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Bacterial fingerprints as a tool for large-scale functional ecology

Posted by Dina Pandya

· Monday, September 20th, 2021

Unravelling the relationship between biological diversity and ecosystem functions is a timeless question which dates back to the expeditions of Alexander von Humboldt in the early 1800’. At the base of the marine foodweb, marine prokaryotes are essential for ecosystem functioning. Measuring their biogeography and functional traits therefore merits investigation as alterations in their alpha and beta diversities could lead to changes in the fluxes of oceanic biogeochemical cycles that sustain the life on Earth.

In a new article, published in Nature Communications, the authors used the genetic fingerprint of marine bacteria to predict their metabolic profiles from the ice edge to the equator in the Pacific Ocean. Their research showed that low-cost, high-throughput bacterial marker gene data can be used as a tool for large-scale functional ecology. They tackled five hypotheses and show how biological diversity influences functional diversity, and how these are related to energy production in the ocean. The authors, furthermore, highlight how - can be nicely integrated with the physical and chemical sampling programs during global ocean monitoring campaigns such as GO-SHIP and GEOTRACES.

Increasing our understanding how bacterial diversity impacts the functional diversity of ecosystems has also broader implications. For example, bacterial fingerprints can help us to improve marine ecosystem monitoring programs, especially in coastal zones and estuaries where the input of nitrogen is predicted to increase. Assessing the changes in the bacterial diversity can also help to assess the environmental footprint of aquaculture cages, which are a source of nutrients such as carbon, nitrogen and phosphorus and have been shown to deteriorate the water quality and life higher up the food chain.

Figure caption: The P15S GO-SHIP line from the ice-edge to the equator along 170o W in the South Pacific Ocean (a). Sea surface temperatures and salinity (b) and a conceptual picture of the functional prokaryotic and microbial-eukaryotic biogeography (c). In winter heterotrophic prokaryotes (blue rods) recycle the organic matter produced in the summer and autumn months in the high nutrient low chlorophyll (HNLC) region of the Southern Ocean (SO). Turbulence and mixing (curved arrows) in the sub-tropical front (STF) results in high primary productivity (PP) driven by phytoplankton rich in chlorophyll-a (green discs). The South Pacific Subtropical Gyre Province (SPSG) is characterized by nutrient co-limitation, low PP, and higher abundances of photosynthetic prokaryotes (yellow circles). The Pacific Equatorial Divergence (PED) is characterized by equatorial upwelling which results in an increase of the N:P ratio in the mixed layer (MLD) relative to the SPSG (d), and results in increased chlorophyll-a concentrations and PP. The MLD is shown as a thick white line. CTD stations (small gray dots), sampling stations for 16S rRNA data (large gray circles) and shotgun metagenome samples (yellow stars) are shown on panel d.

Authors:
Eric J. Raes (CSIRO Oceans and Atmosphere, Australia; Dalhousie University, Canada)
Kristen Karsh (CSIRO Oceans and Atmosphere, Australia)
Swan L. S. Sow (CSIRO Oceans and Atmosphere, Australia; University of Tasmania, Hobart; NIOZ Royal Netherlands Institute for Sea Research, The Netherlands)
Martin Ostrowski (University of Technology Sydney, Australia)
Mark V. Brown (The University of Newcastle, Australia)
Jodie van de Kamp (CSIRO Oceans and Atmosphere, Australia)
Rita M. Franco-Santos (University of Tasmania, Australia)
Levente Bodrossy (CSIRO Oceans and Atmosphere, Australia)
Anya M. Waite (Dalhousie University, Canada)

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Raes, E. J., Bodrossy, L., Van De Kamp, J., Bissett, A., Ostrowski, M., Brown, M. V., ... & Waite, A. M. (2018). Oceanographic boundaries constrain microbial diversity gradients in the South Pacific Ocean. Proceedings of the National Academy of Sciences, 115(35), E8266-E8275.

Raes, E. J., van de Kamp, J., Bodrossy, L., Fong, A. A., Riekenberg, J., Holmes, B. H., ... & Waite, A. M. (2020). N2 fixation and new insights into nitrification from the ice-edge to the equator in the South Pacific Ocean. Frontiers in Marine Science, 7, 389.

Sow, S. L., Trull, T. W., & Bodrossy, L. (2020). Oceanographic Fronts Shape Phaeocystis Assemblages: A High-Resolution 18S rRNA Gene Survey From the Ice-Edge to the Equator of the South Pacific. Frontiers in microbiology, 11, 1847.

Species loss alters ecosystem function in plankton communities

Posted by mmaheigan

· Monday, February 8th, 2021

Climate change impacts on the ocean such as warming, altered nutrient supply, and acidification will lead to significant rearrangement of phytoplankton communities, with the potential for some phytoplankton species to become extinct, especially at the regional level. This leads to the question: What are phytoplankton species’ redundancy levels from ecological and biogeochemical standpoints—i.e. will other species be able to fill the functional ecological and/or biogeochemical roles of the extinct species? Authors of a paper published recently in Global Change Biology explored these ideas using a global three-dimensional computer model with diverse planktonic communities, in which single phytoplankton types were partially or fully eliminated. Complex trophic interactions such as decreased abundance of a predator’s predator led to unexpected “ripples” through the community structure and in particular, reductions in carbon transfer to higher trophic levels. The impacts of changes in resource utilization extended to regions beyond where the phytoplankton type went extinct. Redundancy appeared lowest for types on the edges of trait space (e.g., smallest) or those with unique competitive strategies. These are responses that laboratory or field studies may not adequately capture. These results suggest that species losses could compound many of the already anticipated outcomes of changing climate in terms of productivity, trophic transfer, and restructuring of planktonic communities. The authors also suggest that a combination of modeling, field, and laboratory studies will be the best path forward for studying functional redundancy in phytoplankton.

Figure caption: Examples of the modelled ecological and biogeochemical responses to the extinction of different phytoplankton species.Figure caption: Examples of the modelled ecological and biogeochemical responses to the extinction of different phytoplankton species.

Authors:
Stephanie Dutkiewicz (Massachusetts Institute of Technology)
Philip W. Boyd (Institute for Marine and Antarctic Studies, University of Tasmania)
Ulf Riebesell (GEOMAR Helmholtz Centre for Ocean Research Kiel)

Climate-driven pelagification of marine food webs: Implications for marine fish populations

Posted by mmaheigan

· Friday, January 22nd, 2021

Global warming changes the conditions for all ocean life, with wide-ranging consequences. It is particularly difficult to predict the impact of climate change on fish because fish production is conditioned on both temperature and food resource (zooplankton and benthic organisms) changes. Climate change projections from Earth system models show a negative amplification of changes in global ocean net primary production (NPP), with an approximate doubling of production decreases from net primary producers to mesozooplankton. This “trophic amplification” continues up the marine food web to fishes. A new study published in Frontiers in Marine Science illustrates this amplification clearly when fishes are defined by their maximum body size, which describes their position in the food web (Figure 1a). However, decreases in globally integrated biomass and production were not limited to differences in size alone. Importantly, reduced abundances also varied by fish functional type (Figure 1b).

Figure 1: a) Percent change in net primary production (NPP), mesozooplankton (MesoZ) production, all medium (M) fishes, and all large (L) fishes from Historic (1951-2000) to the RCP 8.5 Projection (2051-2100). b) Percent change in production of forage fish, large pelagic fish, demersal fish, and benthic invertebrates in Projection (2051-2100) from Historic (1951-2000). c) Absolute change in the ratio of zooplankton production to seafloor detrital flux as the difference of the Projection (2051-2100) from the Historic (1951-2000). d) Percent change in zooplankton production (dashed grey), percent change in seafloor detrital flux (solid grey), and absolute change in the ratio of their means during the Historic and Projection time periods relative to 1951.

Despite the “pelagification” of marine food webs caused by unequal decreases in secondary production (Figure 1d) and subsequent increases in pelagic zooplankton production relative to seafloor detritus production (Figure 1c,d), large pelagic fish (e.g., tunas and billfishes) suffered the greatest declines and the highest degree of projection uncertainty. The result was a shift from benthic-based ecosystems historically dominated by large demersal fish (e.g., cods and flounders) towards pelagic-based ones dominated by smaller forage fish (e.g., sardines and herring). Any positive impacts of the pelagification of food resources on large pelagic fish were overwhelmed by the negative impacts of the overall reduction in global productivity, compounded by warming-induced increases in metabolic demands. Both the degree of change in the productivity of large pelagic fish and the magnitude of trophic amplification were sensitive to the temperature dependence of metabolic rates. Thus, better constraints are needed on empirical estimates of the effect of temperature on physiological rates to project the impacts of climate change on fish biomass and marine ecosystem structure.

Ocean fish harvests currently supply ~15% of global protein demand. Reduced primary production will decrease the total amount of fish available to harvest for human food, while the pelagification of ecosystems could require large and expensive structural modifications to fisheries, including gear, location, regional and international management plans, consumer demands, and market values.

Authors:
Colleen M. Petrik (Texas A&M University)
Charles A. Stock (Geophysical Fluid Dynamics Laboratory)
Ken H. Andersen (Technical University of Denmark)
P. Daniël van Denderen (International Council for the Exploration of the Seas)
James R. Watson (Oregon State University)

Austral summer vertical migration patterns in Antarctic zooplankton

Posted by mmaheigan

· Thursday, October 15th, 2020

Sunrise and sunset are the main cues driving zooplankton diel vertical migration (DVM) throughout the world’s oceans. These marine animals balance the trade-off between feeding in surface waters at night and avoiding predation during the day at depth. Near-constant daylight during polar summer was assumed to dampen these daily migrations. In a recent paper published in Deep-Sea Research I, authors assessed austral summer DVM patterns for 15 taxa over a 9-year period. Despite up to 22 hours of sunlight, a diverse array of zooplankton – including copepods, krill, pteropods, and salps – continued DVM.

Figure caption: Mean day (orange) and night (blue) abundance of (A) the salp Salpa thompsoni, (B) the krill species Thysanoessa macrura, (C) the pteropod Limacina helicina, and (D) chaetognaths sampled at discrete depth intervals from 0-500m. Horizontal dashed lines indicate weighted mean depth (WMD). N:D is the night to day abundance ratio for 0-150 m. Error bars indicate one standard error. Sample size n = 12 to 22. Photos by Larry Madin, Miram Gleiber, and Kharis Schrage.

The Palmer Antarctica Long-Term Ecological Research (LTER) Program conducted this study using a MOCNESS (Multiple Opening/Closing Net and Environmental Sensing System) to collect depth-stratified samples west of the Antarctic Peninsula. The depth range of migrations during austral summer varied across taxa and with daylength and phytoplankton biomass and distribution. While most taxa continued some form of DVM, others (e.g., carnivores and detritivores) remained most abundant in the mesopelagic zone, regardless of photoperiod, which likely impacted the attenuation of vertical carbon flux. Given the observed differences in vertical distribution and migration behavior across taxa, ongoing changes in Antarctic zooplankton assemblages will likely impact carbon export pathways. More regional, taxon-specific studies such as this are needed to inform efforts to model zooplankton contributions to the biological carbon pump.

Authors:
John Conroy (VIMS, William & Mary)
Deborah Steinberg (VIMS, William & Mary)
Patricia Thibodeau (VIMS, William & Mary; currently University of Rhode Island)
Oscar Schofield (Rutgers University)

Will global change “stress out” ocean DOC cycling?

Posted by mmaheigan

· Tuesday, September 29th, 2020

The dissolved organic carbon (DOC) pool is vital for the functioning of marine ecosystems. DOC fuels marine food webs and is a cornerstone of the earth’s carbon cycle. As one of the largest pools of organic matter on the planet, disruptions to marine DOC cycling driven by climate and environmental global changes can impact air-sea CO2 exchange, with the added potential for feedbacks on Earth’s climate system.

Figure 1. Simplified view of major dissolved organic carbon (DOC) sources (black text) and sinks (yellow text) in the ocean.

Since DOC cycling involves multiple processes acting concurrently over a range of time and space scales, it is especially challenging to characterize and quantify the influence of global change. In a recent review paper published in Frontiers in Marine Science, the authors synthesize impacts of global change-related stressors on DOC cycling such as ocean warming, stratification, acidification, deoxygenation, glacial and sea ice melting, inflow from rivers, ocean circulation and upwelling, and atmospheric deposition. While ocean warming and acidification are projected to stimulate DOC production and degradation, in most regions, the outcomes for other key climate stressors are less clear, with much more regional variation. This synthesis helps advance our understanding of how global change will affect the DOC pool in the future ocean, but also highlights important research gaps that need to be explored. These gaps include for example a need for studies that allow to understand the adaptation of degradation/production pathways to global change stressors, and their cumulative impacts (e.g. temperature with acidification).

Authors:
C. Lønborg (Aarhus University)
C. Carreira (CESAM, Universidade de Aveiro)
Tim Jickells (University of East Anglia)
X.A. Álvarez-Salgado (CSIC, Instituto de Investigacións Mariñas)

Turning a spotlight on grazing

Posted by mmaheigan

· Thursday, July 23rd, 2020

Microscopic plankton in the surface ocean make planet Earth habitable by generating oxygen and forming the basis of marine food webs, yielding harvestable protein. For over 100 years, oceanographers have tried to ascertain the physical, chemical, and biological processes governing phytoplankton blooms. Zooplankton grazing of phytoplankton is the single largest loss process for primary production, but empirical grazing data are sparse and thus poorly constrained in modeling frameworks, including assessments of global elemental cycles, cross-ecosystem comparisons, and predictive efforts anticipating future ocean ecosystem function. As sunlight decays exponentially with depth, upper-ocean mixing creates dynamic light environments with predictable effects on phytoplankton growth but unknown consequences for grazing.

Figure caption: Rates (d⁻¹) of phytoplankton growth (μ), grazing mortality (g), and biomass accumulation (r) under four mixed layer scenarios simulated using light as a proxy of (a) sustained deep mixing, (b) rapid shoaling, (c) sustained shallow mixing, and (d) rapid mixed layer deepening. Error bars represent one standard deviation of the mean of duplicate experiments. Grazing was measured but not detected in the sustained deep mixing and rapid shoaling conditions, denoted with x.

Using data from a spring cruise in the North Atlantic, authors of a recent study published in Limnology & Oceanography compared the influences of microzooplankton predation and fluctuations in light availability—representative of a mixing water column—on phytoplankton standing stock. Data from at-sea incubations and light manipulation experiments provide evidence that phytoplankton’s instantaneous and zooplankton’s delayed responses to light fluctuations are key modulators of the balance between phytoplankton growth and grazing rates (Figure 1). These results suggest that light is a potential, remotely retrievable predictor of when and where in the ocean zooplankton grazing may represent an important loss term of phytoplankton production. If broadly verified, this approach could be used to systematically assess sparsely measured grazing across spatial and temporal gradients in representative regions of the ocean. Such data will be essential for enhancing our predictive capacity of ocean food web function, global biogeochemical cycles and the many derived processes, including fisheries production and the flow of carbon through the oceans.

Authors:
Françoise Morison (University of Rhode Island)
Gayantonia Franzè (University of Rhode Island, currently Institute of Marine Research, Norway)
Elizabeth Harvey (University of Georgia, currently University of New Hampshire)
Susanne Menden-Deuer (University of Rhode Island)

Modern OMZ copepod dynamics provide analog for future oceans

Posted by mmaheigan

· Thursday, July 23rd, 2020

Global warming increases ocean deoxygenation and expands the oxygen minimum zone (OMZ), which has implications for major zooplankton groups like copepods. Reduced oxygen levels may impact individual copepod species abundance, vertical distribution, and life history strategy, which is likely to perturb intricate oceanic food webs and export processes. In a study recently published in Biogeosciences, authors conducted vertically-stratified day and night MOCNESS tows (0-1000 m) during four cruises (2007-2017) in the Eastern Tropical North Pacific, sampling hydrography and copepod distributions in four locations with different water column oxygen profiles and OMZ intensity (i.e. lowest oxygen concentration and its vertical extent in a profile). Each copepod species exhibited a different vertical distribution strategy and physiology associated with oxygen profile variability. The study identified sets of species that (1) changed their vertical distributions and maximum abundance depth associated with the depth and intensity of the OMZ and its oxycline inflection points, (2) shifted their diapause depth, (3) adjusted their diel vertical migration, especially the nighttime upper depth, or (4) expanded or contracted their depth range within the mixed layer and upper part of the thermocline in association with the thickness of the aerobic epipelagic zone (habitat compression concept) (Figure 1). Distribution depths for some species shifted by 10’s to 100’s of meters in different situations, which also had metabolic (and carbon flow) implications because temperature decreased with depth. This observed present-day variability may provide an important window into how future marine ecosystems will respond to deoxygenation.

Figure caption: Schematic diagram showing how future OMZ expansion may affect zooplankton distributions, based on present-day responses to OMZ variability. The dashed line indicates diel vertical migration (DVM) and highlights the shoaling of the nighttime depth as the aerobic habitat is compressed. The lower oxycline community and the diapause layer for some species, associated with a specific oxygen concentration, may deepen as the OMZ expands.

Authors:
Karen F. Wishner (University of Rhode Island)
Brad Seibel (University of South Florida)
Dawn Outram (University of Rhode Island)

Autonomous platforms yield new insights on North Atlantic bloom phenology

Posted by mmaheigan

· Wednesday, April 22nd, 2020

Phytoplankton produces organic carbon, which serves as a major energy source in marine food webs and plays an important role in the global carbon cycle. Studies of phytoplankton seasonal timing (phenology) have been a major focus in oceanography, especially in the subpolar North Atlantic region, where massive increases in phytoplankton biomass (blooms) occur during the winter-spring transition.

Figure 1. Panel a: Each line represents the trajectory of a profiling Argo float deployed during the North Atlantic Aerosols and Marine Ecosystems Study (NAAMES) expeditions (12 total); the initial float deployment location is denoted by a filled circle. The bar chart (inset right bottom) indicates float deployment durations. Panel b: Seasonal climatologies of C_phyto (green), µ (blue), l (red), and r (grey) from Argo floats for all 4 regions (D1-D4 as indicated on map in Panel a).

Many hypotheses based on data from shipboard discrete sampling or satellite remote sensing have been proposed to explain drivers of phytoplankton bloom formation and dynamics. However, discrete shipboard sampling limits both spatial and temporal coverage, and satellite approaches cannot provide direct information at depth. To address this gap in spatiotemporal coverage, a recent study in Frontiers in Marine Science, applied bio-optical measurements from 12 Argo profiling floats to study the year-round phytoplankton phenology in a north-south section of the western North Atlantic Ocean (40° N to 60° N). The authors calculated phytoplankton division rate (µ), loss rate (l), and carbon accumulation rate (r) using the Argo-based Chlorophyll-a (Chl) and phytoplankton carbon (C_phyto) estimates. Latitudinally varying phytoplankton dynamics were observed, with a higher (and later) C_phyto peak in the north, and stronger μ–r decoupling and increased proportion of winter to total annual production in the south (Figure 1). Seasonal phenology patterns arise from interactions between “bottom-up” (e.g., resources for growth) and “top-down” (e.g., grazing, mortality) factors that involve both biological and physical drivers. The Argo float data are consistent with the disturbance recovery hypothesis (DRH) over a full annual cycle. Float-based mixed layer phytoplankton phenology observations were comparable to satellite remote sensing observations. In a data-model comparison, outputs from an eddy-resolving ocean simulation only reproduced some of the observed phytoplankton phenology, indicating possible biases in the simulated physical forcing, turbulent dynamics, and biophysical interactions.

In addition to seasonal patterns in the mixed layer, float-based measurements provide information on the vertical distribution of physical and biogeochemical quantities and therefore are complementary to the satellite measurements. This powerful combination of observing assets enhances spatiotemporal coverage, thus enabling us to better observe, compare, model, and predict seasonal phytoplankton dynamics in the subpolar North Atlantic.

Authors:
Bo Yang (University of Virginia)
Emmanuel S. Boss (University of Maine)
Nils Haëntjens (University of Maine)
Matthew C. Long (National Center for Atmospheric Research)
Michael J. Behrenfeld (Oregon State University)
Rachel Eveleth (Oberlin College)
Scott C. Doney (University of Virginia)

Can phytoplankton help us determine ocean iron bioavailability?

Posted by mmaheigan

· Wednesday, March 11th, 2020

Iron (Fe) is a key element to sustaining life, but it is present at extremely low concentrations in seawater. This scarcity limits phytoplankton growth in large swaths of the global ocean, with implications for marine food webs and carbon cycling. The acquisition of Fe by phytoplankton is an important process that mediates the movement of carbon to the deep ocean and across trophic levels. It is a challenge to evaluate the ability of marine phytoplankton to obtain Fe from seawater since it is bound by a variety of poorly defined organic complexes.

Figure 1: Schematic representation of the reactions governing dissolved Fe (dFe) bioavailability to phytoplankton (a) Bioavailability of dFe in seawater collected from various basins and depth and probed with different iron-limited phytoplankton species under dim laboratory light and sunlight (b) (See paper for further details on samples and species)

A recent study in The ISME Journal proposes a new approach for evaluating seawater dissolved Fe (dFe) bioavailability based on its uptake rate constant by Fe-limited cultured phytoplankton. The authors collected samples from distinct regions across the global ocean, measured the properties of organic complexation, loaded these complexes with a radioactive Fe isotope, and then tracked the internalization rates from these forms to a diverse set of Fe-limited phytoplankton species. Regardless of origin, all of the phytoplankton acquired natural organic complexes at similar rates (accounting for cell surface area). This confirms that multiple Fe-limited phytoplankton species can be used to probe dFe bioavailability in seawater. Among water types, dFe bioavailability varied by ~4-fold and did not clearly correlate with Fe concentrations or any of the measured Fe speciation parameters. This new approach provides a novel way to determine Fe bioavailability in samples from across the oceans and enables modeling of in situ Fe uptake rates by phytoplankton based simply on measured Fe concentrations.

Authors:
Yeala Shaked (Hebrew University of Jerusalem)
Kristen N. Buck (University of South Florida)
Travis Mellett (University of South Florida)
Maria. T. Maldonado (University of British Columbia)

Pumped up by the cold: Increased elemental density in polar diatoms

Posted by mmaheigan

· Monday, October 28th, 2019

Large diatoms are common in polar phytoplankton blooms, contributing significantly to food webs and carbon export, but relatively little is known about their elemental biogeochemistry. A recent study in Frontiers in Marine Science showed that the size-dependent increase in cell nutrient content for polar diatoms was similar to published values for temperate diatoms, whereas the elemental density (mass per unit volume) of polar diatoms was substantially greater for all elements measured (carbon, nitrogen, silicon and phosphorus). Furthermore, at near freezing culture temperatures, there was a positive relationship between diatom size and realized growth rates near their theoretical maximum (Figure 1). Because of the differences in elemental density between carbon and silica, these diatoms exhibited particulate C:Si ratios that are commonly interpreted as a sign of iron limitation; yet these cultures were trace metal-replete. The observed elemental composition differences suggest that it may be important for polar biogeochemical models to include different representations of diatom biogeochemistry by accounting for the functions of size and near freezing temperature.

Figure 1. Left: Cellular carbon content for polar diatoms across four orders of magnitude in biovolume compared to the same relationship for a wide range of non-polar diatoms (MD&L = Menden-Deuer & Lessard, 2000). The y-intercept is the estimate of the baseline carbon density in these polar diatoms, and is significantly higher than the literature values reviewed in MD&L (2000). Right: Growth rate of the same polar diatoms expressed as a percent of their calculated maximum growth rate at 2°C. Error bars represent the range of values observed in the experiments. Maximum growth rate was estimated by 1) applying the growth rate/biovolume relationships published by Chisholm (1992) and Edwards et al. (2012) to the observed biovolume for each culture, and 2) scaling this growth rate to 2°C growth temperature using the relationship of Eppley (1972).

Authors:
Michael Lomas (Bigelow Laboratory for Ocean Sciences)
Steven Baer (Maine Maritime Academy)
Sydney Acton (Dauphin Island Sea Lab)
Jeffrey Krause (Dauphin Island Sea Lab and University of South Alabama)

Funding for the Ocean Carbon & Biogeochemistry Project Office is provided by the National Science Foundation (NSF) and the National Aeronautics and Space Administration (NASA). The OCB Project Office is housed at the Woods Hole Oceanographic Institution.

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