successional changes in bacterial assemblage structure during epilithic biofilm development. Ecology 82:555-566.
Jackson, C.R., E.E. Roden, and P.F. Churchill. 2000b. Denaturing gradient gel electrophoresis can fail to separate 16S rDNA fragments with multiple base differences. Mol. Biol. Today 1:49-51.
Roden, E.E. 2002. Modeling iron redox cycling and the influence of microbial Fe(III) oxide reduction on methanogenesis in freshwater wetland sediments. Manuscript in preparation.
Roden, E.E., and J.H. Tuttle. 1992. Sulfide release from estuarine sediments underlying anoxic bottom water. Limnol. Oceanogr. 37:725-738.
Roden, E.E., and J.H. Tuttle. 1993. Inorganic sulfur turnover in oligohaline estuarine sediments. Biogeochemistry 22:81-105.
Roden, E.E., and J.H. Tuttle. 1996. Carbon cycling in mesohaline Chesapeake Bay sediments 2: kinetics of particulate and dissolved organic carbon turnover. J. Mar. Sci. 54:343-383.
Roden, E.E., and M.M. Urrutia. 1999. Ferrous iron removal promotes microbial reduction of crystalline iron(III) oxides. Environ. Sci. Technol. 33:1847-1853.
Schnoor, J.L. 1996. Environmental modeling, Wiley Interscience.
Urrutia, M.M., E.E. Roden, and J.M. Zachara. 1999. Influence of aqueous and solid-phase Fe(II) complexants on microbial reduction of crystalline Fe(III) oxides. Environ. Sci. Technol. 33:4022-4028.
Walker, J.C.G. 1991. Numerical adventures with geochemical cycles, Oxford University Press.
Weber, K.A., F.W. Picardal, and E.E. Roden. 2001. Microbially-catalyzed nitrate-dependent oxidation of biogenic solid-phase Fe(II) compounds. Environ. Sci. Technol. 35:1644-1650.
Weber, K.A., P.F. Churchill, and E.E. Roden. 2002. Microbial community structure associated with interaction between nitrogen and iron redox cycles in freshwater sediments. Manuscript in preparation.

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