The microbial nitrogen cycle is one of the most complex and environmentally important
element cycles on Earth, but most studies focus exclusively on the direct involvement
of prokaryotes. Therefore, this Research Topic was launched to attract more attention
to the role of eukaryotic microbes in the nitrogen cycle. In seven contributions,
new findings on intracellular storage and the dissimilatory and assimilatory use of
nitrate by eukaryotic microbes are summarized and discussed.
The Research Topic was inaugurated with a Review Article that provides an overview
of the ecophysiology of nitrate storage and dissimilatory nitrate reduction by diverse
marine eukaryotes (Kamp et al.). The review emphasizes that eukaryotic nitrate storage
and dissimilatory nitrate reduction are far more widespread than previously envisioned.
Even though this field of research is still in its infancies, recent advances further
strengthen the ecological significance of this metabolic trait. Dissimilatory nitrate
reduction has now been confirmed in various species, which are so far covering four
out of eight major lineages in the eukaryotic tree of life, i.e., foraminifers, diatoms,
fungi, and ciliates. Nitrate storage has been found in even six out of the eight lineages,
i.e., foraminifers, gromiids, diatoms, fungi, dinoflagellates, haptophytes, and chlorophytes.
A compilation of intracellular nitrate inventories in various sediments indicates
that the eukaryotic intracellular nitrate pools vastly exceed porewater nitrate pools.
Quantitative estimates on the phylogenetic partitioning of dissimilatory nitrate reduction
suggest that eukaryotes may even rival prokaryotes in certain sediments.
The Review Article was followed by six Original Research Articles. Two of them focus
on nitrate storage and nitrogen turnover in sinking diatom-bacteria aggregates (Kamp
et al.; Stief et al.). Depending on their size and respiration activity, diatom-bacteria
aggregates can develop an anoxic center even at relatively high oxygen concentrations
in the surrounding water. Aggregates sinking through oxygenated waters might thus
be important hot spots for anaerobic nitrogen conversions, including denitrification
and thus fixed-nitrogen loss. Anoxia inside the aggregates enables nitrate-storing
and aggregate-forming diatoms, such as Skeletonema marinoi, to perform Dissimilatory
Nitrate Reduction to Ammonium (DNRA). Interestingly though, the nitrate initially
stored by diatoms also becomes available to the bacterial community of the aggregate
during its descent. This partially uncouples the denitrification activity by aggregate-associated
bacteria from ambient nitrogen supplies. It was also speculated that intracellular
nitrate not converted before the aggregates have settled onto the seafloor might fuel
benthic nitrogen transformations (Marzocchi et al., 2017).
Two articles of this Research Topic deal with foraminifers, which were the first marine
eukaryotes, found to perform denitrification on intracellular nitrate in anoxic conditions
(Risgaard-Petersen et al., 2006). This groundbreaking finding has since stimulated
research on denitrification by foraminifera and their endobionts (e.g., Piña-Ochoa
et al., 2010; Bernhard et al., 2012). Here, additional research activities centering
on foraminifera exposed to anoxic conditions are presented. Nitrate incorporation
and subsequent assimilation by foraminifera, or possibly by their endobionts, in dysoxic
or anoxic conditions has been studied by Nomaki et al. An important conclusion was
that foraminiferal (intracellular) nitrate is not solely used for denitrification,
but can also fuel nitrogen assimilation, even in oxygen-depleted environments. Along
these lines, the in situ experiments with 13C- and 15N-labeled phytodetritus by Enge
et al. provide insights into organic C and N uptake by calcareous foraminifera that
were studied along a depth transect in sediments of the Oxygen Minimum Zone of the
Arabian Sea. The study revealed that the cellular C/N uptake-ratio is lower, if foraminifers
are exposed to lower oxygen concentrations. The authors discuss that the low C/N uptake-ratio
is due to a greater demand or storage of organic (i.e., food-based) nitrogen in anoxic
conditions and that it is potentially used (as nitrate) for denitrification and thus
for energy conservation.
Gromiids are rather large, nitrate-storing protists that, similar to diatom-bacteria
aggregates, may turn anoxic internally due to their own respiration activity. Sources
and sinks of intracellular nitrate in gromiids and the potential role of their bacterial
endobionts in the ensuing nitrate dynamics were studied by Høgslund et al. Tracer
experiments with 15N revealed that intracellular nitrate is both taken up from the
environment and produced internally, probably by bacterial endobionts performing nitrification.
Anoxia triggers denitrification activity that is apparently mediated by bacterial
endobionts since it can be inhibited by antibiotics.
The article by Garcia-Robledo et al. addresses the spatial-temporal dynamics of inorganic
nutrients in the sediment of an intertidal mudflat with previously unseen comprehensiveness.
The magnitude and relative importance of porewater, intracellular, and exchangeable
pools of nitrate, ammonium, and phosphate were correlated with the seasonal dynamics
in abundance and photosynthetic activity of benthic microalgae. Interestingly, exchangeable
nitrate, i.e., nitrate ionically adsorbed to organic matter or clay particles, accounted
for the largest fraction of the total sedimentary nitrate pool, a phenomenon so far
only described for ammonium and phosphate. These results suggest that anoxic sediment
layers may actually harbor two sources of nitrate, i.e., intracellular and exchangeable
nitrate, which might supply electron acceptors to the microbial community.
In summary, this Research Topic reports novel findings on nitrate storage and use
across a broad phylogeny reaching from diatoms (and other microalgae) to foraminifers
and gromiids. The included studies address the ecophysiology of the organisms and
their environmental impact on pelagic and benthic habitats as well as in anoxic micro-niches,
such as diatom-bacteria aggregates or even inside of gromiids. Further, the metabolic
fate of assimilated nitrogen and the biogeochemical role of intracellular vs. adsorbed
nitrogen compounds in sediments were revealed. The new perspectives provided here
are expected to stimulate more research on the eukaryotic players in the nitrogen
cycle, especially since their ecological significance is becoming increasingly clear.
Author contributions
All authors listed have made a substantial, direct and intellectual contribution to
the work, and approved it for publication.
Conflict of interest statement
The authors declare that the research was conducted in the absence of any commercial
or financial relationships that could be construed as a potential conflict of interest.