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Josephine Y. Aller


Ph.D., 1975, University of Southern California

Microbial-biogeochemistry, Marine benthic ecology, Biosensors




Research Interests

My research group is currently involved in several distinct areas of inquiry supported through grants from NSF and NOAA. One major area of long term research focuses on the geomicrobiology of animal-sediment interactions, the bacterial dominance of benthic biological communities and processes in tropical deltaic environments, 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. 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. The biological communities also closely reflect properties of the physical environment and depositional facies, and therefore they can be useful indicators of hydrodynamic and transport processes past and present, particularly in remote locales where it is not possible to extensively instrument and continuously monitor sedimentary dynamics. We are particularly interested in the reworked and fluidized fine grained deposits that characterize vast areas of the world’s coastlines today particularly in the tropics and which were almost certainly one of the dominant microbial ecosystems of the early Earth. As a result of frequent physical disturbance there is little evidence of macro- or meiofaunal activities in these sediments. Instead, they contain very abundant and active populations of phylogenetically and metabolically diverse microbes. This research involves collaborations with R. Aller and J. Mak at SBU and colleagues at the University of Louisiana, Lafayette, University of Hawaii, and Australian Institute of Marine Science, Townsville, AU. Our research areas include the Amazon – Guianas dispersal system off French Guiana), and the Fly River dispersal system in the Gulf of Papua, Papua New Guinea.

My research group continues to be interested in microbial dynamics at the sea-air boundary. We are particularly concerned with mechanisms involved in the concentration and transfer of microorganisms from the ocean through the sea surface microlayer (SML) to the atmosphere as aerosols, the formation and characteristics of these aerosols, and transport in the atmosphere as an important means of dispersal of viable microorganisms. The sea-surface microlayer (SML) at the atmosphere/hydrosphere boundary is the upper 0-1 mm and represents a unique biological, physical and chemical habitat where microbial and other organisms, organic matter, and a variety of anthropogenic substances can be greatly enriched in comparison to subsurface waters. As an interface, it serves as a source and a sink for materials in the atmosphere and the water column. Most marine aerosols originate when air bubbles burst at the surface ejecting material from the sea surface microlayer and bubble surface layer into the atmosphere and thus contain inorganic salts, organic matter, and microorganisms similar to those in seawater. One of my current projects in collaboration with Daniel Knopf involves examining ocean sea spray aerosol particles including sea-salts and mixed inorganic/organic matter in ice cloud formation.

Another area of active 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 colleagues from Electrical Engineering at SBU, the University of Hawaii, and the Monterey Bay Aquarium Research Institute (MBARI). In situ biosensors have been identified repeatedly as a high priority for effective and reliable in situ instrumentation to provide long-term, high-resolution observations of critical environmental parameters in the ocean in recent workshops and conferences. However, few microbial biosensors have been developed, and fewer still are capable of remotely sensing aquatic microbial populations and processes. Over the past several years we developed the Capillary Waveguide Biosensor (CWB) a bench top instrument capable of rapid, quantitative detection of picogram quantities of specific, targeted nucleic acid sequences through repeated cycles over long intervals n samples of marine microbial communities. We are now working to transform the CWB into an automated, in situ monitoring device by changing it to an interchangeable sensor module for deployment as an analytical module within the Environmental Sample Processor (ESP) developed by Dr. Christopher Scholin and colleagues at MBARI.

Additional research concerns factors that influence the persistence and transmission of human enteric viruses in marine coastal environments including the water, benthic organisms particularly molluscs, in sediments, and in aerosols over coastal waters. Viral pollution in the marine environment is of great concern due to the discharge of human viral pathogens into coastal waters via wastewater discharges and land runoff.

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


Aller, J.Y. and P. F. Kemp. 2008. Archaeal versus bacterial phylogenetic diversity: A comparison across environments. FEMS Microbiology Ecology 65:74-87.

Dhadwal, H. S., B. Mukherjee, P. Kemp, J. Aller, Y. Liu, and J. Radway. 2007. A Dual Detector Capillary Waveguide Sensor for Detection and Quantification of Hybridized Target Species. Analytica Chimica Acta. 598: 147-154

Aller, J. Y., D. M. Alongi, and R. C. Aller. 2008. Biological indicators of sedimentary dynamics in the central Gulf of Papua: Seasonal and decadal perspectives, In: The Papuan Continuum: Source to Sink through the Fly River System and the Gulf of Papua JGR Earth Surface MARGINS Special Issue Journal of Geophysical Research, 113, F01S08, doi:10.1029/2007JF000823.

Madrid, V.M., R.C. Aller, J.Y. Aller and A.Y. Chistoserdov. 2006. Evidence of the activity of dissimilatory sulfate-reducing prokaryotes in nonsulfidogenic tropical mobile muds. FEMS Microbial Ecology 57:169-181.

Aller, J.Y., M.M. Kuznetsova, C.J. Jahns, P.F. Kemp. 2005. Enrichment of viruses and bacteria in the sea surface microlayer and marine aerosols. Journal of Aerosol Science 36(5/6): 801-812.

Kuznetsova M., C. Lee, J. Aller. 2005. Characterization of the proteinaceous matter in marine aerosols. Marine Chemistry 96:59-377.

Kemp, P. F. and J.Y. Aller. 2004. Bacterial diversity in aquatic and other environments: what can we learn from 16S rDNA libraries FEMS Microbiology Ecology 47(2):161-177.

Kemp, P. F. and J.Y. Aller. 2004. Estimating prokaryotic diversity: When are libraries large enough? Limnology and Oceanography Methods 2: 114-125.

Aller, J.Y. and R.C. Aller. 2004. Physical Disturbance creates bacterial dominance of benthic biological communities in tropical deltaic environments of the Gulf of Papua. Continental Shelf Research 24:2395-2416

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 Part II 49: 4599-4626.

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 Microbiol. Ecol 37: 197-209

Aller, J.Y., R.C. Aller, and S. A. Woodin. (Editors) Organism-Sediment Interactions. 2001. Univ. So. Carolina Press, Columbia S.C. 403 pp. Proceedings of a symposium/workshop held in October 1998 dedicated to D.C. Rhoads and addressing important research issues regarding the interactions of benthic organisms and the sediments.

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. 315-333.

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


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