Holden Group Research Statement
3-08


Our group studies microbes: who’s in the environment, what they do, and how they do it.   The unifying theme is physical and biochemical structuring of molecules, cells, populations, and communities.  How does where microbes are influence what they do?  How does what they do influence where they are?  The research is at several scales (nm to m), and for many environmental compartments (soil, sediments, water).  The specific problems are both basic, i.e. fundamental feedbacks between unsaturated biofilm extracellular polymeric substances (EPS) and microbial growth, and applied, i.e. microbial communities as indicators of pollution along gradients (sediments, surface waters, soil profiles).  The research approaches depend on the particular question, but often include field sampling, laboratory analysis, laboratory experimentation, modeling, and using tools from molecular biology, microbial physiology, analytical chemistry, biophysics, microscopy and mathematics.

 

Currently, we have three main, funded areas of research:

1) vadose zone microbial ecology,

2) microbiological water quality in coastal environments, and

3) interactions of bacteria with engineered nanomaterials.

 

1)  In our vadose zone microbial ecology research, we work in collaboration with Josh Schimel's lab in EEMB (http://www.lifesci.ucsb.edu/eemb/faculty/schimel/) to study controls on microbial community composition, diversity, and process in surface and deep soils in a California grassland.  Our field sites are in the Sedgwick Natural Reserve which is part of the overall UC Natural Reserve System (http://nrs.ucop.edu/).  We are generally interested in "who's there" and "what they are doing", but the current thrust in this now decade-long collaboration regards understanding how resource (namely C and N) availability and stress (namely water availability and temperature) together structure microbial communities and populations along the soil profile from surface to deep (1 m or below).  Resource availability and stressful water conditions (defined here as severe desiccation and rapid moisture cycling) decline from surface to deep in the grassland soils that we study.  Microbes cope with stress by investing more energy and nutrition towards survival.  Yet water, as an environmental variable, also strongly controls resource availability by creating solute diffusion paths and reducing air-filled pore space.  In a possible future scenario of a changing climate, soil moisture profiles could change such that wetting/ drying penetrates more deeply into the subsurface.  Under such conditions, microbes may access previously, physically-unavailable C.  We aim to learn how microbes in deep versus surface soils respond to changing wetting and drying regimes, including their population structures, respiration dynamics and physiological impairment.  This work is funded by the National Science Foundation (Ecology Program and Microbial Observatories Program). 

 

Related to this work is our long term interest in the microscale growth habits of bacteria in surface and deep soils.  We wish to understand the biofilm growth habit in the vadose zone, i.e., its prevalence and biophysical characteristics that affect pollutant biodegradation. While biofilms in wet environments are increasingly recognized as an important growth mode for bacteria, little is known regarding biofilms in dry systems. Our work is towards providing fundamental knowledge of unsaturated biofilm physiology, ecology, chemistry and physics.  This orientation towards biofilms cross cuts our work in all three main thrust areas of our funded research, and is a lens through which we plan and execute experiments, and field sample analysis.

 

2) In our microbiological water quality research, our applied interest is in determining the presence and origins of pathogen-containing, fecal material in coastal freshwaters that discharge into coastal oceans. Worldwide, coastal development results in periodically high levels of disease indicators in coastal waters. Estuaries and wetlands are expected to cleanse, to some degree, the pollution that is carried by dry weather and stormwater runoff, but they may also have the opposite effect. Indicators of waste are insufficient for unequivocally relating human activities in watersheds to coastal contamination. Watershed management is guided by incomplete scientific knowledge because scientifically-based information and solutions are not available. Our research is towards understanding both how to diagnose surface waters for the presence of human fecal contamination and how to apply that knowledge in a 'systems context" where biotic markers are subject to decay as well as accumulation or growth as they are transported from upstream in a watershed to coastal beach waters.  Tools turn out to be useful for gaining such understanding: we have been complementing waste indicators with whole community, phylogenetically-based fingerprinting as metrics for water quality, using quantitative PCR-based markers specific to human waste, and employing other culture-independent techniques.  We have recently completed a 3-year study with the City of Santa Barbara to determine the presence and origins of human waste in two urban creek systems: Arroyo Burro and Mission Creeks.  Community analysis proved to be a very useful tool for these purposes: both fingerprinting and microarray based community analysis (i.e. the PhyloChip)--the latter through a collaboration with Gary Andersen's group at LBNL (http://www-esd.lbl.gov/ECO/MME/staff_andersen.htm) --revealed patterns and individual groups of organisms indicative of waste sources.  Sources were identified, and the research provided very rich implications for feedbacks between civil infrastructure and surface water pollution.  We are continuing to work in this area with the support of the Clean Beaches Program in the State of California.  Projects include developing transferable source tracking approaches for use in urban areas, understanding the fate of a treated wastewater effluent plume in the coastal zone, and further characterizing human waste extents in urban Santa Barbara.  We enjoy that this research is contributing both fundamental insights into surface water microbial ecology, including spatial structuring of microbial communities in urban waterscapes, while also providing needed scientific information that our agency collaborators can use in water quality management.

 

Our interest in microbial communities as “tracers” for gradients, i.e. gradients created by microbes that also feedback to structure communities, extends more broadly to sediments (coastal and marine) and particle-associated bacteria, where we have studied hydrocarbon seep petroleum and associated communities, and estuarine sedimentary and particle-associated bacterial communities (total and denitrifying) along pollution gradients.

 

3) In our research regarding the interactions of engineered nanomaterials with bacteria, we are trying to understand how engineered nanomaterials affect bacterial cells and populations and, in turn, how bacteria modify the structure and function of nanomaterials.  The physical interactions and structuring of nanomaterials and cells, at the microbe-scale, significantly determine effects and feedbacks.  Importantly, nanomaterials exist in our environment naturally but they will also enter the environment through industrial and consumer pathways.  How bacteria respond to nanoscale particles is an important, yet relatively unexplored, dimension of microbial ecology in soil and water; it may also be a key to how introduced synthetic nanomaterials affect ecosystems.  We’ve been working with two model bacteria taxa that we've studied in pure culture extensively: Pseudomonas putida and Pseudomonas aeruginosa.  Nanomaterials that we study range from metal oxides (e.g. various titania or TiO2) to CdSe quantum dots.  Our work is both physiologically-oriented, i.e. towards understanding how nanoparticle integrity changes in the presence of growing bacteria and how growth of bacteria is altered by nanoparticles, and oriented towards understanding mechanisms of interactions at the gene expression level in bacteria.  We are funded through the EPA STAR program and the DOE.  Our collaborators are within the groups of Jay Nadeau (McGill University, http://www.mcgill.ca/microimm/department/associate_adjunct_prof/nadeau/), Galen Stucky (UCSB, http://www.chem.ucsb.edu/~stuckygroup/stuckygroup/),  and Ed Orias (UCSB, http://www.lifesci.ucsb.edu/mcdb/emeriti/orias/index.html).