Research Topics:

Want to learn more about Raman microspectroscopy and atomic force microscopy and how they can be applied to single cell analysis? Tune in to this YouTube video.

My group’s research efforts have focused on (i) microbial mediation of biogeochemical processes (particularly carbon cycling), (ii) food web interactions among microorganisms (bacteria, protozoans, algae and viruses), and (iii) and linking ecological function to specific microbial community members. Microbiological and chemical exchange processes through the water column and at oxic/anoxic, solid/water and air/water boundaries have been particular foci of our group.

Microbiological processes are intimately linked to the fate of carbon in the ocean and are responsive to climatic changes. As founding members of the NSF-funded CARIACO Ocean Time Series Program (1995-2017), our team’s research in the anoxic Cariaco Basin has improved understanding of current carbon cycling dynamics in the southern Caribbean Sea on the continental margin of Venezuela. Beyond being intrinsically fascinating, the Cariaco Basin serves as a model for other oxygen-depleted bodies of water (e.g., the Gulf of Mexico “Dead Zone”, Long Island Sound, Black Sea, the Baltic and Mediterranean Deeps, major Oxygen Minimum Zones, and fjords), which are expanding geographically as climate changes and as human populations impact coastal waters, a process referred to as ocean deoxygenation. Our group has focused on microbial dynamics, biogeochemistry and transformations of organic materials transported from oxic to anoxic waters. We are particularly motivated to understand the process of chemoautotrophy. The reason being that chemoautotrophic carbon fixation is globally important to food webs and can link carbon, nitrogen and sulfur cycles. Our group combines traditional microbial ecological and geochemical measurements with modern molecular techniques, such as SSU rRNA libraries, stable isotope probing (SIP), fluorescence in situ hybridization (FISH), and quantitative PCR of functional genes and their expression, to unravel the interplay between chemical gradients, elemental cycling and microbial population dynamics.

Our holy grail has been to understand the role(s) of specific microbial populations across wide-ranging geochemical seascapes. Making such linkages improves inferences about the role of specific microorganisms discovered within massive genomic databases. To that end, we have built an exciting analytical service center within SoMAS - the NAno-Raman Molecular Imaging Laboratory (NARMIL), through NSF’s Major Research Instrumentation funding. NARMIL houses a novel, state-of-the-art Renishaw inVia confocal laser Raman microspectrophotometer which permits 3-D mapping of biomolecules, minerals, and synthetic materials, while also providing fluorescent, bright field and differential interference contrast (DIC) images. By combining SIP, phylogenetic FISH probes and Raman mapping, we determine identity of individual cells and their activity in assimilating isotopic labels. NARMIL also houses a Bruker Innova Atomic Force Microscope (AFM), which produces topographic images comparable to scanning electron microscopy, but under standard lab conditions. Coupling these instruments enables nanometer-scale chemical maps of specimen surfaces. NARMIL provides SoMAS with unique and powerful analytical tools with countless applications throughout the natural sciences, biomedicine, and engineering. We are enthusiastically exploring new research frontiers with these novel capabilities! For example, Raman microspectroscopy has enabled identification and quantification of microplastics (0.5-500 mm diameter) and microbial degradation in the ocean. This technology has also allowed us to measure single-cell growth rates of heterotrophic and autotrophic microorganisms. To learn more about our facility, please visit: http://you.stonybrook.edu/nanoraman/.