incorporate those substrates can be detected, and even quantified, with various tools,
providing a quantitative measurement. Combining this incubation approach with
mass spectrometry can provide further detail, particularly if the instrument has single
cell resolution, such as the NanoSIMS (Nanoscale secondary ion mass spectrometer). NanoSIMS stable isotope probing, also known as NanoSIP (Pett-Ridge and
Weber 2012), enables the quantification of biogeochemical activity at the single cell
level, which at least partially addresses two scientific needs: (1) linking activity and
identity for microbial biogeochemistry and (2) studying microbes at the scale at
which they behave (the single-cell scale). For more information, I refer the reader to
a recent review on this topic (Mayali 2020). Although NanoSIP, unfortunately,
cannot measure biochemical activities not linked to growth (such as catabolic
processes, e.g., respiration), it still provides useful data on microbial biogeochemical
activities coupled to substrate incorporation into biomass. Several other drawbacks
include the fact that the instrument used for this type of spectrometry is very
expensive, requires highly skilled technicians to operate it, and analytically is slow
(i.e., not high throughput). Still, in my opinion, it remains a state-of-the-art method
to measure microbial biogeochemical activity in situ at the single cell level and will
continue to yield exciting discoveries over the next decades.
13.3 Algal-Bacteria Interactions in the Face of Climate
Change
Most of the increased CO 2 from the atmosphere is absorbed by the oceans, which
among other impacts causes ocean acidification (Doney et al. 2009). Phytoplankton
photosynthesis supports aquatic carbon sequestration; thus these organisms directly
impact and are impacted by increasing CO 2 concentrations. Climate change also has
led to increasing ocean temperatures. A number of studies have investigated the
impacts of temperature and CO 2 on carbon cycling in aquatic environments, but
these studies are still too few and far-between and generally suffer from the caveats
described above (lack of activity measurements, inability to link small and large
scales). In particular, there is a lack of mechanistic studies that investigate how
climate impacts small-scale biogeochemical interactions. For example, how is climate change going to impact the exchange of metabolites between microbial cells in
the ocean? Do phytoplankton make more or less utilizable organic material when
stressed by climate impacts? More research is needed in this area, even beyond
studies related to climate change. More importantly, new approaches need to be
developed that can bridge the small and large scales and that offer mechanistic and
predictive abilities. Most likely, these methods will be computational in nature, since
modeling can in some cases successfully investigate phenomena that are not possible
to reproduce experimentally (Stubbendieck et al. 2016; Gould et al. 2018; Diener
et al. 2020).
208
X. Mayali
providing a quantitative measurement. Combining this incubation approach with
mass spectrometry can provide further detail, particularly if the instrument has single
cell resolution, such as the NanoSIMS (Nanoscale secondary ion mass spectrometer). NanoSIMS stable isotope probing, also known as NanoSIP (Pett-Ridge and
Weber 2012), enables the quantification of biogeochemical activity at the single cell
level, which at least partially addresses two scientific needs: (1) linking activity and
identity for microbial biogeochemistry and (2) studying microbes at the scale at
which they behave (the single-cell scale). For more information, I refer the reader to
a recent review on this topic (Mayali 2020). Although NanoSIP, unfortunately,
cannot measure biochemical activities not linked to growth (such as catabolic
processes, e.g., respiration), it still provides useful data on microbial biogeochemical
activities coupled to substrate incorporation into biomass. Several other drawbacks
include the fact that the instrument used for this type of spectrometry is very
expensive, requires highly skilled technicians to operate it, and analytically is slow
(i.e., not high throughput). Still, in my opinion, it remains a state-of-the-art method
to measure microbial biogeochemical activity in situ at the single cell level and will
continue to yield exciting discoveries over the next decades.
13.3 Algal-Bacteria Interactions in the Face of Climate
Change
Most of the increased CO 2 from the atmosphere is absorbed by the oceans, which
among other impacts causes ocean acidification (Doney et al. 2009). Phytoplankton
photosynthesis supports aquatic carbon sequestration; thus these organisms directly
impact and are impacted by increasing CO 2 concentrations. Climate change also has
led to increasing ocean temperatures. A number of studies have investigated the
impacts of temperature and CO 2 on carbon cycling in aquatic environments, but
these studies are still too few and far-between and generally suffer from the caveats
described above (lack of activity measurements, inability to link small and large
scales). In particular, there is a lack of mechanistic studies that investigate how
climate impacts small-scale biogeochemical interactions. For example, how is climate change going to impact the exchange of metabolites between microbial cells in
the ocean? Do phytoplankton make more or less utilizable organic material when
stressed by climate impacts? More research is needed in this area, even beyond
studies related to climate change. More importantly, new approaches need to be
developed that can bridge the small and large scales and that offer mechanistic and
predictive abilities. Most likely, these methods will be computational in nature, since
modeling can in some cases successfully investigate phenomena that are not possible
to reproduce experimentally (Stubbendieck et al. 2016; Gould et al. 2018; Diener
et al. 2020).
208
X. Mayali