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Diatoms commit iron piracy with stolen bacterial gene

Posted by mmaheigan

· Tuesday, February 4th, 2020

Since diatoms carry out much of the primary production in iron-limited marine environments, constraining the details of how these phytoplankton acquire the iron they need is paramount to our understanding of biogeochemical cycles of iron-depleted high-nutrient low-chlorophyll (HNLC) regions. The proteins involved in this process are largely unknown, but McQuaid et al. (2018) scientists described a carbonate-dependent uptake protein that enables diatoms to access inorganic iron dissolved in seawater. As increasing atmospheric CO₂ results in decreased seawater carbonate ion concentrations, this iron uptake strategy may have an uncertain future. In a recent study published in PNAS, authors used CRISPR technology to characterize a parallel uptake system that requires no carbonate and is therefore not impacted by ocean acidification.

This system targets an organically complexed form of iron (siderophores, molecules that bind and transport iron in microorganisms) that is only produced by co-occurring microbes. Two genes are required to convert siderophores from a potent toxicant to an essential nutrient. One of these (FBP1) is a receptor that was horizontally acquired from siderophore-producing bacteria. The other (FRE2) is a eukaryotic reductase that facilitates the dissociation of Fe-siderophore complexes.

Figure caption: (A) Growth curves of diatom cultures ( • = WT, ◇ = ΔFBP1, ☐ = ΔFRE2) in low iron media. (B) Growth in same media with siderophores added. (C) Diatoms under 1000x magnification, brightfield. (D) mCherry-FBP1. (E) Plastid autofluorescence. (F) YFP-FRE2. (G) Phylogenetic tree of FBP1 and related homologs.

Are diatoms really stealing siderophores from hapless bacteria? The true nature of this interaction is unknown and may at times be mutualistic. For example, when iron availability limits the carbon supply to a microbial community, heterotrophic bacteria may benefit from using siderophores to divert iron to diatom companions. Further work is needed to understand the true ecological basis for this interaction, but these results suggest that as long as diatoms and bacteria co-occur, iron limitation in marine ecosystems will not be exacerbated by ocean acidification.

Authors:
Tyler Coale (Scripps Institution of Oceanography, J.Craig Venter Institute)
Mark Moosburner (Scripps Institution of Oceanography, J.Craig Venter Institute)
Aleš Horák (Biology Centre CAS, Institute of Parasitology, University of South Bohemia)
Miroslav Oborník (Biology Centre CAS, Institute of Parasitology, University of South Bohemia)
Katherine Barbeau (Scripps Institution of Oceanography)
Andrew Allen (Scripps Institution of Oceanography, J.Craig Venter Institute)

Also see joint post on the GEOTRACES website

What really controls deep-seafloor calcite dissolution?

Posted by mmaheigan

· Monday, December 16th, 2019

On time scales of tens to millions of years, seawater acidity is primarily controlled by biogenic calcite (CaCO₃) dissolution on the seafloor. Our quantitative understanding of future oceanic pH and carbonate system chemistry requires knowledge of what controls this dissolution. Past experiments on the dissolution rate of suspended calcite grains have consistently suggested a high-order, nonlinear dependence on undersaturation that is independent of fluid flow rate. This form of kinetics has been extensively adopted in models of deep-sea calcite dissolution and pH of benthic sediments. However, stirred-chamber and rotating-disc dissolution experiments have consistently demonstrated linear kinetics of dissolution and a strong dependence on fluid flow velocity. This experimental discrepancy surrounding the kinetic control of seafloor calcite dissolution precludes robust predictions of oceanic response to anthropogenic acidification.

In a recent study published in Geochimica et Cosmochimica Acta, authors have reconciled these divergent experimental results through an equation for the mass balance of the carbonate ion at the sediment-water interface (SWI), which equates the rate of production of that ion via dissolution and its diffusion in sediment porewaters to the transport across the diffusive sublayer (DBL) at the SWI. If the rate constant derived from suspended-grain experiments is inserted into this balance equation, the rate of carbonate ion supply to the SWI from the sediment (sediment-side control) is much greater in the oceans than the rate of transfer across the DBL (water-side control). Thus, calcite dissolution at the seafloor, while technically under mixed control, is strongly water-side dominated. Consequently, a model that neglects boundary-layer transport (sediment-side control alone) invariably predicts CaCO₃-versus-depth profiles that are too shallow compared to available data (Figure 1). These new findings will inform future attempts to model the ocean’s response to acidification.

Figure 1: Plots of the calcite (CaCO₃) content of deep-sea sediments as a function of oceanic depth. Left panel: data from the Northwestern Atlantic Ocean. Right panel: data from the Southwest Pacific Ocean. The blue line represents predicted CaCO₃ content assuming no boundary-layer effects (pure sediment-side control). The red line is the prediction that includes both sediment and water effects (mixed control), and the green line is the prediction with pure water-side control. The agreement between the red and green lines signifies that calcite dissolution is essentially water-side controlled at the seafloor. These results are duplicated for all tested regions of the oceans.

Authors:
Bernard P. Boudreau (Dalhousie University)
Olivier Sulpis (University of Utrecht)
Alfonso Mucci (McGill University)

A role for tropical nitrogen fixers in glacial CO2 drawdown

Posted by mmaheigan

· Wednesday, December 4th, 2019

Iron fertilization of marine phytoplankton by Aeolian dust is a well-established mechanism for atmospheric carbon dioxide (CO₂) drawdown by the ocean. When atmospheric CO₂ decreased by 90-100 ppm during previous ice ages, fertilization of iron-limited phytoplankton in the high latitudes was thought to have contributed up to ¹/₃ (30 ppm) of the total CO₂ drawdown. Unfortunately, recent modeling studies suggest that substantially less CO₂ (only 2-10 ppm) is sequestered by the ocean in response to high latitude fertilization.

The limited capacity for high latitude CO₂sequestration in response to iron enrichment motivated the authors of a new study published in Nature Communications to address how lower latitude phytoplankton could contribute to CO₂ drawdown. The authors used an ocean model to show that in response to Aeolian iron fertilization, dinitrogen (N₂) fixers, specialized phytoplankton that introduce bioavailable nitrogen to tropical surface waters, drive the sequestration of an additional 7-16 ppm of CO₂ by the ocean.

Figure 1: Scenarios of Fe supply to the tropical Pacific. In the low iron scenario, analogous to the modern climate, N₂ fixation (yellow zone and dots) is concentrated in the Northwest and Southwest subtropical Pacific where aeolian dust deposition is greatest. Non-limiting PO₄ concentrations (green zone and dots) exist within the tropics and spread laterally from the area of upwelling near the Americas and at the equator (blue zone). In the high Fe scenario, analogous to the glacial climate, N₂ fixation couples to the upwelling zones in the east Pacific, enabling strong utilisation of PO₄, the vertical expansion of suboxic zones (grey bubbles) and a deeper injection of carbon-enriched organic matter (downward squiggly arrows).

These results provide evidence of a tropical ocean CO₂ sequestration pathway, the mere existence of which is hotly debated. Importantly, the study describes an additional mechanism of CO₂ drawdown that is complementary to the high latitude mechanism. When combined, their contributions elevate iron-driven CO₂ drawdown towards the expected 30 ppm, making iron fertilization a driver of a stronger biological pump on a global scale.

Authors:
Pearse Buchanan (University of Liverpool, University of Tasmania, CSIRO Oceans and Atmosphere, ARC Centre of Excellence in Climate System Science)
Zanna Chase (University of Tasmania)
Richard Matear (CSIRO Oceans and Atmosphere, ARC Centre of Excellence in Climate Extremes)
Steven Phipps (University of Tasmania)
Nathaniel Bindoff (University of Tasmania, CSIRO Oceans and Atmosphere, ARC Centre of Excellence in Climate Extremes, Antarctic Climate and Ecosystems Cooperative Research Centre)

The arsenic respiratory cycle in pelagic waters of Oxygen Deficient Zones

Posted by mmaheigan

· Wednesday, October 30th, 2019

Oxygen Deficient Zones (ODZs) are naturally occurring functionally anoxic regions of the open ocean which can act as proxies for early Earth’s anoxic ocean. Without free oxygen, microorganisms in these regions use alternative electron acceptors to oxidize organic material. These functionally anoxic regions are also hotspots for chemoautotrophic pathways. Some microorganisms can use arsenic based compounds to oxidize organic material, and others can couple nitrate reduction with arsenic oxidation supporting autotrophic carbon fixation thus linking arsenic respiration with carbon and nitrogen cycling. While arsenic concentrations in modern oceans are relatively low, the Precambrian ocean likely had periods of high arsenic concentrations. Integrating over time and space of anoxic waters, arsenic-based metabolisms may have had significant implications for the biogeochemical cycling of not only arsenic, but also carbon and nitrogen.

Figure 1: Arsenotrophic genes identified in the Eastern Tropical North Pacific Oxygen Deficient Zone. (A) Genomic complement for dissimilatory arsenate reduction assembled from metagenomes which likely supports respiration of organic matter. (B) Genomic complement for putative chemoautotrophic arsenite oxidation pathway assembled from metagenomes which may couple with nitrate reduction to support organic matter production. (C) Relative abundance of genes associated with arsenite oxidase (aioA), dissimilatory arsenate reduction (arrA), and forward dissimilatory sulfite reductase (dsrA) associated with sulfur reduction; abundance shown as a relative contribution to the total microbial community as estimated by abundance of RNA polymerase genes (rpoB). The genes arrA and forward-dsrA are more abundant in the particulate fraction, whereas aioA is more abundant in the free-living fraction. (D) Relative abundance of genes in the microbial community for the more abundant genes aioA-like and reverse form of dsrA associated with sulfur oxidation. aioA-like genes are relatively more abundant within the particulate fraction, with no strong partitioning between fractions identified for the reverse-dsrA genes. Arsenical reduction and chemoautotrophic arsenical oxidation are likely performed by different microbial groups within the ODZ communities.

Recent work in PNAS identified gene sequences for a complete arsenic respiratory cycle from Eastern Tropical North Pacific (ETNP) ODZ metagenomes. The authors identified arsenotrophic genes for dissimilatory arsenate reduction from one group of microorganisms and genes for a putative chemoautotrophic arsenite oxidation pathway from another group within the ETNP ODZ microbial community. Analysis of genomic sequences from a free-living sample and from particulate-associated sample indicate niche differentiation of these pathways—arsenate reduction genes enriched within the particulate fraction and arenite oxidation enriched in the free-living water column. In addition to the presence of these genes in metagenomes, the authors identified the active expression of these arsenotrophic genes in publicly available metatranscriptomes from the ETNP and Eastern Tropical South Pacific ODZs. Theyalso found an abundance of sequences in the ETNP ODZ for the gene aioA-like, which is a closely related enzyme to arsenite oxidase (aioA), but with an unconfirmed function. The identification of these actively expressed genes in modern ODZs enables further investigation of these cycles that were likely important in early oceans. These findings also highlight that there are still yet to be discovered respiratory pathways in ODZs. Arsenotrophy, in conjunction with other niche respiratory pathways – both known and as yet undiscovered – likely sum to a considerable contribution of energy flow and elemental cycling through these anoxic systems.

Authors:
Jaclyn Saunders (University of Washington; present affiliation Woods Hole Oceanographic Institution)
Clara Fuchsman (University of Washington; present affiliation Horn Point Laboratory)
Cedar McKay & Gabrielle Rocap (University of Washington)

See related University of Washington press-release

Air-sea gas exchange estimates biased by multi-day surface trapping

Posted by mmaheigan

· Tuesday, August 20th, 2019

Routine measurements of air-sea gas exchange assume a homogeneous gas concentration across the upper few meters of the ocean. But is this assumption valid? A recent study in Biogeosciences revealed substantial systematic gradients of nitrous oxide (N₂O) in the top few meters of the Peruvian upwelling regime. These gradients lead to a 30% overestimate of integrated N₂O emissions across the entire region, with local emissions overestimated by as much as 800%.

Figure caption: Air-sea gas exchange estimates can be biased by gas concentration gradients within the upper few meters of the ocean; in particular, surface trapping over several days’ duration can generate substantial gradients.

The N₂O gradients off Peru form during multi-day events of surface trapping, in which near-surface stratification dampens turbulent mixing. Until now, surface trapping was assumed to be a diurnal (driven by solar warming) process without memory, whereby only weak gradients would form during the hours of trapping and then dissipate. It is likely that multi-day surface trapping occurs in other ocean regions as well. The total impact on emission estimates of different greenhouse gases is yet to be quantified, but given the findings in the Peruvian upwelling system, could be significant globally.

Authors:
Tim Fischer, Annette Kock, Damian L. Arévalo-Martínez, Marcus Dengler, Peter Brandt, Hermann W. Bange (GEOMAR)

Regional circulation changes and a growing atmospheric CO2 concentration drive accelerated anthropogenic carbon uptake in the South Pacific

Posted by mmaheigan

· Tuesday, August 6th, 2019

About one tenth of human CO₂ emissions are currently being taken up by the Pacific Ocean, which makes the seawater more corrosive to the calcium carbonate shells and skeletons of the plants and animals that live there. Now, thanks to hard work by international teams of scientists from the Global Ocean Ship-based Hydrographic Investigations Program (GO-SHIP), there are decades of data, enough to test how much this anthropogenic CO₂ accumulation varies throughout the Pacific Ocean and regionally on the timescales of decades.

Figure caption: Map of the concentration of human-emitted CO₂ along the sections where data were available from more than one decade, estimated for the year 2015.

Using a new take on an old technique, along with a wide variety of repeat biogeochemical measurements, a study in Biogeochemical Cycles revealed that Pacific anthropogenic CO₂ accumulation increased from the 1995-2005 decade to the 2005-2015 decade. While the magnitude of the decadal increase was consistent with increases in human CO₂ emissions over this period for most of the Pacific, the rate of change was greater than expected in the South Pacific subtropical gyre. The authors suggest that recent increases in circulation in the gyre region could have delivered an unexpectedly large amount of anthropogenic CO₂-laden seawater from the surface to the ocean interior. Programs like GO-SHIP will continue to be critical for tracking the fate of human CO₂emissions and associated feedbacks on climate and marine ecosystems.

Authors:
B. R. Carter (Univ. Washington and PMEL)
R. A. Feely, G. C. Johnson, J. L. Bullister (PMEL)
R. Wanninkhof (NOAA AOML)
S. Kouketsu, A. Murata (JAMSTEC
R. E. Sonnerup, S. Mecking (Univ. Washington)
P. C. Pardo (Univ. Tasmania)
C. L. Sabine (Univ. Hawai‘i, Mānoa)
B. M. Sloyan, B. Tilbrook (CSIRO, Australia)
K. Speer (Florida State University
L. D. Talley (Scripps Institution of Oceanography)
F. J. Millero (Univ. Miami)
S. E. Wijffels (CSIRO and WHOI)
A. M. Macdonald (WHOI)
N. Gruber (ETH Zurich)

The causes of the 90-ppm glacial atmospheric CO2 drawdown still strongly debated

Posted by mmaheigan

· Tuesday, July 9th, 2019

Joint feature with GEOTRACES

Figure: Illustration of the two main mechanisms identified by this study to explain lower atmospheric CO₂ during glacial periods. Left: present-day conditions; right: conditions around 19,000 years ago during the Last Glacial Maximum. The obvious explanation for lower CO₂ during glacial periods – cooler ocean temperatures (darker blue shade) making CO₂ more soluble, much as a glass of sparkling wine will remain fizzier for longer when it is colder – has long been dismissed as not being a significant factor. However, previous calculations assumed that the ocean cooled uniformly and was saturated in dissolved CO₂. The model, consistent with reconstructions of sea surface temperature, predicts more cooling at mid latitudes compared with polar regions and also accounts for undersaturation. This nearly doubles the effect of temperature change and accounts for almost half the 90 ppm glacial-interglacial atmospheric CO₂ difference. Another quarter is explained in this model by increased growth of marine algae (green blobs and inset) in the waters off Antarctica. Algae absorb CO₂ from the atmosphere during photosynthesis and “pump” it into the deep ocean when they die and sink. But their growth in the present-day ocean, especially the waters off Antarctica, is limited by the availability of iron, an essential micronutrient primarily supplied by wind-borne dust. In our model an increased supply of iron to the Southern Ocean, likely originating from Patagonia, Australia and New Zealand, enhances their growth and sucks CO₂ out of the atmosphere. This “fertilization” effect was greatly underestimated by previous studies. The study also finds that, contrary to the current consensus, a large expansion of sea ice off Antarctica and reconfiguration of ocean circulation may have played only a minor role in glacial-interglacial CO₂ changes. Credit: Illustration by Andrew Orkney, University of Oxford.

Using an observationally constrained earth system model, S. Khatiwala and co-workers compare different processes that could lead to the 90-ppm glacial atmospheric CO₂drawdown, with an important improvement on the deep carbon storage quantification (i.e. Biological Carbon Pump efficiency). They demonstrate that circulation and sea ice changes had only a modest net effect on glacial ocean carbon storage and atmospheric CO₂, whereas temperature and iron input effects were more important than previously thought due to their effects on disequilibrium carbon storage.

Authors:
Samar Khatiwala (University of Oxford, UK)
Andreas Schmittner and Juan Muglia (Oregon State University)

Forecasting air-sea CO2 flux variations several years in advance

Posted by mmaheigan

· Tuesday, July 9th, 2019

Year-to-year changes in the flux of CO₂ between the atmosphere and the ocean impact the global carbon cycle and climate system, and challenge our ability to verify fossil fuel CO₂ emissions. A new study published in Earth System Dynamics suggests that these air-sea CO₂ flux variations are predictable several years in advance.

A novel set of initialized forecasts of past air-sea CO₂ flux from an Earth system model (Figure 1a) confidently predicts year-to-year variations in the globally-integrated flux up to two years in advance. At regional scales, the forecast lead time increases. The predictability of CO₂ flux from the initialized forecast system exceeds that obtained solely from foreknowledge of variations in external forcing (e.g., volcanic eruptions) or a simple persistence forecast (e.g., CO₂ flux this year will be the same as next year). The longest-lasting forecast enhancements are in the subantarctic Southern Ocean and the northern North Atlantic (Figure 1b).

Figure 1: (a) Forecasts of the past evolution of air-sea CO2 flux in the South Pacific using an Earth System model indicate the potential to predict the future evolution of this quantity. (b) In each biome, the maximum forecast lead time in which the initialized forecast of air-sea CO2 flux beats out other forecast methods.

These results are particularly meaningful for those forecasting year-to-year changes in the global carbon budget, especially as these forecasting efforts are blind to the externally-forced variability in advance (i.e., the external forcing of the future is unknown). In this way, forecasts of air-sea CO₂ flux variations can help to inform future predictions of land-air CO₂ flux and atmospheric CO₂ concentration.

Authors:
Nicole Lovenduski (University of Colorado Boulder)
Stephen G. Yeager (National Center for Atmospheric Research)
Keith Lindsay (National Center for Atmospheric Research)
Matthew C. Long (National Center for Atmospheric Research)

See also the OCB Ocean-Atmosphere Interactions: Scoping directions for U.S. research Workshop to be held in October 1-3, 2019

Suddenly shallow: A new aragonite saturation horizon will soon emerge in the Southern Ocean

Posted by mmaheigan

· Monday, May 27th, 2019

Earth System Models (ESMs) project that by the end of this century, the aragonite saturation horizon (the boundary between shallower, saturated waters and deeper, undersaturated waters that are corrosive to aragonitic shells) will shoal all the way to the surface in the Southern Ocean, yet the temporal evolution of the horizon has not been studied in much detail. Rather than a gradual shoaling, a new shallow aragonite saturation horizon emerges suddenly across many locations in the Southern Ocean between now and the end of the century (Figure 1, left), as detailed in a new study published in Nature Climate Change.

Figure 1: Maximum step-change in the depth of the aragonite saturation horizon (left), timing of the step-change (center), and cause of the change (right). Xs on the time axis (center) indicate when the shallow horizon emerges in each ensemble member. (click image to enlarge)

The emergence of the shallow aragonite saturation horizon is apparent in each member of an ensemble of climate projections from an ESM, but the step change occurs during different years (Figure 1, center). The shoaling is driven by the gradual accumulation of anthropogenic CO₂ in the Southern Ocean thermocline, where the carbonate ion concentration exhibits a local minimum and approaches undersaturation (Figure 1, right).

The abrupt shoaling of the Southern Ocean aragonite saturation horizon occurs under both business-as-usual and emission-stabilizing scenarios, indicating an inevitable and sudden decrease in the volume of suitable habitat for aragonitic organisms such as shelled pteropods, foraminifers, cold-water corals, sea urchins, molluscs, and coralline algae. Widespread reductions in these habitats may have far-reaching consequences for fisheries, economies, and livelihoods.

Authors:
Gabriela Negrete-García (Scripps Institution of Oceanography)
Nicole Lovenduski (University of Colorado Boulder)

See also OCB2019 plenary session: Carbon cycle feedbacks from the seafloor (Wednesday, June 26, 2019)

Pteropod populations stable or increasing according to long-term study along the Western Antarctic Peninsula

Posted by mmaheigan

· Thursday, March 21st, 2019

Shelled pteropods (pelagic snails) are abundant planktonic predators and prey, linking grazers and higher trophic levels and contributing to the carbon cycle via consumption and excretion. Pteropods have been heralded as bioindicators of ocean acidification, given their aragonitic shell’s susceptibility to dissolution, which could ultimately lead to declining abundance. However, pteropod population dynamics are understudied, particularly in the Southern Ocean, a region predicted to be highly impacted by both warming and ocean acidification. In a recent publication in Limnology and Oceanography, long-term data sets from the Western Antarctic Peninsula show that while there is considerable interannual variability in pteropod abundance, populations have remained stable over the past 25 years, with some pteropod species (gymnosomes (non-shelled pteropod) overall, L. antarctica and C. pyramidata (shelled pteropods) regionally) even increasing during this period (Figure 1).

Figure 1. Annual pteropod abundance anomalies for the entire Palmer Antarctica Long-Term Ecological Research (LTER) study region along the Western Antarctic Peninsula. (a) Limacina helicina antarctica (shelled pteropod), (b) Gymnosomes – nonshelled pteropods that prey on shelled pteropods (p = 0.007, r² = 0.27), and (c) Clio pyramidata (shelled pteropod). Effect of environment on pteropod abundance. (d) SST vs. L. antarctica abundance, e) Sea ice advance vs. L. antarctica and Gymnosome abundance, (f) Sea ice retreat vs. C. pyramidata abundance. Data plotted are annual anomalies for each year of the time series (1993–2017). Sea ice advance is lagged 2-yr behind pteropod abundance (e.g., 2017 pteropod annual anomaly is plotted against 2015 sea ice advance annual anomaly) SST are lagged 1-yr behind L. antarctica abundance (e.g., 2017 L. antarctica annual anomaly is plotted against 2016 SST). Regression lines for significant linear relationships are shown, regression statistics are as follows: (d) SST vs. L. antarctica (circles): n = 25, p = 0.006, r² = 0.25 (e) sea ice advance vs. L. antarctica (filled-circles) and Gymnosomes (empty-circles): n = 25, p = 0.003, r² = 0.30 (dashed line); (f) sea ice retreat vs. C. pyramidata (squares): n = 14, p = 0.0003, r² = 0.64.

There was no significant influence of carbonate chemistry parameters (e.g., aragonite saturation state) on pteropod abundance, since the Western Antarctic Peninsula has yet to experience prolonged conditions characteristic of ocean acidification. However, other environmental factors such as warming and associated sea ice retreat were more influential. For example, warmer, ice-free waters in one year typically led to higher pteropod abundances the following year, suggesting that pteropods may be better adapted than expected to warming conditions due to climate change. The authors propose that earlier sea ice retreat promotes recruitment and subsequent expansion of pteropods further South, which could explain their increased abundance in this subregion. These results increase our understanding of pteropod responses to environmental variability, which is important for predicting future effects of climate change on regional carbon cycling and plankton trophic interactions in the Southern Ocean.

Authors:
Patricia S. Thibodeau (VIMS)
Deborah K. Steinberg (VIMS)
Sharon E. Stammerjohn (University of Colorado at Boulder)
Claudine Hauri (University of Alaska Fairbanks)

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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