03.2020 | THE SCIENTIST 15Notebook
NEWS AND ANALYSISTHIBAUT BRUNET, KING LAB
Rhodopsins on
Loan
A
few years ago, Alexandra Worden
was watching as an $800,
medical-grade fluorescence
activated single-cell sorter dangled
from a crane, about to be loaded onto
a research vessel—and hoping the crane
operator appreciated just how delicate
the equipment was. The marine micro-
bial ecologist and her colleagues were
about to set sail on the Atlantic Ocean
to collect unicellular eukaryotes and
sequester them individually for single-
cell whole-genome sequencing. The trip
was part of a survey that also includedexpeditions on the Pacific Ocean to find
archaea, bacteria, and other organisms
associated with these microbes. Worden
and her collaborators wanted to avoid
bringing the seawater samples back to
the lab, which would risk distorting the
bio diversity of the sample—“some guys
just don’t make it,” says Worden, espe-
cially when it can take days to steam
back to shore. So instead, they’d decided
to bring the lab to the field.
With the crane operation well-
executed and the instrument safely on
board, the crew set off on its journey. The
researchers gathered seawater, fluores-
cently stained cells for a food vacuole to
label those organisms that were actively
eating, and fed samples to the cell sorterto sift out the fluorescent cells from the
rest. The vast majority of cells selected
turned out to be choano flagellates, pred-
atory eukaryotes that feed on bacteria.
The team then began looking for bac-
teria and archaea among the choano-
flagellates, but in doing the sequencing to
identify prokaryote genomes, “we weren’t
getting a big signal,” says Worden, a pro-
fessor at GEOMAR, the Helmholtz Cen-
tre for Ocean Research in Kiel, Germany,
and a senior scientist at the Monterey Bay
Aquarium Research Institute (MBARI)
in California.MARCH 2020MARINE PREDATORS: Choanoflagellates
(pictured here in a multicellular state) are
eukaryotes that feed on bacteria in the ocean.