MICROBIAL ECOLOGY:

RICK LOVELL'S LAB

 

This site contains information on research conducted by current and former students in my lab.  As indicated in my Department of Biological Sciences homepage, we have a lot of things going on.  Most projects examine various aspects of microbial community composition and dynamics.  A major project in this area is the North Inlet Microbial Observatory, which examines the diazotrophic bacteria associated with salt marsh plants.  Additional projects have a more physiological focus and we have also worked on the biochemistry of aryl dehalogenation, aromatic catabolism, and the structure and catalysis of a key enzyme in acetogenesis.  A brief description of our field research sites and lists of publications and current collaborators are also provided.

Goat Island field site in the North Inlet salt marsh system.

 

Contents:

Personnel

Field Research Sites

Field Photos

Publication List

List of Current Collaborators

Personnel:

Former Postdoctoral Associates:

Yung Pin Chen, Research Professor

Background:

BS, Microbiology, Fu Dan University, Shanghai, China
MS, Ph.D., Murdoch University, Western Australia

Major projects:

"Catabolism of aromatic compounds by diazotrophic bacteria"
"Halogenation and dehalogenation enzymes in marine invertebrates, algae, and bacteria"

Project notes:

 

Notomastus lobatus in its native habitat.

Yung Pin has been involved in many projects, including several with other faculty in the Departments of Biological Sciences and Chemistry and Biochemistry.  Our projects have been focused primarily on characterization of novel enzymes from bacteria and invertebrates.  Some examples of these include ring cleavage dioxygenases from soil diazotrophs, reductive dehalogenases from marine bacteria, and haloperoxidases and dehaloperoxidases from marine polychaetes.  The flavin containing chloroperoxidase from Notomastus lobatus and the dehaloperoxidase from Amphitrite ornata both represent novel types of enzymes Yung Pin has purified.  Yung Pin has also worked on catabolism of aromatic compounds by marine microalgae in collaboration with Dr. Alan Lewitus.

Publications:

Lovell, C.R., A.J. Lewitus, N. Eriksen, and Y.P. Chen. 2002. Resistance of the marine diatom Thalassiosira sp. to toxicity of phenolic compounds. Marine Ecology Progress Series 229:11-18.

Roach, M.P., Y.P. Chen, S.A. Woodin, D.E. Lincoln, C.R. Lovell, and J.H. Dawson. 1997. Notomastus lobatus chloroperoxidase and Amphitrite ornata dehaloperoxidase both contain histidine as their proximal heme iron ligand. Biochemistry 36:2197-2202.

Chen, Y.P., S.A. Woodin, D.E. Lincoln, and C.R. Lovell. 1996. An unusual dehalogenating peroxidase from the marine terebellid polychaete Amphitrite ornata. Journal of Biological Chemistry 271:4609-4612.

Zhang, E., Y.P. Chen, M.P. Roach, D.E. Lincoln, C.R. Lovell, S.A. Woodin, J.H. Dawson, and L. Lebioda. 1996. Crystallization and initial spectroscopic characterization of the heme-containing dehaloperoxigenase from the marine polychaete Amphitrite ornata. Acta Crystallographica D52:1191-1193.

Steward, C.C., T. Dixon, Y.P. Chen and C.R. Lovell. 1995. Enrichment and isolation of a reductively debrominating bacterium from the burrow of a bromometabolite producing marine hemichordate. Canadian Journal of Microbiology 41:637-642.

Chen, Y.P. and C.R. Lovell. 1994. Purification and properties of a homodimeric protocatechuate 4,5-dioxygenase from Rhizobium leguminosarum. Archives of Microbiology 161:191-195.

Yoon, K.S., Y.P. Chen, D.E. Lincoln, C.R. Lovell, L.W. Knapp, and S.A. Woodin. 1994. Localization of the chloroperoxidase of the capitellid polychaete Notomastus lobatus. Biological Bulletin 187:215-222.

Chen, Y.P., G. Lopez-de-Victoria and C.R. Lovell. 1993. Utilization of aromatic compounds as carbon and energy sources during growth and N2-fixation by free-living nitrogen fixing bacteria. Archives of Microbiology 159:207-212.

Chen, Y.P., D.E. Lincoln, S.A. Woodin and C.R. Lovell. 1991. Purification and properties of a unique flavin-containing chloroperoxidase from the capitellid polychaete Notomastus lobatus. Journal of Biological Chemistry 266:23909-23915.

Chen, Y.P., and C.R. Lovell. 1990. Purification and characterization of catechol-1,2-dioxygenase from Rhizobium leguminosarum biovar viceae Strain USDA 2370. Applied and Environmental Microbiology 56:1971-1973.

Current Ph.D. students:

Julie Criminger

Started program August 2004.

Background:

BS, Biological Sciences, University of South Carolina

 

Julie’s project examines the association of diazotrophic species of the genus Vibrio with salt marsh plants.  These organisms are readily isolated from roots of various salt marsh plants and one species has been shown to express nifH in the rhizosphere of Spartina alterniflora. 

 

 

Debra Davis

Started program August 2003.

Background:

BS, Birkbeck College, University of London

MS, University of Massachusetts Dartmouth

 

Debra’s project examines the expression of nifH in the rhizosphere of salt marsh grasses.  Specific research questions address the impact of rhizosphere ventilation and sediment porewater salinity on expression of nifH and on rates of nitrogen fixation.

Current M.S. students:

Melissa Cramer

Started program January 2004.

Background:

BS, Virginia Polytechnic Institute

 

Melissa’s project examines some novel diazotrophs isolated from roots of salt marsh plants with the goal of characterizing these organisms and producing formal taxonomic descriptions of them.

 

Current undergraduate research students:

 

Nicole Haghshenas: 2004-present

 

“Horizontal transfer of nifH-encoding plasmids among rhizosphere bacteria” 

 

Howard Hughes Summer Undergraduate Research Award, 2004

 

Former graduate students:

George Matsui

Background:

BS, Marine Science, University of South Carolina, Honors College

Dissertation Title:

“Microbial Ecology of Sulfate Reducing Bacteria within Selected Marine Infaunal Tubes”

Completed Ph.D. program:  December, 2003.

Dissertation Abstract:

Sulfate reducing bacteria (SRB) play an important role in the biogeochemical cycling of carbon and sulfur.  They are responsible for over 90% of sulfate reduction and up to 50% of carbon oxidation in marine sediments.  These obligate anaerobes are commonly found at the oxic/anoxic interface and have been found within clearly oxic sediments.  SRB have been detected and high rates of sulfate reduction have been measured in the tubes and burrows of marine infauna.  The presence of SRB in the tubes of the marine polychaete Diopatra cuprea and the effects of sediment properties and oxygen on the assemblage were examined using molecular and biochemical techniques.  SRB were found in all D. cuprea tubes examined in this study.  The SRB assemblages were limited to members of the Desulfobacteriaceae.  Assemblages from sediment sites having different amounts of silt and clay differed.  Differing amounts of oxygen exposure of tubes also produced SRB assemblages that differed.  Certain members of the SRB assemblage did not appear to be as sensitive to oxygen as others detected in D. cuprea tubes.  SRB in tubes of Chaertopterus variopedatus were compared to those in D. cuprea tubes and found to be different.  SRB from C. variopedatus tubes were not among those recovered from the D. cuprea clonal library but were detected by hybridization in tubes of D. cuprea.  D. cuprea tubes displayed greater potential SRB diversity than C. variopedatus tubes.  This may reflect differences in the behavior of the animals or in the habitat.

 

The results of this study have important implications for biogeochemical cycling of sulfur and carbon.  Tubes and burrows increase the surface area available for sulfate reduction.  Some of the polychaete tube SRB have been shown to at least persist under oxic conditions for prolonged periods.  This may imply a wider range of habitats in which sulfate reduction can occur.

 

Publications:

Matsui, G.Y., D.B. Ringelberg, and C.R. Lovell. 2004. Sulfate reducing bacteria in tubes constructed by the marine infaunal polychaete Diopatra cuprea. Applied and Environmental Microbiology 70:7053-7065.

Watson, J., G.Y. Matsui, A. Leaphart, F.A. Rainey, J. Wiegel, and C.R. Lovell. 2000. Reductively debrominating strains of Propionigenium maris from burrows of bromophenol producing marine infauna.  International Journal of Systematic and Evolutionary Microbiology 50:1035-1042.

Adam Leaphart

Background:

BS, Biological Sciences, University of South Carolina, Honors College

Dissertation Title:

"The Ecology and Biochemistry of Formyltetrahydrofolate Synthetase"
Completed Ph.D. program:  August, 2002.

Dissertation Abstract:

Acetogens are anaerobic bacteria that utilize the Acetyl-CoA pathway for the reductive synthesis of acetyl-CoA from C1 compounds in an electron-accepting, energy conserving manner.  As a group these bacteria are highly diverse in terms of their metabolic capabilities, physiology, and phylogeny.  As a result of this diversity, acetogens are ubiquitous in all anaerobic environments.  A major product of acetogenesis is acetate, a crucial carbon cycle intermediate in many ecosystems.  Acetogenic bacteria produce an estimated 10% of the 1013 kg of acetate formed annually, and thus are important contributors to the global fixation of carbon.  Although acetogens are readily isolted, little is known of their abundance, distribution and activities in natural environments.  Natural bacteria are often refractory to isolation by classical pure culture techniques involving laboratory media.  Owing to the diverse nature of the acetogenic bacteria, this would certainly be expected.  In these studies, a highly conserved enzyme in the methyl branch of the Acetyl-CoA pathway, formyltetrahydrofolate synthetase (FTHFS), has been examined from both ecological and biochemical perspectives.  FTHFS catalyzes the ATP-dependent addition of formate to tetrahydrofolate, thus bringing formate into the pool of C1 intermediates and supplying the methyl group of Acetyl-CoA.  Degenerate polymerase chain reaction primers were constructed from the existing FTHFS sequences and used to examine the distribution and diversity of FTHFS containing bacteria on the roots of selected salt marsh plants.  Although a great deal of diversity was observed, only a small portion of the recovered sequences grouped within the known acetogen cluster.  The entirety of these sequences originated from the roots of Spartina alterniflora, implying specificity for either the host plant or the environmental conditions it develops.  Other partial FTHFS sequences, while also quite similar to the acetogenic sequences, clustered away from the known acetogen clade.  These may be representative of divergent sequences from true acetogens, sequences from non-acetogenic, FTHFS-containing bacteria (including sulfate reducing bacteria), or a highly similar non-FTHFS gene (such as the Sphingomonas paucimobilis ligH).  In accordance with the sequence information provided from these studies and the three dimensional structure data established for FTHFS, biochemical studies were initiated using site-directed mutagenesis to examine key catalytic and structural amino acid residues.  Glutamate 98 was shown to be directly responsible for the binding of monovalent cations and resulting increased thermostability.  Arginine 97 was shown to be the binding site for the formyl phosphate intermediate in the formation of N10 -formyltetrahydrofolate.
 

Publications:

Leaphart, A.B., M.J. Friez, and C.R. Lovell. 2003. Formyltetrahydrofolate synthetase sequences from salt marsh plant roots reveal a diversity of acetogenic bacteria and other bacterial functional groups. Applied and Environmental Microbiology 69:693-696.

Leaphart, A.B., H.T. Spencer, and C.R. Lovell. 2002. Site directed mutagenesis of a putative catalytic and formyl phosphate binding site and substrate inhibition of N10-formyltetrahydrofolate synthetase. Archives of Biochemistry and Biophysics 408:137-143.

Leaphart, A.B., and C.R. Lovell. 2001. Recovery and analysis of formyltetrahydrofolate synthetase gene sequences from natural populations of acetogenic bacteria. Applied and Environmental Microbiology 67:1392-1395.

Radfar, R., A. Leaphart, J.M. Brewer, W. Minor, J.D. Odom, R.B. Dunlap, C.R. Lovell, and L. Lebioda. 2000. Cation binding and thermostability of FTHFS monovalent cation binding sites and thermostability of N10-formyltetrahydrofolate synthetase from Moorella thermoacetica. Biochemistry 39:14481-14486.

Watson, J., G.Y. Matsui, A. Leaphart, F.A. Rainey, J. Wiegel, and C.R. Lovell. 2000. Reductively debrominating strains of Propionigenium maris from burrows of bromophenol producing marine infauna.  International Journal of Systematic and Evolutionary Microbiology 50:1035-1042.

 

Michelle Brown

Background:

BS, Marine Science, University of Hawaii
 

Thesis Title:

"Expression of nifH Genes by Diazotrophic Bacteria in the Rhizosphere of Short Form Spartina alterniflora as Determined Using Reverse Transcriptase PCR"
Completed M.S. program:  May, 2002
 

Thesis Abstract:

A diverse assemblage of diazotrophic bacteria exists in the rhizosphere of the smooth cordgrass, Spartina alterniflora, but the taxa actively involved in nitrogen fixation have not been determined.  In order to identify the diazotrophs that were actively expressing nifH, the gene encoding the nitrogenase iron protein, we extracted mRNA from Spartina rhizosphere samples and performed nifH-specific reverse transcriptase-PCR.  The products recovered were sequenced and the sequences analyzed.  The expressed nifH sequences recovered were from organisms affiliated with the (gamma- + beta-) Proteobacteria and the anaerobes.  Most of the expressed nifH sequences we recovered were highly similar (> 95% similarity) to sequences recovered from Spartina rhizosphere DNA using conventional nifH-specific PCR.  These sequences were also similar, but not identical to the nifH sequences of Pseudomonas stutzeri, Vibrio diazotrophicus, Desulfovibrio africanus, and Desulfovibrio gigas.
 

Publication:

Brown, M.M., M.J. Friez, and C.R. Lovell. 2003. Expression of nifH genes by diazotrophic bacteria in the rhizosphere of short form Spartina alterniflora. FEMS Microbiology Ecology 43:411-417.
 

Hongyue Dang

Background:

BS, Marine Sciences, Ocean University of Qingdao, Quingdao, China
MS, Marine Sciences, Ocean University of Qingdao, Quingdao, China
 

Dissertation Title:

"Determination of bacterial primary colonists of surfaces in coastal marine waters by 16S rDNA sequence analyses and fluorescence in situ hybridization"
Completed Ph.D. program  May, 2001.
 

Dissertation Abstract:

The near-universal colonization of surfaces in marine waters and the formation of biofilms and biofouling communities have important implications for ecological function and industrial processes.  However, the dynamics of surface colonization in situ, particularly in the early stages of biofilm establishment, are not well understood.  A 2-phase 16S rRNA based phylogenetic study was employed to determine the composition and abundance of key bacterial primary colonists on submerged artificial surfaces, as well as on naturally occurring suspended particles in coastal seawater.  Phylogenetic analyses of the most common sequences recovered from submerged artificial surfaces showed that the sequenced colonists were related to bacteria known to inhabit surfaces or particles in marine systems.  Thirty four of the 55 clones sequenced were affiliated with the marine Rhodobacter group.  The quantitative contribution of this group to colonization of artificial surfaces and naturally occurring particles in seawater was determined by fluorescence in situ hybridization (FISH) with DNA probes targeting 16S or 23S rRNA, combined with confocal laser scanning microscopy (CLSM) quantification.  In addition to their remarkable phylotype diversity, the numerical dominance of the marine Rhodobacter group on artificial and naturally occurring surfaces was demonstrated.  More than 28% of the total bacterial cells detected by fluorescence staining and 40% of the cells detected by EUB338 on an artificial test surface were affiliated with the marine Rhodobacter group.  The FISH results also indicated that bacterial abundance increased significantly on the artificial surface over short-term incubations, mainly due to the growth of the marine Rhodobacter group organisms.  The alpha Proteobacteria, especially those from the marine Rhodobacter group, were abundance on naturally occurring suspended particles in seawater and as free-living planktonic cells year round.  The marine Rhodobacter group accounted for more than 25% of the particle-associated bacteria and more than 18% of the free-living bacteria.  The numerical dominance and genotypic diversity of the marine Rhodobacter group organisms as determined in this study indicate that the marine Rhodobacter group is a widespread and significant bacterial lineage in coastal marine systems and a dominant colonizing group on both artificial and natural surfaces.

Publications:

Dang, H., and C.R. Lovell. 2002. Numerical dominance and phylotype diversity of marine Rhodobacter during early Colonization of submerged surfaces in coastal marine waters as determined by 16S rDNA sequence analysis and fluorescence in situ hybridization. Applied and Environmental Microbiology 68:496-504.

Dang, H., and C.R. Lovell. 2002. Seasonal dynamics of particle-associated and free-living marine Proteobacteria in a salt marsh tidal creek as determined using fluorescence in situ hybridization. Environmental Microbiology 4:287-295.

Dang, H., and C.R. Lovell. 2000. Bacterial primary colonization and early succession on surfaces in marine waters as analyzed by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Applied and Environmental Microbiology 66:467-475.
 

Christopher (Kitt) Bagwell

Background:

BS, Biological Sciences, University of South Carolina
Vernberg Award for the Outstanding Exiting Graduating Student, 2001

Dissertation Title:

"Physiological Microdiversity of Rhizoplane Diazotrophs of Intertidal Grasses: Evidence for Functional Redundancy via Niche Specialization"
Completed Ph.D. program:  March, 2001


 

Dissertation Abstract:

Spartina alterniflora dominated salt marshes extend along the eastern and northern Gulf coasts of temperate North America, and are among the most productive ecosystems known.  Despite high levels of productivity, Spartina marshes are largely considered to be nitrogen limited.  Diazotrophs (N2-fixers) are expected to be an ecologically significant supply of biologically available nitrogen in these systems, however we know relatively little about these organisms.  This study examined the physiological and phylogenetic diversity of the culturable, O2 utilizing fraction of the rhizoplane diazotroph assemblage from Spartina growth forms, as well as from other wetlands grasses (Juncus roemerianus and Spartina patens) and a high marsh plant (Salicornia virginica).  Diazotroph strains demonstrated physiological adaptation to their high or low marsh origins, and more specifically to the host plant from which they were isolated.  These findings imply niche specialization by diazotrophs, providing new insight into the observed stability (compositional and functional) of the diazotroph assemblage.  The responses of selected diazotroph populations were examined quantitatively to long-term fertilization of short Spartina to assess the physiological competitiveness of diazotrophs under nutrient enriched conditions.  The relative abundances of select diazotrophs and diazotrophic activity were found to be persistent and resilient despite significant changes in abiotic and biotic environmental conditions.  The physiological traits that differentiate diazotroph populations presumably support competitiveness and niche specialization, lending support to a hypothesis of functional redundancy for the diazotroph assemblage.

Publications:

LaRocque, J., P.W. Bergholz, C.E. Bagwell, and C.R. Lovell. 2004. Influence of host plant-derived and abiotic environmental parameters on the composition of the diazotroph assemblage associated with roots of Juncus roemerianus. Antonie van Leeuwenhoek 68:249-261.    

 

Bagwell, C.E., and C.R. Lovell. 2004. A DNA-DNA hybridization method for the detection and quantification of specific bacterial taxa in natural environments.  In: J.F.T Spencer and A.L. Ragout de Spencer (eds.) Environmental Microbiology, pp. 169-174. Methods in Biotechnology Series, Humana Press, Totowa, NJ.

Bagwell, C.E., J.R. La Rocque, G.W. Smith, S.W. Polson, M.J. Friez, J.W. Longshore, and C.R. Lovell. 2002. Molecular diversity of diazotrophs in oligotrophic seagrass bed communities. FEMS Microbiology Ecology 39:113-119.

Beeson, K., D.L. Erdner, C.E. Bagwell, C.R. Lovell, and P.A. Sobecky. 2002. Differentiation of plasmids in marine diazotroph assemblages determined by randomly amplified polymorphic DNA analysis. Microbiology 148:179-189.

Bagwell, C.E., M. Dantzler, P.W. Bergholz, and C.R. Lovell. 2001. Host-specific ecotypic diversity of rhizoplane diazotrophs of the perennial glasswort, Salicornia virginica and selected salt marsh grasses. Aquatic Microbial Ecology 23:293-300.

Bergholz, P.W., C.E. Bagwell, and C.R. Lovell. 2001. Physiological diversity of rhizoplane diazotrophs of the saltmeadow cordgrass, Spartina patens.  Implications for host specific ecotypes. Microbial Ecology 42:466-473.

Lovell, C.R., C.E. Bagwell, M. Czako, L. Marton, Y.M. Piceno, and D.B. Ringelberg. 2001. Stability of a rhizosphere microbial community exposed to natural and manipulated environmental variability. FEMS Microbiology Ecology 38:69-76.

Lovell, C.R., M.J. Friez, J.W. Longshore, and C.E. Bagwell. 2001. Recovery and phylogenetic analysis of nifH sequences from diazotrophic bacteria associated with dead aboveground biomass of Spartina alterniflora. Applied and Environmental Microbiology 67:5308-5314.

Bagwell, C.E., and C.R. Lovell. 2000. Persistence of selected Spartina alterniflora rhizoplane diazotrophs exposed to natural and manipulated environmental variability. Applied and Environmental Microbiology 66:4625-4633.

Bagwell, C.E. and C.R. Lovell. 2000. Microdiversity of culturable diazotrophs from the rhizoplanes of the salt marsh grasses Spartina alterniflora and Juncus roemerianus. Microbial Ecology 39:128-136.

Lovell, C.R., Y.M. Piceno, J.M. Quattro, and C.E. Bagwell. 2000. Molecular analysis of diazotroph diversity in the rhizosphere of the smooth cordgrass, Spartina alterniflora. Applied and Environmental Microbiology 66:3814-3822.

Bagwell, C.E., Y.M. Piceno, A.L. Ashburne, and C.R. Lovell. 1998. Physiological diversity of the rhizosphere diazotroph assemblages of selected salt marsh grasses. Applied and Environmental Microbiology 64:4276-4282.

Yvette Piceno

Background:

BS, Biology, University of New Hampshire
NSF Predoctoral Fellow, 1993-96
Vernberg Award for the Outstanding Exiting Graduating Student, 1999

Dissertation title:

"Molecular Analysis of Diazotroph Assemblage Composition in Spartina alterniflora Rhizosphere"
Completed Ph.D. Program:  April, 1999

Dissertation Abstract:

Microbial community composition and structure and the environmental factors influencing them are an area of active research.  Of particular interest is the concept of microbial community plasticity in changing environments.  Salt marshes are dynamic environments with both biotic and abiotic differences along tidal gradients from the creek bank to the upper marsh.  The dominant macrophyte in Southeastern US salt marshes is Spartina alterniflora and it has two main growth forms: the tall form grows along creek banks, whereas the short form grows farther inland.  The differences in plant height are thought to be caused by biogeochemical differences along the gradient from the creek bank to the upper marsh.  Plant roots supply carbon and energy to the rhizosphere microbes and differences in plant productivity are expected to affect the rhizosphere microbes and differences in plant productivity are expected to affect the rhizosphere microbial community.  Therefore, bacteria living in these marsh sediments will be exposed not only to the biogeochemical differences along this tidal gradient, but also to differences in carbon/energy availability derived from S. alterniflora root growth and exudation.  An initial study was conducted to determine the diazotroph assemblage composition in these two marsh zones over a seasonal cycle.  Spatial and temporal variability within each zone as well as the variability in diazotroph composition between zones was assessed.  Rhizosphere samples were collected from each zone in March, June, September, and December of 1997.  DNA was extracted and a portion of the nifH gene (required for N2fixation) was amplified via the polymerase chain reaction (PCR).  The PCR products were analyzed using denaturing gradient gel electrophoresis, and gel profiles were compared within and between zones.  The diazotroph assemblage composition was remarkably stable within a zone over one year, and the gel profiles were very similar between zones, indicating a similar diazotroph assemblage in both zones.  Field experiments then were conducted in which nutrient availability was increased or plant resources were directed away from the rhizosphere (by clipping or shading the plants) for two or eight weeks.  The diazotroph assemblage composition was monitored as described above.  The assemblage composition was very stable during these experiments.  This was a surprising result since microbial communities are thought to respond rapidly to environmental changes.  Results from these experiments and the seasonal study suggest there is greater stability in some natural systems than anticipated.

Publications:

Lovell, C.R., C.E. Bagwell, M. Czako, L. Marton, Y.M. Piceno, and D.B. Ringelberg. 2001. Stability of a rhizosphere microbial community exposed to natural and manipulated environmental variability. FEMS Microbiology Ecology 38:69-76.

Lovell, C.R., Y.M. Piceno, J.M. Quattro, and C.E. Bagwell. 2000. Molecular analysis of diazotroph diversity in the rhizosphere of the smooth cordgrass, Spartina alterniflora. Applied and Environmental Microbiology 66:3814-3822.

Piceno, Y.M. and C.R. Lovell. 2000. Stability of natural bacterial communities: I. Nutrient addition effects on rhizosphere diazotroph assemblage composition. Microbial Ecology 39:32-40.

Piceno, Y.M. and C.R. Lovell. 2000. Stability of natural bacterial communities: II. Plant resource allocation effects on rhizosphere diazotroph assemblage composition. Microbial Ecology 39:41-48.

Piceno, Y.M., P.A. Noble, and C.R. Lovell. 1999. Spatial and temporal assessment of diazotroph assemblage composition in vegetated salt marsh sediments using denaturing gradient gel electrophoresis analysis. Microbial Ecology 38:157-167.

Bagwell, C.E., Y.M. Piceno, A.L. Ashburne, and C.R. Lovell. 1998. Physiological diversity of the rhizosphere diazotroph assemblages of selected salt marsh grasses. Applied and Environmental Microbiology 64:4276-4282.

Pinckney, J., Y. Piceno and C.R. Lovell. 1994. Short-term changes in the vertical distribution of benthic microalgal biomass in intertidal, muddy sediments. Diatom Research 9:143-153.

Lovell, C.R. and Y. Piceno. 1994. Purification of DNA from estuarine sediments. Journal of Microbiological Methods 20:161-174.

Steward, C.C., J. Pinckney, Y. Piceno and C.R. Lovell. 1992. Bacterial numbers and activity, microalgal biomass and productivity and meiofaunal distribution in sediments naturally contaminated with biogenic bromophenols. Marine Ecology Progress Series 90:61-71.
 

Tina Phillips

Background:

BS, Biology, Jacksonville University

Thesis title:

"Distribution of Bacterial Cells and Biovolume in Diopatra cuprea Burrow Lining Biofilms"
Completed M.S. Program:  May, 1998

Thesis abstract:

Recent studies have shown that the bulk microbial community associated with macrofaunal burrow linings is distinctly different from those at the sediment water interface and in the surrounding bulk sediments.  Activities of the macrofaunal host, such as type of burrow, exudates released, and irrigation frequency may affect the spatial distribution of bacteria within burrow lining biofilms and the potential for interactions among different species.  Bacterial distributions were determined in Diopatra cuprea tube lining biofilms using scanning confocal laser microscopy.  Distributions were examined on three spatial scales: (1) among different tubes, (2) at different locations within the tube, and (3) at different depths in the biofilm.  Bacterial cells were heterogeneously distributed within tubes.  The average concentration of cells among all tubes was 5.61 x 108 per cm3.  There was no trend in the distribution of cell numbers along the length of the tube or with increasing depth into the biofilm.  Average cell size across all tubes analyzed was 0.085 um3.  Two distinct trends were observed in the distribution of cell size.  As depth below the sediment surface increased in the tube, mean cell size increased.  As depth into the biofilm increased, mean cell size decreased.  Microcolonies were abundant and were not confined to specific depths within the biofilm or locations within the tube.  The distribution of potentially active cells was also examined.  Potentially active cells were observed at all depths within the biofilm and at least 46% of the cells at any given site within the tubes were potentially active.  The constituents of the biofilm rely mainly on the irrigation activity of the burrow host to deliver oxygen and/or nutrients.  We hypothesize that the rate and intensity of burrow irrigation have profound effects on the spatial organization of the biofilm community.

Publications:

Lovell, C.R., T.M. Phillips, and C.C. Steward. 1999. Activity of marine sediment bacterial communities exposed to increasing concentrations of 4-bromophenol, a polychaete secondary metabolite. Marine Ecology Progress Series 179:241-246.

Phillips, T.M. and C.R. Lovell. 1999. Distributions of total and active bacteria in biofilms lining tubes of the onuphid polychaete Diopatra cuprea. Marine Ecology Progress Series 183:169-178.

Jamey Watson

Background:

BS, Biological Sciences, University of South Carolina
Master of Arts in Teaching, University of South Carolina

Thesis title:

"Reductively Debrominating Strains of Propionigenium maris from Burrows of Bromophenol Producing Marine Infauna"
Completed M.S. Program:  May, 1998

Thesis abstract:

Two strains of Propionigenium maris able to reductively debrominate 2,4,6-tribromophenol, producing monobromophenols, were isolated from marine hemichordate (C.C. Steward et al., 1995) and polychaete burrows.  These strains, which are anaerobic, nonmotile, stain Gram negative, and are rod-shaped, grew in the presence of 0.05% yeast extract.  One strain (DSL-1) could ferment pyruvate and succinate, the other (ML-1) glucose and succinate, producing primarily butyrate and propionate, respectively.  No inorganic terminal electron acceptors were identified.  The pH and temperature optima for growth of DSL-1 were 7.6 and 30oC; 7.0 and 32oC for ML-1.  Doubling times for these strains under these conditions were 0.50 and 0.43 h, respectively.  Both strains required 2-3% (w/v) NaCl for optimal growth.  16S rRNA sequence analysis showed these to be new strains of Propionigenium maris.  They differ from the P. maris type stain (DSM 9537) in a number of respects, including their ability to debrominated di- and tribromophenols.

Publications:

Watson, J., G.Y. Matsui, A. Leaphard, F.A. Rainey, J. Wiegel, and C.R. Lovell. 2000. Reductively debrominating strains of Propionigenium maris from burrows of bromophenol producing marine infauna.  International Journal of Systematic and Evolutionary Microbiology 50:1035-1042.
 

Geralyne Lopez-de-Victoria

Background:

BS, Microbiology, University of Puerto Rico
MS, Microbiology, University of Puerto Rico
1993-95 DOE/EPSCoR Predoctoral Fellow

Dissertation Title:

"Analysis of Motility and Chemotaxis in the  Free-Living Nitrogen-Fixing Azospirillum spp."
Completed Ph.D. program:  December, 1995

Dissertation Abstract:

Azospirillum spp. are free-living nitrogen-fixing bacteria abundant in the rhizosphere of important crops such as rice, corn, and wheat.  The rhizosphere is relatively rich in potential carbon sources, including a variety of aromatic compounds.  The ability to detect and to utilize these compounds as growth substrates would contribute to survival and persistence of Azospirillum spp. and may enhance their ability to colonize the rhizosphere.

The ability of the free-living nitrogen fixing bacteria, Azomonas agilis, Azospirillum brasilense, Azospirillum lipoferum, Azotobacter chroococcum, Azotobacter vinelandii, and Beijerinckia mobilis, to grow and fix nitrogen using aromatics as their only carbon source was first evaluated.  All species grew and expressed nitrogenase activity on benzoate, catechol, 4-hydroxybenzoate, naphthalene, protocatechuate, and 4-toluate.  This study demonstrated that the ability to use aromatic compounds is more wide-spread among soil bacteria than previously thought.  In the second part of this project, chemotaxis of three Azospirillum strains to aromatic compounds was evaluated.  Some of these compounds are strong chemoattractants of Azospirillum species when supplied at levels well below the detection thresholds of other soil bacteria and within the concentration ranges reported for soils.  Distinct differences in chemotaxis between the two Azospirillum spp. studied were also observed.  Chemotaxis may contribute to survival, rhizosphere colonization, and the initiation of interactions with plants by Azospirillum spp.

The differences in the motility mechanisms between these two Azospirillum spp. were then evaluated using computer-assisted video motion analysis to measure speed, rate of change in direction, and net to gross displacement ratio of the organisms.  The experimental design used and analysis of data generated through this approach are reviewed in detail.  It was shown that A. lipoferum swims faster and in more circular patterns than A. brasilense.  The distinct differences in swimming behavior observed in response to aromatic compounds may be of ecological significance in soils.

These results confirm the hypotheses that aromatic compounds are utilizable by soil bacteria and that they are significant chemoattractants of Azospirillum spp.

Publications:

Lopez-de-Victoria, G., R.K. Zimmer-Faust, and C.R. Lovell. 1995. Computer assisted video motion analysis: a precise method for the study of motility and chemotaxis. Journal of Microbiological Methods 23:329-341.

Lopez-de-Victoria, G., D.R. Fielder, R.K. Zimmer-Faust and C.R. Lovell. 1994. Motility behavior of Azospirillum species in response to aromatic compounds. Canadian Journal of Microbiology 40:705-711.

Lopez-de-Victoria, G., and C.R. Lovell. 1993. Chemotactic behavior of Azospirillum species to aromatic compounds. Applied and Environmental Microbiology 59:2951-2955.

Chen, Y.P., G. Lopez-de-Victoria and C.R. Lovell. 1993. Utilization of aromatic compounds as carbon and energy sources during growth and N2-fixation by free-living nitrogen fixing bacteria. Archives of Microbiology159:207-212.
 

Charles Steward

Background:

BS, Biology, Fuhrman University

Dissertation Title:

"The Microbial Ecology of Estuarine Sediments Containing Biogenic Bromophenols"
Completed Ph.D. program:  August, 1994

Dissertation Abstract:

Infaunal worms producing halogenated secondary metabolites are common in marine sediments.  Haloaromatic compounds, such as bromophenols, are released from these animals and can be found at very high levels in the worm burrow sediments and at lower levels in nearby consolidated sediments.  Levels of bromophenols produced by the capitellid polychaete Notomastus lobatus typically reach levels of 100 ng/g sediment in consolidated sediments.  The specific role(s) of these compounds is not fully known but three hypotheses concerning their function have been proposed.  1) Halometabolites may serve as antimicrobial compounds, limiting bacterial growth on the animals and in their burrows.  2) The compounds may have an antipredator function, imparting an unpalatable taste to the animal.  3) The compounds may serve as positive or negative cues for recruitment of larvae.  The last two hypotheses have been addressed by other investigators.  The research described here addresses the antimicrobial hypothesis.

One goal of the project was to evaluate sediment microbial activity in the presence and absence of bromophenols.  A particularly useful index of microbial growth is their assimilation of growth substrates.  A new method for the extraction of assimilated radiolabel from estuarine sediments was developed in order to facilitate measurement of substrate assimilation rates.  Radiolabeled sediment cores underwent a series of washes to remove unincorporated radiolabel, followed by an alkaline extraction to recover assimilated radiolabel.  This method was highly successful in all sediments in which it was tested.

With the addition of the new method for recovering assimilated radiolabel from sediment bacteria, all of the methods needed for a detailed comparison of microbial communities in bromophenol contaminated and uncontaminated sediments were available.  Adjacent field sites (North Inlet salt marsh, Georgetown, SC) having markedly different levels of bromophenol contamination were selected and numerous microbial parameters including bacterial numbers, bacterial organic substrate assimilation and respiration rates, microalgal biomass and primary productivity and meiofaunal numbers were determined at these sites.  In addition, the distributions of bacteria and microalgae around N. lobatus burrows were examined in order to determine if these were affected by proximity to burrows containing high levels of bromophenols.  No significant impact of bromophenols on the biomass, distributions, or activities of microbial communities in consolidated sediments was identified.

The microbial communities of the bromophenol containing infaunal burrows were of great interest since the levels of these compounds are much higher in burrow lining sediments than in surrounding consolidated sediments.  The antimicrobial hypothesis predicts inhibition, resulting in lower biomass and species diversity in these burrows.  Microbial biomass and community structure were investigated in the burrows of three marine worms, two producing bromophenols and one non-bromophenol producer, using phospholipid fatty acid (PLFA) analysis.  PLFA analysis was also performed on nearby surface sediments and subsurface sediments collected for each of the three species of worms.  No impact of biogenic bromophenols on worm burrow microbial biomass and community structure was observed.  Rather, the worm burrows are microenvironments supporting abundant and diverse microbial communities.

The observation that levels of bromophenols are much lower in surrounding consolidated sediments than in worm burrow lining sediments raised the question of turnover of these compounds.  Specifically, are sediment bacteria responsible for significant degradation of these compounds?  Rates of degradation of 4-bromophenol (4-BP) were determined in undisturbed sediment cores by measuring respiration and assimilation of 14C-4BP.  Similar rates of 4-BP degradation were found at a field site containing 4-BP and a comparable site lacking this compound.  Respiration rates followed a clear seasonal trend, with higher rates measured during the warmer months.  This pattern was consistent with the results of temperature response experiments.  It appears that 4-BP is a labile carbon source which can be readily utilized by estuarine sediment bacteria.

Laboratory studies were completed on anaerobic enrichment cultures and an obligately anaerobic bacterium (DSL-1) isolated from the burrow of a bromophenol producing hemichordate.  Both the enrichments and DSL-1 reductively dehalogenated 2,4,6-tribromophenol to 2,4-dibromophenol, 4-bromophenol and finally phenol.  Cultures were grown on a basal salts recipe, supplemented with 1 mM 2,4,6-tribromophenol and 0.5% yeast extract.  The cultures were not capable of utilizing the phenol as a carbon source. One (1) mM tribromophenol could be dehalogenated to micromolar levels in 36 hours.  These studies provide evidence that debrominating bacteria are found in worm burrow sediments and can be easily recovered from bromophenol containing worm burrows.

All of the data collected during these studies support the conclusion that biogenic bromophenols do not inhibit growth or activity of sediment microorganisms.  Consequently, the antimicrobial hypothesis is rejected.
 

Lining of the N. lobatus burrow showing oxidized sediment surrounded by reduced bulk sediment.
Publications:

Lovell, C.R., T.M. Phillips, and C.C. Steward. 1999. Activity of marine sediment bacterial communities exposed to increasing concentrations of 4-bromophenol, a polychaete secondary metabolite. Marine Ecology Progress Series 179:241-246.

Steward, C.C. and C.R. Lovell. 1997. Respiration and assimilation of 4-bromophenol by estuarine sediment bacteria. Microbial Ecology 33:198-205.

Steward, C.C., S.C. Nold, D.B. Ringelberg, D.C. White, and C.R. Lovell. 1996. Microbial biomass and community structure in the burrows of bromophenol producing and non-producing marine worms and surrounding sediments. Marine Ecology Progress Series 133:149-165.

Steward, C.C., T. Dixon, Y.P. Chen and C.R. Lovell. 1995. Enrichment and isolation of a reductively debrominating bacterium from the burrow of a bromometabolite producing marine hemichordate. Canadian Journal of Microbiology 41:637-642.

Steward, C.C., J. Pinckney, Y. Piceno and C.R. Lovell. 1992. Bacterial numbers and activity, microalgal biomass and productivity and meiofaunal distribution in sediments naturally contaminated with biogenic bromophenols. Marine Ecology Progress Series 90:61-71.

Steward, C.C. and C.R. Lovell. 1992. Improved method for recovery and quantitation of assimilated radiolabel from sediment bacteria. Journal of Microbiological Methods 16:221-230.

Former undergraduate students (chronological listing):

Yvonne Hui: 1988-90

"Sequence homology of formyltetrahydrofolate synthetase genes"

Publications:

Lovell, C.R. and Y. Hui. 1991. Design and testing of a functional group specific DNA probe for the study of natural populations of acetogenic bacteria. Applied and Environmental Microbiology 57:2602-2609.

Lewinski, K., Y. Hui, C.G. Jakob, C.R. Lovell and L. Lebioda. 1993. Crystallization and preliminary crystallographic data for formyltetrahydrofolate synthetase from Clostridium thermoaceticum.  Journal of Molecular Biology 229:1153-1156.

Linda Layman: 1989

"Techniques in molecular biology"

Todd Engles: 1991

"Techniques in molecular biology"

Jamie Watson: 1991

"Techniques in molecular biology"

Brooke Bickley: 1991-92

"Techniques in molecular biology", "Microbial degradation of  haloaromatics"

Terry Dixon: 1992-94

Honors Senior Thesis Title:

"Reductive Dehalogenation:  Characterization of a Reductively Debrominating Organism and  Purification of a Reductive Dehalogenase"

South Carolina College Research Fellowship, 1992-93
Howard Hughes Summer Undergraduate Research Fellow, 1993
Goldwater Scholarship, 1993.

Publication:

Steward, C.C., T. Dixon, Y.P. Chen and C.R. Lovell. 1995. Enrichment and isolation of a reductively debrominating bacterium from the burrow of a bromometabolite producing marine hemichordate. Canadian Journal of Microbiology 41:637-642.

Christopher Bagwell: 1993-95

"Molecular characterization of nitrogen fixing bacteria"

Howard Hughes Summer Undergraduate Research Fellow, 1994.
Department of Biological Sciences Outstanding Senior Award, 1995.

Publication:

Bagwell, C.E., Y.M. Piceno, A.L. Ashburne, and C.R. Lovell. 1998. Physiological diversity of the rhizosphere diazotroph assemblages of selected salt marsh grasses. Applied and Environmental Microbiology 64:4276-4282.

See the "Former graduate students" section for publications from Kitt's graduate program.

Jeffrey Stephens: 1994-95

Honors Senior Thesis Title:

"Biochemistry of Dehalogenation".

Adam Leaphart: 1993-96

Honors Senior Thesis Title:

"Formyltetrahydrofolate Synthetase"

Nominated for the Goldwater Scholarship, 1995.
Howard Hughes Summer Undergraduate Research Fellow, 1995.
Current Ph.D. student.

Amy Ashburn: 1995-96

"Molecular characterization of nitrogen fixing bacteria".

Howard Hughes Academic Year Undergraduate Research Fellow, 1995

Publication:

Bagwell, C.E., Y.M. Piceno, A.L. Ashburne, and C.R. Lovell. 1998. Physiological diversity of the rhizosphere diazotroph assemblages of selected salt marsh grasses.  Applied and Environmental Microbiology 64:4276-4282.

Tae Uk Ho: 1995-96

"Sulfate reduction"

Julia Smith: 1996-97

"Physiological characterization of nitrogen fixing bacteria"

Howard Hughes Summer Undergraduate Research Fellow, 1996.

Lorone Washington: 1996-97

"Physiological characterization of nitrogen fixing bacteria".

EPSCoR Undergraduate Research Fellow, 1996-97.
Howard Hughes Summer Undergraduate Research Fellow, 1997.

Daniel Boyer: 1997-98

"Dehalogenation by bacteria growing on or in bromometabolite producing marine polychaetes and hemichordates".

Howard Hughes Summer Undergraduate Research Fellow, 1998.

Corey Wilson: 1998

"Phylogenetic analysis of protein families".

Eugene Wang: 1999

"Analysis of bacterial communities".

Peter Bergholz:  1998-99

"Isolation and characterization of diazotrophic bacteria from the rhizosphere of Spartina patens".
"Physiological responses of rhizosphere diazotrophs to toxins".

Howard Hughes Summer Undergraduate Research Fellow, 1999.

Research Technician 1999-2001.

Publications:

LaRocque, J., P.W. Bergholz, C.E. Bagwell, and C.R. Lovell. 2004. Influence of host plant-derived and abiotic environmental parameters on the composition of the diazotroph assemblage associated with roots of Juncus roemerianus. Antonie van Leeuwenhoek 68:249-261.    

 

Bagwell, C.E., M. Dantzler, P.W. Bergholz, and C.R. Lovell. 2001. Host-specific ecotypic diversity of rhizoplane diazotrophs of the perennial glasswort, Salicornia virginica and selected salt marsh grasses. Aquatic Microbial Ecology 23:293-300.

Bergholz, P.W., C.E. Bagwell, and C.R. Lovell. 2001. Physiological diversity of rhizoplane diazotrophs of the saltmeadow cordgrass, Spartina patens.  Implications for host specific ecotypes. Microbial Ecology 42:466-473.

 

Megan Dantzler: 1999-2001

Honors Senior Thesis Title:

"Physiological diversity of culturable, oxygen utilizing diazotrophic bacteria associated with the oligohaline grass Spartina cynosuroides"

Howard Hughes Academic Year Undergraduate Research Fellow, 1999-00.
SC EPSCoR Undergraduate Research Fellow, Summer 2000.

Publications:

Bagwell, C.E., M. Dantzler, P.W. Bergholz, and C.R. Lovell. 2001. Host-specific ecotypic diversity of rhizoplane diazotrophs of the perennial glasswort, Salicornia virginica and selected salt marsh grasses. Aquatic Microbial Ecology 23:293-300.

Jeannine (Jan) LaRoque: 1999-2002

"Physiological responses of diazotrophic bacteria to toxins"
"Diversity and distributions of diazotrophic bacteria associated with two populations of the black needle rush, Juncus roemerianus."

T.L. McMeekin Scholarship, 2001-2002.
Howard Hughes Academic Year Undergraduate Research Fellowship, 2001-2002.

Publications:

LaRocque, J., P.W. Bergholz, C.E. Bagwell, and C.R. Lovell. 2004. Influence of host plant-derived and abiotic environmental parameters on the composition of the diazotroph assemblage associated with roots of Juncus roemerianus. Antonie van Leeuwenhoek 68:249-261.    

 

Bagwell, C.E., J.R. La Rocque, G.W. Smith, S.W. Polson, M.J. Friez, J.W. Longshore, and C.R. Lovell. 2002. Molecular diversity of diazotrophs in oligotrophic seagrass bed communities. FEMS Microbiology Ecology 39:113-119.

 

Clint Page: 2000-2002

"Physiological characterization of rhizosphere bacteria and their products"
"Phylogenetic affiliations of culturable diazotrophic bacteria from roots of selected salt marsh plants"

Howard Hughes Summer Undergraduate Research Fellow, 2001.

Chris Freeman: 2000-2002

"Diazotrophic bacteria from the rhizosphere of Thalassia testudinum"

 

Peter V. Decker: 2001-2002

"A comparison of methods for analysis of microbial assemblages"

Kanika McAlpine: 2001-2002

 

“Phylogenetic analysis of diazotrophic bacteria”

 

 

Daniel Gilstrap: 2001-2002

 

“Recovery and molecular analysis of diazotroph diversity present in sediment and separated root samples in a Salicornia virginica and Spartina alterniflora mixed zone”

 

Howard Hughes Summer Undergraduate Research Award, 2002

 

Julie Criminger: 2002-2003 

“Phylogenetic analysis of diazotrophic bacteria”

Howard Hughes Summer Undergraduate Research Award, 2002

 

Forrest Snipes:  2003

 

“Characterization of novel diazotrophic bacteria”

 

Howard Hughes Summer Undergraduate Research Award, 2003

 

Field Research Sites:

Most projects in my lab have strong field research components.  We often use pure culture or microcosm studies to extend our results from field observations and experimentation, but most projects begin and end in the field.  My favorite location for field research is the North Inlet salt marsh system near Georgetown, SC.  This system is a euhaline estuary dominated by the salt marsh cordgrass, Spartina alterniflora. The system contains numerous small creeks, intertidal sandflats, and oyster reefs, providing a nice variety of research sites.  The North Inlet marsh is a part of the Hobcaw Barony property managed by the Baruch Foundation and is the major research site of the Baruch Institute.  The Hobcaw Barony property has been set aside for marine research and preservation and access to it is strictly controlled.  The North Inlet system is one of the last pristine east coast salt marshes and is a vital comparison site in the National Estuarine Research Reserve System.   The Institute maintains a modern field laboratory facility at North Inlet and provides lab space, housing, and boats for field research projects. Extensive synoptic data on the North Inlet system are also available through the Institute.  The North Inlet Microbial Observatory is based in the Crab Haul Creek basin, near to the Baruch Institute Field Laboratory.
 

Baruch Institute Field Laboratory at North Inlet.

Several nearby sites offer additional research opportunities.  Murrells Inlet is located just north of North Inlet and is also a NERRS site.  This system is structurally similar to North Inlet, but has extensive commercial and residential development.  Winyah Bay is located just south of North Inlet and is an open estuarine system, also with substantial human impact via urban development, and urban, industrial, and agricultural runoff.  We have also done a little sampling in the Charleston Harbor area, which has been heavily impacted by urban development and industrial pollution.

This document last modified December 3, 2004.