Protist grazing contributes to microbial food web at the upper boundary of the twilight zone in the subarctic Pacific

2020 ◽  
Vol 636 ◽  
pp. 235-241 ◽  
Author(s):  
HM McNair ◽  
S Menden-Deuer
Keyword(s):  
Primary Production ◽  
Food Web ◽  
Single Cell ◽  
Euphotic Zone ◽  
Twilight Zone ◽  
Particulate Carbon ◽  
Surface Ocean ◽  
Tropical Environments ◽  
The Impact ◽  
Upper Boundary

Grazing by herbivorous protists (microzooplankton) is a major loss pathway of primary production in the surface ocean, yet its impact below the well-lit surface ocean is largely unknown. The upper boundary of the twilight zone is critically important to understanding carbon cycling and is often the depth of highest attenuation of particulate carbon flux. Available measurements of primary production and grazing below the well-lit surface ocean suggest that the upper boundary of the twilight zone may harbor active but poorly constrained food web processes. Previous grazing rates from the base of the euphotic zone were measured in subtropical and tropical environments. Thus, the impact of protist grazing on prey populations remains unknown in colder conditions at higher latitudes. To advance understanding and provide mechanistic insight into processes occurring at the base of the euphotic zone (0.4-0.7% PAR), we measured predation rates on both phytoplankton and heterotrophic prokaryotes in the North Pacific, using a novel method that amplified the grazing signal by concentrating the predator community, enabling detection of grazing rates far below previous limits. Protists consumed 0.6% of the phytoplankton population daily and 12% of daily heterotrophic prokaryote growth. These conservative rate measurements document marginal removal of phytoplankton even in these colder regimes, implying flows of energy from single-cell primary producers and prokaryotes to single-cell protists at rates far below previous detection limits in this twilight region of a low-productivity system.

scholarly journals Quantifying carbon fluxes from primary production to mesopelagic fish using a simple food web model

2018 ◽  
Vol 76 (3) ◽  
pp. 690-701 ◽  
Author(s):  
Thomas R Anderson ◽  
Adrian P Martin ◽  
Richard S Lampitt ◽  
Clive N Trueman ◽  
Stephanie A Henson ◽  
...  
Keyword(s):  
Primary Production ◽  
Food Web ◽  
Flow Analysis ◽  
World Ocean ◽  
Field Studies ◽  
Mesopelagic Fish ◽  
Fish Biomass ◽  
Analysis Model ◽  
Surface Ocean ◽  
Carbon Transfer

Abstract An ecosystem-based flow analysis model was used to study carbon transfer from primary production (PP) to mesopelagic fish via three groups of copepods: detritivores that access sinking particles, vertical migrators, and species that reside in the surface ocean. The model was parameterized for 40°S to 40°N in the world ocean such that results can be compared with recent estimates of mesopelagic fish biomass in this latitudinal range, based on field studies using acoustic technologies, of ∼13 Gt (wet weight). Mesopelagic fish production was predicted to be 0.32% of PP which, assuming fish longevity of 1.5 years, gives rise to predicted mesopelagic fish biomass of 2.4 Gt. Model ensembles were run to analyse the uncertainty of this estimate, with results showing predicted biomass >10 Gt in only 8% of the simulations. The work emphasizes the importance of migrating animals in transferring carbon from the surface ocean to the mesopelagic zone. It also highlights how little is known about the physiological ecology of mesopelagic fish, trophic pathways within the mesopelagic food web, and how these link to PP in the surface ocean. A deeper understanding of these interacting factors is required before the potential for utilizing mesopelagic fish as a harvestable resource can be robustly assessed.

scholarly journals The role of mixotrophic protists in the biological carbon pump

2014 ◽  
Vol 11 (4) ◽  
pp. 995-1005 ◽  
Author(s):  
A. Mitra ◽  
K. J. Flynn ◽  
J. M. Burkholder ◽  
T. Berge ◽  
A. Calbet ◽  
...  
Keyword(s):  
Climate Change ◽  
Primary Production ◽  
Food Web ◽  
Nutrient Recycling ◽  
Biogeochemical Cycling ◽  
Trophic Levels ◽  
Biological Pump ◽  
Nutrient Regeneration ◽  
New Paradigm ◽  
The Impact

Abstract. The traditional view of the planktonic food web describes consumption of inorganic nutrients by photoautotrophic phytoplankton, which in turn supports zooplankton and ultimately higher trophic levels. Pathways centred on bacteria provide mechanisms for nutrient recycling. This structure lies at the foundation of most models used to explore biogeochemical cycling, functioning of the biological pump, and the impact of climate change on these processes. We suggest an alternative new paradigm, which sees the bulk of the base of this food web supported by protist plankton communities that are mixotrophic – combining phototrophy and phagotrophy within a single cell. The photoautotrophic eukaryotic plankton and their heterotrophic microzooplankton grazers dominate only during the developmental phases of ecosystems (e.g. spring bloom in temperate systems). With their flexible nutrition, mixotrophic protists dominate in more-mature systems (e.g. temperate summer, established eutrophic systems and oligotrophic systems); the more-stable water columns suggested under climate change may also be expected to favour these mixotrophs. We explore how such a predominantly mixotrophic structure affects microbial trophic dynamics and the biological pump. The mixotroph-dominated structure differs fundamentally in its flow of energy and nutrients, with a shortened and potentially more efficient chain from nutrient regeneration to primary production. Furthermore, mixotrophy enables a direct conduit for the support of primary production from bacterial production. We show how the exclusion of an explicit mixotrophic component in studies of the pelagic microbial communities leads to a failure to capture the true dynamics of the carbon flow. In order to prevent a misinterpretation of the full implications of climate change upon biogeochemical cycling and the functioning of the biological pump, we recommend inclusion of multi-nutrient mixotroph models within ecosystem studies.

scholarly journals Morphodynamic signatures of MDA-MB-231 single cells and cell doublets undergoing invasion in confined microenvironments

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xingjian Zhang ◽  
Trevor Chan ◽  
Michael Mak
Keyword(s):  
Single Cell ◽  
Single Cells ◽  
Leading Edge ◽  
Cell Group ◽  
Collective State ◽  
Long Term Effects ◽  
Cell Metastasis ◽  
Geometric Confinement ◽  
Short And Long Term ◽  
The Impact

AbstractCancer cell metastasis is a major factor in cancer-related mortality. During the process of metastasis, cancer cells exhibit migratory phenotypes and invade through pores in the dense extracellular matrix. However, the characterization of morphological and subcellular features of cells in similar migratory phenotypes and the effects of geometric confinement on cell morphodynamics are not well understood. Here, we investigate the phenotypes of highly aggressive MDA-MB-231 cells in single cell and cell doublet (an initial and simplified collective state) forms in confined microenvironments. We group phenotypically similar single cells and cell doublets and characterize related morphological and subcellular features. We further detect two distinct migratory phenotypes, fluctuating and non-fluctuating, within the fast migrating single cell group. In addition, we demonstrate an increase in the number of protrusions formed at the leading edge of cells after invasion through geometric confinement. Finally, we track the short and long term effects of varied degrees of confinement on protrusion formation. Overall, our findings elucidate the underlying morphological and subcellular features associated with different single cell and cell doublet phenotypes and the impact of invasion through confined geometry on cell behavior.

scholarly journals Optimizing expression quantitative trait locus mapping workflows for single-cell studies

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anna S. E. Cuomo ◽  
Giordano Alvari ◽  
Christina B. Azodi ◽  
Davis J. McCarthy ◽  
Marc Jan Bonder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quantitative Trait Locus ◽  
Single Cell ◽  
Quantitative Trait ◽  
Cell Types ◽  
Expression Quantitative Trait Locus ◽  
Eqtl Mapping ◽  
Trait Locus ◽  
The Impact

Abstract Background Single-cell RNA sequencing (scRNA-seq) has enabled the unbiased, high-throughput quantification of gene expression specific to cell types and states. With the cost of scRNA-seq decreasing and techniques for sample multiplexing improving, population-scale scRNA-seq, and thus single-cell expression quantitative trait locus (sc-eQTL) mapping, is increasingly feasible. Mapping of sc-eQTL provides additional resolution to study the regulatory role of common genetic variants on gene expression across a plethora of cell types and states and promises to improve our understanding of genetic regulation across tissues in both health and disease. Results While previously established methods for bulk eQTL mapping can, in principle, be applied to sc-eQTL mapping, there are a number of open questions about how best to process scRNA-seq data and adapt bulk methods to optimize sc-eQTL mapping. Here, we evaluate the role of different normalization and aggregation strategies, covariate adjustment techniques, and multiple testing correction methods to establish best practice guidelines. We use both real and simulated datasets across single-cell technologies to systematically assess the impact of these different statistical approaches. Conclusion We provide recommendations for future single-cell eQTL studies that can yield up to twice as many eQTL discoveries as default approaches ported from bulk studies.

scholarly journals Enhanced Viral Activity in the Surface Microlayer of the Arctic and Antarctic Oceans

2021 ◽  
Vol 9 (2) ◽  
pp. 317
Author(s):  
Dolors Vaqué ◽  
Julia A. Boras ◽  
Jesús Maria Arrieta ◽  
Susana Agustí ◽  
Carlos M. Duarte ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Food Web ◽  
Physicochemical Characteristics ◽  
The Arctic ◽  
Microbial Food Web ◽  
Surface Microlayer ◽  
Polar Regions ◽  
Nutrient Inputs ◽  
Viral Activity ◽  
The Impact

The ocean surface microlayer (SML), with physicochemical characteristics different from those of subsurface waters (SSW), results in dense and active viral and microbial communities that may favor virus–host interactions. Conversely, wind speed and/or UV radiation could adversely affect virus infection. Furthermore, in polar regions, organic and inorganic nutrient inputs from melting ice may increase microbial activity in the SML. Since the role of viruses in the microbial food web of the SML is poorly understood in polar oceans, we aimed to study the impact of viruses on prokaryotic communities in the SML and in the SSW in Arctic and Antarctic waters. We hypothesized that a higher viral activity in the SML than in the SSW in both polar systems would be observed. We measured viral and prokaryote abundances, virus-mediated mortality on prokaryotes, heterotrophic and phototrophic nanoflagellate abundance, and environmental factors. In both polar zones, we found small differences in environmental factors between the SML and the SSW. In contrast, despite the adverse effect of wind, viral and prokaryote abundances and virus-mediated mortality on prokaryotes were higher in the SML than in the SSW. As a consequence, the higher carbon flux released by lysed cells in the SML than in the SSW would increase the pool of dissolved organic carbon (DOC) and be rapidly used by other prokaryotes to grow (the viral shunt). Thus, our results suggest that viral activity greatly contributes to the functioning of the microbial food web in the SML, which could influence the biogeochemical cycles of the water column.

scholarly journals The impact of intraspecific variation on food web structure

Ecology ◽  
2018 ◽  
Vol 99 (12) ◽  
pp. 2712-2720 ◽  
Author(s):  
Tom Clegg ◽  
Mohammad Ali ◽  
Andrew P. Beckerman
Keyword(s):  
Food Web ◽  
Intraspecific Variation ◽  
Food Web Structure ◽  
Web Structure ◽  
The Impact

scholarly journals Regional variability of acidification in the Arctic: a sea of contrasts

2014 ◽  
Vol 11 (2) ◽  
pp. 293-308 ◽  
Author(s):  
E. E. Popova ◽  
A. Yool ◽  
Y. Aksenov ◽  
A. C. Coward ◽  
T. R. Anderson
Keyword(s):  
Climate Change ◽  
Primary Production ◽  
Arctic Ocean ◽  
Canadian Arctic ◽  
Atmospheric Co2 ◽  
The Arctic ◽  
Canadian Arctic Archipelago ◽  
Regional Variability ◽  
The Arctic Ocean ◽  
The Impact

Abstract. The Arctic Ocean is a region that is particularly vulnerable to the impact of ocean acidification driven by rising atmospheric CO2, with potentially negative consequences for calcifying organisms such as coccolithophorids and foraminiferans. In this study, we use an ocean-only general circulation model, with embedded biogeochemistry and a comprehensive description of the ocean carbon cycle, to study the response of pH and saturation states of calcite and aragonite to rising atmospheric pCO2 and changing climate in the Arctic Ocean. Particular attention is paid to the strong regional variability within the Arctic, and, for comparison, simulation results are contrasted with those for the global ocean. Simulations were run to year 2099 using the RCP8.5 (an Intergovernmental Panel on Climate Change (IPCC) Fifth Assessment Report (AR5) scenario with the highest concentrations of atmospheric CO2). The separate impacts of the direct increase in atmospheric CO2 and indirect effects via impact of climate change (changing temperature, stratification, primary production and freshwater fluxes) were examined by undertaking two simulations, one with the full system and the other in which atmospheric CO2 was prevented from increasing beyond its preindustrial level (year 1860). Results indicate that the impact of climate change, and spatial heterogeneity thereof, plays a strong role in the declines in pH and carbonate saturation (Ω) seen in the Arctic. The central Arctic, Canadian Arctic Archipelago and Baffin Bay show greatest rates of acidification and Ω decline as a result of melting sea ice. In contrast, areas affected by Atlantic inflow including the Greenland Sea and outer shelves of the Barents, Kara and Laptev seas, had minimal decreases in pH and Ω because diminishing ice cover led to greater vertical mixing and primary production. As a consequence, the projected onset of undersaturation in respect to aragonite is highly variable regionally within the Arctic, occurring during the decade of 2000–2010 in the Siberian shelves and Canadian Arctic Archipelago, but as late as the 2080s in the Barents and Norwegian seas. We conclude that, for future projections of acidification and carbonate saturation state in the Arctic, regional variability is significant and needs to be adequately resolved, with particular emphasis on reliable projections of the rates of retreat of the sea ice, which are a major source of uncertainty.

scholarly journals A stochastic, Lagrangian model of sinking biogenic aggregates in the ocean (SLAMS 1.0): model formulation, validation and sensitivity

2016 ◽  
Vol 9 (4) ◽  
pp. 1455-1476 ◽  
Author(s):  
Tinna Jokulsdottir ◽  
David Archer
Keyword(s):  
Primary Production ◽  
Degradation Kinetics ◽  
Mechanistic Model ◽  
Euphotic Zone ◽  
Lagrangian Model ◽  
Zooplankton Grazing ◽  
Aggregate Model ◽  
Size Spectra ◽  
Sea Floor ◽  
Individual Particles

Abstract. We present a new mechanistic model, stochastic, Lagrangian aggregate model of sinking particles (SLAMS) for the biological pump in the ocean, which tracks the evolution of individual particles as they aggregate, disaggregate, sink, and are altered by chemical and biological processes. SLAMS considers the impacts of ballasting by mineral phases, binding of aggregates by transparent exopolymer particles (TEP), zooplankton grazing and the fractal geometry (porosity) of the aggregates. Parameterizations for age-dependent organic carbon (orgC) degradation kinetics, and disaggregation driven by zooplankton grazing and TEP degradation, are motivated by observed particle fluxes and size spectra throughout the water column. The model is able to explain observed variations in orgC export efficiency and rain ratio from the euphotic zone and to the sea floor as driven by sea surface temperature and the primary production rate and seasonality of primary production. The model provides a new mechanistic framework with which to predict future changes on the flux attenuation of orgC in response to climate change forcing.

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