Thamdrup, B. New Pathways and processes in the global nitrogen cycle. Annu. Rev. Ecol. Evol. Syst. 43, 407–428 (2012).
Lam, P. et al. Revising the nitrogen cycle in the Peruvian oxygen minimum zone. Proc. Natl. Acad. Sci. USA 106, 4752–4757 (2009).
Google Scholar
Behrendt, A., de Beer, D. & Stief, P. Vertical activity distribution of dissimilatory nitrate reduction in coastal marine sediments. Biogeosciences 10, 7509–7523 (2013).
Fossing, H. et al. Concentration and transport of nitrate by the mat-forming sulphur bacterium. Thioploca. Nature 374, 713–715 (1995).
Google Scholar
McHatton, S. C., Barry, J. P., Jannasch, H. W. & Nelson, D. C. High nitrate concentrations in vacuolate, autotrophic marine Beggiatoa spp. Appl. Environ. Microbiol. 62, 954–958 (1996).
Google Scholar
Kamp, A., Høgslund, S., Risgaard-Petersen, N. & Stief, P. Nitrate storage and dissimilatory nitrate reduction by eukaryotic microbes. Front. Microbiol. 6, 1492 (2015).
Eppley, R. W. & Rogers, J. N. Inorganic nitrogen assimilation of Ditylum brightwellii, a marine plankton diatom. J. Phycol. 6, 344–351 (1970).
Google Scholar
Lomas, M. & Glibert, P. Comparisons of nitrate uptake, storage, and reduction in marine diatoms and flagellates. J. Phycol. 36, 903–913 (2000).
Google Scholar
Jørgensen, B. B. & Gallardo, A. Thioploca spp.: filamentous sulfur bacteria with nitrate vacuoles. FEMS Microbiol. Ecol. 28, 301–313 (1999).
Schulz, H. N. et al. Dense populations of a giant sulfur bacterium in Namibian shelf sediments. Science 284, 493–495 (1999).
Google Scholar
Risgaard-Petersen, N. et al. Evidence for complete denitrification in a benthic foraminifer. Nature 443, 93–96 (2006).
Google Scholar
Kamp, A., de Beer, D., Nitsch, J. L., Lavik, G. & Stief, P. Diatoms respire nitrate to survive dark and anoxic conditions. Proc. Natl. Acad. Sci. USA 108, 5649–5654 (2011).
Google Scholar
Stief, P. et al. Dissimilatory nitrate reduction by Aspergillus terreus isolated from the seasonal oxygen minimum zone in the Arabian Sea. BMC Microbiol. 14, 35 (2014).
Høgslund, S., Cedhagen, T., Bowser, S. S. & Risgaard-Petersen, N. Sinks and sources of intracellular nitrate in gromiids. Front. Microbiol. 8, 617 (2017).
Harold, F. M. The Vital Force: A Study of Bioenergetics (WH Freeman & Co., 1986).
Katz, M. E., Finkel, Z. V., Grzebyk, D., Knoll, A. H. & Falkowski, P. G. Evolutionary trajectories and biogeochemical impacts of marine eukaryotic phytoplankton. Annu. Rev. Ecol. Evol. Syst. 35, 523–556 (2004).
Villareal, T. A., Altabet, M. A. & Culverrymsza, K. Nitrogen transport by vertically migrating diatom mats in the North Pacific Ocean. Nature 363, 709–712 (1993).
Google Scholar
Kamp, A., Stief, P. & Schulz, H. N. Anaerobic sulfide oxidation with nitrate by a freshwater Beggiatoa enrichment culture. Appl. Environ. Microbiol. 72, 4755–4760 (2006).
Google Scholar
Merz, E. et al. Nitrate respiration and diel migration patterns of diatoms are linked in sediments underneath a microbial mat. Environ. Microbiol. 23, 1422–1435 (2021).
Google Scholar
Leblanc, K. et al. A global diatom database–abundance, biovolume and biomass in the world ocean. Earth Syst. Sci. Data 4, 149–165 (2012).
Benoiston, A. S. et al. The evolution of diatoms and their biogeochemical functions. Phil. Trans. R. Soc. B 372, 20160397 (2017).
Nelson, D. M., Tréguer, P., Brzezinski, M. A., Leynaert, A. & Queguiner, B. Production and dissolution of biogenic silica in the ocean-revised global estimates, comparison with regional data and relationship to biogenic sedimentation. Global Biogeochem. Cycl. 9, 359–372 (1995).
Google Scholar
Sarthou, G., Timmermans, K. R., Blain, S. & Tréguer, P. Growth physiology and fate of diatoms in the ocean: a review. J. Sea Res. 53, 25–42 (2005).
Google Scholar
Dortch, Q., Clayton, J. R., Thoresen, S. S. & Ahmed, S. I. Species differences in accumulation of nitrogen pools in phytoplankton. Mar. Biol. 81, 237–250 (1984).
Google Scholar
Kamp, A., Stief, P., Knappe, J. & de Beer, D. Response of the ubiquitous pelagic diatom Thalassiosira weissflogii to darkness and anoxia. PLoS ONE 8, e82605 (2013).
Kamp, A., Stief, P., Bristow, L. A., Thamdrup, B. & Glud, R. N. Intracellular nitrate of marine diatoms as a driver of anaerobic nitrogen cycling in sinking aggregates. Front. Microbiol. 7, 1669 (2016).
Needoba, J. A. & Harrison, P. J. Influence of low light and a light:dark cycle on NO3− uptake, intracellular NO3−, and nitrogen isotope fractionation by marine phytoplankton. J. Phycol. 40, 505–516 (2004).
Google Scholar
Lomas, M. W. & Glibert, P. M. Temperature regulation of nitrate uptake: A novel hypothesis about nitrate uptake and reduction in cool-water diatoms. Limnol. Oceanogr. 44, 556–572 (1999).
Google Scholar
Lomas, M. W., Rumbley, C. J. & Glibert, P. M. Ammonium release by nitrogen sufficient diatoms in response to rapid increases in irradiance. J. Plankton Res. 22, 2351–2366 (2000).
Google Scholar
Van Tol, H. M. & Armbrust, E. V. Genome-scale metabolic model of the diatom Thalassiosira pseudonana highlights the importance of nitrogen and sulfur metabolism in redox balance. PLoS ONE 16, e0241960 (2021).
Piña-Ochoa, E. et al. Widespread occurrence of nitrate storage and denitrification among Foraminifera and Gromiida. Proc. Natl. Acad. Sci. USA 107, 1148–1153 (2010).
García-Robledo, E., Corzo, A., Papaspyrou, S., Jimenez-Arias, J. L. & Villahermosa, D. Freeze-lysable inorganic nutrients in intertidal sediments: dependence on microphytobenthos abundance. Mar. Ecol. Prog. Ser. 403, 155–163 (2010).
Marchant, H. K., Lavik, G., Holtappels, M. & Kuypers, M. M. M. The fate of nitrate in intertidal permeable sediments. PLoS ONE 9, e104517 (2014).
Villareal, T. A. & Lipschultz, F. Internal nitrate concentrations in single cells of large phytoplankton from the Sargasso Sea. J. Phycol. 31, 689–696 (1995).
Google Scholar
Smith, G. J., Zimmerman, R. C. & Alberte, R. S. Molecular and physiological responses of diatoms to variable levels of irradiance and nitrogen availability: Growth of Skeletonema costatum in simulated upwelling conditions. Limnol. Oceanogr. 37, 989–1007 (1992).
Google Scholar
Montagnes, D. J. S. & Franklin, D. J. Effect of temperature on diatom volume, growth rate, and carbon and nitrogen content: Reconsidering some paradigms. Limnol. Oceanogr. 46, 2008–2018 (2001).
Google Scholar
Smith, S. R. et al. Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom. Nat. Commun. 10, 4552 (2019).
Behrenfeld, M. J. et al. Thoughts on the evolution and ecological niche of diatoms. Ecol. Monogr. 91, e01457 (2021).
Bourke, M. F. et al. Metabolism in anoxic permeable sediments is dominated by eukaryotic dark fermentation. Nat. Geosci. 10, 30–35 (2017).
Google Scholar
Härnström, K., Ellegaard, M., Andersen, T. J. & Godhe, A. Hundred years of genetic structure in a sediment revived diatom population. Proc. Natl. Acad. Sci. USA 108, 4252–4257 (2011).
Pelusi, A., Santelia, M. E., Benvenuto, G., Godhe, A. & Montresor, M. The diatom Chaetoceros socialis: spore formation and preservation. Europ. J. Phycol. 55, 1–10 (2020).
Google Scholar
Petterson, K. & Sahlsten, E. Diel patterns of combined nitrogen uptake and intracellular storage of nitrate by phytoplankton in the open Skagerrak. J. Exp. Mar. Biol. Ecol. 138, 167–182 (1990).
Petterson, K. Seasonal uptake of carbon and nitrogen and intracellular storage of nitrate in planktonic organisms in the Skagerrak. J. Exp. Mar. Biol. Ecol. 151, 121–1137 (1991).
Bode, A., Botas, J. A. & Fernandez, E. Nitrate storage by phytoplankton in a coastal upwelling environment. Mar. Biol. 129, 399–406 (1997).
Google Scholar
Stief, P., Kamp, A., Thamdrup, B. & Glud, R. N. Anaerobic nitrogen turnover by sinking diatom aggregates at varying ambient oxygen levels. Front. Microbiol. 7, 98 (2016).
Jensen, M. M. et al. Intensive nitrogen loss over the Omani Shelf due to anammox coupled with dissimilatory nitrite reduction to ammonium. ISME J. 5, 1660–1670 (2011).
Google Scholar
Magalhaes, C. M., Wiebe, W. J., Joye, S. B. & Bordalo, A. A. Inorganic nitrogen dynamics in intertidal rocky biofilms and sediments of the Douro River estuary (Portugal). Estuaries 28, 592–607 (2005).
Google Scholar
Burgin, A. J. & Hamilton, S. K. Have we overemphasized the role of denitrification in aquatic ecosystems? A review of nitrate removal pathways. Front. Ecol. Environ. 5, 89–96 (2007).
Kühl, M., Glud, R. N., Ploug, H. & Ramsing, N. B. Microenvironmental control of photosynthesis and photosynthesis-coupled respiration in an epilithic cyanobacterial biofilm. J. Phycol. 32, 799–812 (1996).
Heisterkamp, I. M. et al. Shell biofilm-associated nitrous oxide production in marine molluscs: processes, precursors and relative importance. Environ. Microbiol. 15, 1943–1955 (2013).
Google Scholar
Fernandez-Mendez, M. et al. Composition, buoyancy regulation and fate of ice algal aggregates in the Central Arctic Ocean. PLoS ONE 9, e107452 (2014).
Boetius, A. et al. Export of algal biomass from the melting Arctic sea ice. Science 339, 1430–1432 (2013).
Google Scholar
Abed, R. M. M. & Garcia-Pichel, F. Long-term compositional changes after transplant in a microbial mat cyanobacterial community revealed using a polyphasic approach. Environ. Microbiol. 3, 53–62 (2001).
Google Scholar
Al-Najjar, M. A. A., de Beer, D., Kühl, M. & Polerecky, L. Light utilization efficiency in photosynthetic microbial mats. Environ. Microbiol. 14, 982–992 (2012).
Google Scholar
Heisterkamp, I. M., Kamp, A., Schramm, A. T., de Beer, D. & Stief, P. Indirect control of the intracellular nitrate pool of intertidal sediment by the polychaete Hediste diversicolor. Mar. Ecol. Prog. Ser. 445, 181–192 (2012).
García-Robledo, E., Corzo, A. & Papaspyrou, S. A fast and direct spectrophotometric method for the sequential determination of nitrate and nitrite at low concentrations in small volumes. Mar. Chem. 162, 30–36 (2014).
Grasshoff, K. In Methods of Seawater Analysis (eds Grasshoff, K., Ehrhardt, M., Kremling, K.) 143–150 (Verlag Chemie Weinheim, 1983).
Braman, R. S. & Hendrix, S. A. Nanogram nitrite and nitrate determination in environmental and biological materials by vanadium(III) reduction with chemiluminescence detection. Anal. Chem. 61, 2715–2718 (1989).
Google Scholar
Meier, D. V. et al. Limitation of microbial processes at saturation-level salinities in a microbial mat covering a coastal salt flat. Appl. Environ. Microbiol. 87, e00698–21 (2021).
Google Scholar
Sode, K., Horikoshi, K., Takeyama, H., Nakamura, N. & Matsunaga, T. Online monitoring or marine cyanobacterial cultivation based on phycocyanin fluorescence. J. Biotechnol. 21, 209–217 (1991).
Google Scholar
Berns, D. S., Scott, E. & Oreilly, K. T. C-phycocyanin-minimum molecular weight. Science 145, 1054–1055 (1964).
Google Scholar
Hillebrand, H., Durselen, C. D., Kirschtel, D., Pollingher, U. & Zohary, T. Biovolume calculation for pelagic and benthic microalgae. J. Phycol. 35, 403–424 (1999).
Zimmermann, J., Jahn, R. & Gemeinholzer, B. Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols. Org. Divers. Evol. 11, 173–192 (2011).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Google Scholar
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl. Acids Res. 41, D590–D596 (2013).
Google Scholar
Round, F. E., Crawford, R. M. & Mann, D. G. The Diatoms: Biology and Morphology of the Genera. 747p (Cambridge University Press, 1990).
Medlin, L. K. Evolution of the diatoms: major steps in their evolution and a review of the supporting molecular and morphological evidence. Phycologia 55, 79–103 (2016).
Google Scholar
McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
Google Scholar
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer Verlag, 2016).
Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5-7. https://CRAN.R-project.org/package=vegan (2020).
Stief, P. Intracellular Nitrate Storage by Diatoms-Source data. figshare. Dataset. https://doi.org/10.6084/m9.figshare.19790176.v1 (2022).
Source: Ecology - nature.com
