Preliminary experiment for cell count using flow cytometry: Expedition 329

Abstract

One of the major challenges in microbial ecology is to evaluate the accurate number of living cells in a natural environment. Cell count using flow cytometry is a powerful, high-throughput technique that has widely been used for aquatic habitats but not for sedimentary environments because mineral grains interfere with cell detection. During Integrated Ocean Drilling Program Expedition 329, we tested several sample preparation methods for onboard cell counting using flow cytometry with various pelagic sediments from the South Pacific Gyre. The cell numbers acquired from shallow sediments are almost consistent with microscopic direct counts (i.e., ~105 cells/cm3). Yet, the method needs improvement and standardization to reduce the background signal and to lower the minimum detection limit for deep sedimentary habitats with very low cell densities (i.e., <1000 cells/cm3).