Roberta Hansman
Scripps Institution of Oceanography
Geosciences Research Division
9500 Gilman Drive
La Jolla, CA 92093-0208
email: rhansman (at) ucsd (dot) edu
phone: 858-822-0988
CV:
Rapid advances in molecular biological techniques have enabled a more detailed study of microorganisms and microbial communities in their environments. DNA isolation and genomic sequencing from environmental samples have revolutionized what is known about microbial diversity and abundance in a way that could never have been previously determined from culture dependent studies. Previously unknown phylogenetic groups and domains of life that were believed to be unique to extreme environments appear to be ubiquitous in the water. This newly exposed phylogenetic diversity highlights the vast physiological capabilities of the microbial community. However, genetic studies alone cannot elucidate the microbial ecology of the oceans or the biogeochemical role microorganisms play in the environment.Contrary to the hypothesis that prokaryotes are primarily heterotrophic and consume only the new fraction of DOC, the carbon isotopic signature of particular cellular biochemicals suggest that prokaryotes in the water column contain (and therefore, incorporate) aged carbon and that planktonic Archaea are chemoautotrophs. Several questions arise from these findings: Are Archaea obligate chemoautotrophs? Can both Archaea and bacteria consume refractory organic carbon? Is there a refractory organic matter specialist or is there some plasticity to these metabolic roles?
Recently, "molecular biogeochemical" studies (the combination of molecular biology and molecular-level geochemistry) have been very successful at identifying the ecological niches occupied by particular phylogenetic groups. These studies used a combination of fluorescence in-situ hybridization using specific16S rRNA-targeted oligonucleotide probes and molecular-level isotopic studies of specific lipid biomarkers to identify the biogeochemical role of Archaea and bacteria in sediments. Based on the success of these studies we suggest that molecular-level organic geochemistry, when combined with the existing and ongoing molecular biological studies, will provide valuable insight into the particular ecological and biogeochemical niches occupied by diverse members of the microbial community.
My research focuses on the interactions between prokaryotes and the various carbon pools in the sub-surface ocean: DOC (dissolved organic carbon), DIC (dissolved inorganic carbon), and POC (particulate organic carbon)/fresh DOC. More specifically, I am interested in determining which carbon sources fuel prokaryotic production in the deep ocean. We can use the radiocarbon (14C) concentration of cellular biochemicals to trace the sources of carbon assimilated by the prokaryotic community. Heterotrophic prokaryotes assimilate organic compounds as DOC either directly into biomass, or for subsequent breakdown and re-synthesis of new molecules. Autotrophic prokaryotes access the inorganic carbon pool and fix DIC to create their cellular components. Since the building blocks for new biochemicals are assimilated from the environment, intracellular compounds will bear the isotopic signature of the compounds obtained from surrounding deep waters. The 14C concentrations of the DOC and DIC pools are quite different in the deep ocean; thus it is possible to distinguish these carbon source(s) to the pelagic organisms. 
In my research, the biomarker for total prokaryotes in the meso- and bathypelagic ocean will be nucleic acids. Nucleic acids, like most other organic compounds in prokaryotes, are synthesized de novo in cells using building blocks such as carbon, nitrogen and phosphorous, acquired from the environment. The source of this carbon may be either organic (heterotrophic production) or inorganic (autotrophic production); and all viable cells will contain a nucleic acid component, while dead, ghost, or detrital cells will not. Hence, nucleic acid analysis will provide a snapshot of the active community at each sampling location.As a supplement to this isotope work, I am also interested in analyzing the microbial ecology of my study sites. Through a suite a molecular biological techniques, I hope to gain a better understanding of the diversity and interactions of the microorganisms present. Prokaryotic abundances are determined using DAPI staining and epifluorescence microscopy counting. Samples are collected for fluorescent in-situ hybridization (FISH) analyses to determine the quantitative contribution of bacteria and archaea to total prokaryotic abundance. PCR (polymerase chain reaction) combined with DGGE (denaturing gradient gel electrophoresis) is performed on extracted nucleic acids to qualitatively address the prokaryotic community composition of both bacteria and archaea, as well as to visualize potential biases in our extraction method. Bands of interest from DGGE can then be cloned and sequenced to further elucidate the components of the microbial community.
