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Genome Streamlining in Ocean Bacterioplankton

2015/7/19 2500

2015-07-21 10:00-11:30

Dr. Stephen J. Giovannoni, Professor

B103, Jinquan Bldg (College of the Environment and Ecology)

Abstract:

The simplest free-living chemoheterotrophic bacteria known are the SAR11 clade of alphaproteobacteria. Paradoxically, with genome sizes of only 1.2-1.5 Mbp they oxidize 5-20% of all carbon fixed each day on Earth. Recently it has been recognized that small genome size is a common feature of uncultured bacteria from many environments. Small genomes raise questions about the strategies used by chemoheterotrophic cells to interact with complex organic matter. Small cells and genomes have been attributed to selection that favors minimization of cell size and complexity in nutrient-limited systems to reduce the resources required for replication, a process known as streamlining. Regardless of the cause of genome reduction, lost coding potential eventually dictates loss of function, raising the questions, what genome features are expendable, and how do cells become highly successful with a minimal genomic repertoire? One consequence of reductive evolution in streamlined organisms is atypical patterns of prototrophy, for example the recent discovery of a requirement for the thiamin precursor 4-amino-5-hydroxymethyl-2-methylpyrimidine in some plankton taxa. Examples such as this fit within the framework of the Black Queen Hypothesis, which describes genome reduction that results in reliance on community goods and increased community connectivity. Other examples of genome reduction include losses of regulatory functions, or replacement with simpler regulatory systems, and increased metabolic integration. In one such case, in the order Pelagibacterales, the P_IIsystem for regulating responses to N limitation has been replaced with a simpler system composed of fewer genes. Both the absence of common regulatory systems and atypical patterns of prototrophy have been linked to difficulty in culturing Pelagibacterales, lending credibility to the idea that streamlining might broadly explain the phenomenon of the uncultured microbial majority. The success of streamlined osmotrophic bacterioplankton suggests that they successfully compete for labile organic matter and capture a large share of this resource, but an alternative theory postulates they are not good resource competitors and instead prosper by avoiding predation. The answers to these complex questions hinge on translating gene frequencies into trait based ecological models that reflect the systems biology of cells.

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