Research Interests (Global Research Projects: 1, 2)

The activities of bottom-dwelling organisms modify the physical and chemical properties of sediments very near the sediment-water interface and thereby influence a variety of ecological processes. My research interests concern 1) the importance of macrofauna and meiofauna to microbial activities, particularly as they affect the decomposition of organic matter in marine sediments; 2) the bacterial dominance of benthic biological communities and processes in tropical deltaic environments; 3) the impact of physical disturbance on the structure and functioning of benthic communities in marine environments and the identification of biological indicators of those physical processes; and 4) the development of biosensors for the study of microbial processes in sediments.

In collaboration with colleagues at SoMAS (Robert Aller, Paul Kemp, and Ph.D student Vanessa Madrid), Andrei Chistoserdov (ULa Lafayette), and Dan Alongi and Gregg Brunskill (AIMS, Townsville, AU) my research group continues to study the structure and dynamics (recruitment, growth, survival, and activities) of benthic communities in tropical coastal regions off French Guiana and Papua New Guinea. We are interested in elucidating the major physical, chemical, and biological factors controlling diagenetic and benthic community patterns, evaluating the importance of biological activities to sedimentary and geochemical processes in these environments, and identifying biological indicators of these processes. Of particular interest is to understand the association of the sedimentary microbial community with metal-sulfur-and carbon cycles in mobile mud belts and high sedimentation deltaic/margin regions in general.

My other active research area involves the development of biosensor technology for the study of microbial processes in the marine environment. This work involves a continued collaborative effort with Paul Kemp, Harbans Dhadwal (Electrical Engineering), and Ph.D. student Megan Dantzler to develop and optimize an optical nucleic-acid hybridization biosensor for rapid, quantitative detection of the abundance and expression of targeted bacterial genes, and the activity of targeted organisms in a mixed microbial community. Additionally efforts with Andrei Y. Chistoserdov (Ula Lafayette), Paul F. Kemp and Harbans S. Dhadwal are directed toward the development of microarray technology for multiparamenter assessments of the presence, physiological status, and activity of pathogens or harmful microorganisms in the marine environment.

In addition to my research and teaching activities, I coordinate a NSF/NY State Sea Grant sponsored summer undergraduate research experience (REU) site program, which brings 8 undergraduate students from universities throughout the U.S. to SoMAS for 8 weeks during the summer.

Recent Selected Publications

Aller J.Y. and R.C. Aller. 2003. Bacterial dominance of benthic communities in tropical deltaic environments of the Gulf of Papua. Continental Shelf Research Special Volume (in press).

Aller J.Y., R.C. Aller, and M.A. Green 2002. Benthic Faunal Assemblages and Carbon Supply along the Continental Shelf/Shelf Break-Slope off Cape Hatteras, North Carolina. Deep-Sea Research II Special Volume: Biogeochemistry and cycling of carbon in the northwest Atlantic continental margin: findings of the Ocean Margins Program 49(20), 4599-4628.

Aller, R.C., J.Y. Aller, and P.F. Kemp. 2001. Effects of particle and solute transport on rates and extents of remineralization in bioturbated sediments. In: Organism-Sediment Interactions (J.Y. Aller, R.C. Aller, and S. Woodin, eds.) Univ. So. Carolina Press, Columbia S.C. pp. 315-334.

Rhoads, D.C., R. Ward, J.Y. Aller, and R.C. Aller. 2001 The importance of technology in benthic research and monitoring: Looking back to see ahead. In: Organism-Sediment Interactions (J.Y. Aller, R.C. Aller, and S. Woodin, eds.) Univ. So. Carolina Press, Columbia S.C. pp. 1-17.

Madrid, V.M., J.Y. Aller, R.C. Aller, and A.Y. Chistoserdov. 2001. Analysis of high prokaryote diversity and community structure in mobile muds off French Guiana: identification of two new sediment-specific bacterial candidate divisions. FEMS Microbiology Ecology 37, 197-209

Todorov, J.R., J.Y. Aller, A.Y. Chistoserdov, and R.C. Aller. 2000. Molecular microbial diversity in physically disturbed coastal sediments of southeastern Papua New Guinea. FEMS Microbiology Ecology 33(2), 147-155

Aller, R.C. and J.Y. Aller. 1998. The effect of biogenic irrigation intensity and solute exchange on diagenetic reaction rates in marine sediments. Journal of Marine Research. 56, 905-936.

Gerino, M., R. Aller, C. Lee, K. Cochran, J. Aller, M. Green, and D. Hirschberg. 1998. Comparison of different tracers and methods (in situ, laboratory) used to quantify bioturbation during a spring bloom: 234-Thorium, luminophores, and Chl-a. Estuarine Coastal Shelf Science 46, 531-547.

Aller, J.Y. and J.R. Todorov. 1997. Seasonal and spatial patterns of deeply buried calanoid copepods on the Amazon Shelf: Evidence for periodic erosion and deposition cycles. Estuarine Coastal Shelf Science. 44, 57-66.

Aller, J.Y. 1997. Benthic community response to temporal and spatial gradients in physical disturbance within a deep-sea Western Boundary Region. Deep-Sea Research. 44, 39-69.

Aller, J.Y. and I. Stupakoff. 1996. The distribution and seasonal characteristics of benthic communities on the Amazon Shelf as indicators of physical processes. Continental Shelf Research 16, 717-751.

Aller, J.Y. 1995. Molluscan death assemblages on the Amazon Shelf: implications for physical and biological controls on benthic populations. Palaeogeography, Palaeoclimatology, Palaeoecology 118, 181-212.