In a paper published April 26th in mSystems, a team of researchers led by microbiologists at Oregon State University, in Corvallis, describe a successful trial of a new method of identifying the carbon uptake of specific marine bacterioplankton taxa. The technique uses proteomics – the large-scale study of proteins – to observe directly the metabolic processes of communities of microorganisms.
Oregon State microbiologist Ryan Mueller, senior author on the paper, says the technique illuminates the carbon uptake process at three levels. “It shows how much is being used, by which microbes, and how they’re using it to produce new proteins,” he says. “It provides information about which organisms are taking up different substrates.”
Marine bacterioplankton play a critical role in the carbon cycle. They recycle chemicals and decompose carbon-rich material like dissolved free amino acids (DFAA), which can result from many processes including lysing cells or phytoplankton bloom die-offs. Bacterioplankton process half of the organic carbon fixed by phytoplankton and other microbes through photosynthesis, but not all microbial communities have the same uptake rates. Linking particular taxa to metabolic responses has been an open question in the field for decades.
The researchers tested their new method, called proteomic stable isotopic probing, or proteomic-SIP, on eight seawater samples, including six collected from the ocean at Monterey Bay, California, and two from Newport, Oregon. To those samples they added DFAAs enriched with the isotope carbon-13. Using high-resolution mass spectrometry, they extracted and analyzed proteins from the samples – half of the samples after 15 hours, and the other half after 32 hours. They used software developed by researchers at Oak Ridge National Laboratory, in Tennessee, to analyze the proteomics data.