MASUMI STADLER28 THE SCIENTIST | the-scientist.com
methane, and thereby making the carbon
available to other organisms. But research-
ers still don’t know much about how fresh-
water microbes participate in that cycle.
Stadler got the chance to tackle this
topic when she started her PhD. Her lab,
led by biogeochemist Paul del Giorgio,
was already immersed in a massive proj-
ect designed to trace the carbon footprint
of the Romaine before, during, and after
the development of a hydroelectric com-
plex currently under construction along
the river. This meant the team had already
selected hundreds of sampling sites across
hundreds of kilometers, starting from the
river’s headwaters and spanning down to
estuaries opening into the Gulf of St. Law-
rence, passing through streams, lakes, and
reservoirs along the way.
To learn which microbes were present
in different habitats along the river’s water-
shed, Stadler and colleagues took advan-
tage of the group’s existing sampling sites,
going out into the field for a few weeks at a
time during spring, summer, and autumn
to collect water and soil from around 50 to
70 sites at a time—braving mosquitoes and
biting black flies in the summer and snow
in the spring and autumn.After collecting samples during the day,
Stadler and her lab mates spent the eve-
nings processing the samples in a rented
space that operated as their makeshift lab,
a 13-hour drive from the group’s actual lab
space in Montreal. Eventually, after at least
three months of field sampling spread over
a few years, the team sent samples from
nearly 400 sites out for sequencing.
When the results came in, Stadler and
del Giorgio analyzed the bacterial com-
munities, identifying nearly 600 families,and published their findings in The ISME
Journal last November (doi:10.1038/
s41396-021-01146-y, 2021). The most
abundant bacterial taxa overall included
the phyla Proteobacteria (now Pseudomo-
nadota) and Verrucomicrobia (now Ver-
rucomicrobiota), plus the superphylum
Patescibacteria, the researchers report
in their paper; however, the composi-
tion of the microbial communities varied
depending on whether the samples camefrom soil, groundwater, or river water.
Composition changed along the length
of the river, too, from northern headwa-
ters down toward the ocean. Because the
researchers sampled at different times
of year, they also saw that the bacterial
communities changed with the seasons.
Although there were only two authors on
the paper, “this was a real team effort,”
Stadler says, noting the hard work of
graduate students, postdocs, and under-
graduates who contributed to the project.Eva Lindström, a microbial ecolo-
gist and limnologist at the University of
Uppsala, agrees that the project repre-
sented an enormous amount of work. She
adds that it’s “very uncommon that you
manage to get such a nice data set with
so many different types of environments.”
Lindström was a postdoctoral fellow in
del Giorgio’s lab in 2004 and collaborates
on editorial work with him, but was not
involved with the current study. “We have
a good case here of getting to understand
a bit more about the biogeography and
the biodiversity of bacteria,” she says, sup-
plementing work from other groups sug-
gesting that there is considerable spatial
diversity among microbial communities
within particular landscapes.
To distinguish between living bacteria
and dead or dormant ones, the researchers
performed RNA sequencing in addition to
standard DNA sequencing. RNA is less sta-
ble than DNA and doesn’t stick around for
a long time, so it’s a better proxy for living
bacteria. The team classified bacteria that
were only detected by DNA sequencing as
“unreactive” and bacteria with detectable
RNA as “reactive.”
Stadler and colleagues found that the
ratio of unreactive to reactive bacteriaFROM AFAR: Some locations the researchers
visited were so remote they could only be
accessed by seaplane.Researchers might be missing something important if they
exclude less-abundant bacterial species from their analyses.NOTEBOOK