Proteomics directed environmental genomics

Proteomic approaches are ideal for in situ verification of microbial processes.  In a preliminary study, we identified multiple cyanobacterial nutrient uptake proteins in a sample taken at 60m in the Sargasso Sea, demonstrating feasibility of environmental proteomics to query the nutrient status of dominant community members.  In a collaboration with the Rocap lab, we are conducting a proteomic and genomic survey of Prochlorococcus and Synechococcus to explore the role of nutrient and stress response genes in shaping community structure of marine cyanobacteria.  

Specific Objectives:

• Identify membrane associated nutrient uptake and stress response proteins from diverse ecotypes of marine cyanobacteria in culture
• Survey vertical variability in the membrane meta-proteome of picoplankton populations in distinct nutrient regimes in the South Atlantic

 Bacterioplankton-phytoplankton interactions

Bacteria and Archaea play important roles in the global carbon cycle by assimilating dissolved organic carbon (DOC) produced and released by phytoplankton and processing it through the microbial loop.  However, it is unknown why bacterioplankton assimilate such a broad range (30 to 60%) of DOC produced by phytoplankton.  Previous studies have indicated that bacteria increase in abundance during bloom periods and that some marine bacteria produce allelopathic compounds.  One explanation for these observations is that algicidal bacteria act as pathogens, infecting algal hosts and assimilating DOC that is released following cell death.  An alternative hypothesis is that bacterial responses are passive, which suggests that the DOC assimilated by bacteria is released by phytoplankton though sloppy feeding by zooplankton or by viral lysis. Although both active and passive processes have been demonstrated in the laboratory, the mechanisms of DOC release for consumption by bacteria in nature are not well understood.  The objective in this project is to identify mechanisms of DOC release and assimilation by bacterioplankton during phytoplankton blooms.

 Cultivation

Although most microbial lineages in nature have evaded cultivation, improved high throughput cultivation (HTC) strategies have lead to the cultivation of several novel marine isolates, including the first representative from the ubiquitous and abundant SAR11 clade (Rappe et al., 2002).  One of our research objectives is to continue to develop high throughput cultivation based approaches to isolate novel  representatives from previously uncultured groups of marine bacteria.  The metabolism of novel isolates obtained by HTC will be characterized using genomic and proteomic approaches.