Publications

@article{2366,

title = {Development, calibration, and evaluation of a model of Pseudo-nitzschia and domoic acid production for regional ocean modeling studies},

author = {Allison R Moreno and Clarissa Anderson and Raphael M Kudela and Martha Sutula and Christopher Edwards and Daniele Bianchi},

url = {https://www.sciencedirect.com/science/article/pii/S156898832200124X},

isbn = {1568-9883},

year  = {2022},

date = {2022-01-01},

journal = {Harmful Algae},

volume = {118},

pages = {102296},

publisher = {Elsevier},

abstract = {Pseudo-nitzschia species are one of the leading causes of harmful algal blooms (HABs) along the western coast of the United States. Approximately half of known Pseudo-nitzschia strains can produce domoic acid (DA), a neurotoxin that can negatively impact wildlife and fisheries and put human life at risk through amnesic shellfish poisoning. Production and accumulation of DA, a secondary metabolite synthesized during periods of low primary metabolism, is triggered by environmental stressors such as nutrient limitation. To quantify and estimate the feedbacks between DA production and environmental conditions, we designed a simple mechanistic model of Pseudo-nitzschia and domoic acid dynamics, which we validate against batch and chemostat experiments. Our results suggest that, as nutrients other than nitrogen (i.e., silicon, phosphorus, and potentially iron) become limiting, DA production increases. Under Si limitation, we found an approximate doubling in DA production relative to N limitation. Additionally, our model indicates a positive relationship between light and DA production. These results support the idea that the relationship with nutrient limitation and light is based on direct impacts on Pseudo-nitzschia biosynthesis and biomass accumulation. Because it can easily be embedded within existing coupled physical-ecosystem models, our model represents a step forward toward modeling the occurrence of Pseudo-nitzschia HABs and DA across the U.S. West Coast.​​​​​​},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2365,

title = {Controls and characteristics of biomass quantization in size-structured planktonic ecosystem models},

author = {Jordyn E Moscoso and Daniele Bianchi and Andrew L Stewart},

url = {https://www.sciencedirect.com/science/article/pii/S0304380022000321},

isbn = {0304-3800},

year  = {2022},

date = {2022-01-01},

journal = {Ecological Modelling},

volume = {468},

pages = {109907},

publisher = {Elsevier},

abstract = {Strong relationships between size and other traits have long motivated studies of the size structure and dynamics of planktonic food webs. Size structured ecosystem models (SSEMs) are often used to represent the behavior of these ecosystems, with organism size as a first order approximation of the axis of biological diversity. Previous studies using SSEMs have reported the emergence of localized “peaks” in the size spectrum, a phenomenon that will be referred to in this study as “quantization”. However, SSEMs that are used routinely in Earth System Models (ESMs), they tend to be too coarsely discretized to resolve quantization. Observational studies of plankton biomass have also shown qualitatively similar patterns, with localized peaks along the size spectrum. The conditions under which quantization occurs and the ecosystem parameters that control the locations of the biomass “peaks” along the size spectrum have not been systematically explored. This study serves to simultaneously advance our understanding of the constraints on quantization in size-structured ecosystems, and to suggest an approach to discretizing SSEMs that leverages quantization to select a greatly reduced number of size classes. A size-structured model of the pelagic food web, similar to those implemented in global models, is used to investigate the sensitivity of biomass peaks to predator–prey interactions, and nutrient forcing. This study shows that the location of biomass peaks along the size spectrum is strongly controlled by the size selectivity of predation, and the location of biomass peaks along the size spectrum is less sensitive to variations in nutrient supply, external ecosystem forcing, and vertical heterogeneity. Taking advantage of a robust localization of biomass peaks, the dynamics of a continuous planktonic size spectrum to be represented using a few selected size classes, corresponding to locations of the peaks along the size spectrum. These findings offer an insight on how to approach discretization of size structured ecosystem model in Earth system models.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2364,

title = {Trophic level decoupling drives future changes in phytoplankton bloom phenology},

author = {Ryohei Yamaguchi and Keith B Rodgers and Axel Timmermann and Karl Stein and Sarah Schlunegger and Daniele Bianchi and John P Dunne and Richard D Slater},

url = {https://www.nature.com/articles/s41558-022-01353-1},

isbn = {1758-6798},

year  = {2022},

date = {2022-01-01},

journal = {Nature Climate Change},

volume = {12},

number = {5},

pages = {469-476},

publisher = {Nature Publishing Group},

abstract = {Climate change can drive shifts in the seasonality of marine productivity, with consequences for the marine food web. However, these alterations in phytoplankton bloom phenology (initiation and peak timing), and the underlying drivers, are not well understood. Here, using a 30-member Large Ensemble of climate change projections, we show earlier bloom initiation in most ocean regions, yet changes in bloom peak timing vary widely by region. Shifts in both initiation and peak timing are induced by a subtle decoupling between altered phytoplankton growth and zooplankton predation, with increased zooplankton predation (top-down control) playing an important role in altered bloom peak timing over much of the global ocean. Only in limited regions is light limitation a primary control for bloom initiation changes. In the extratropics, climate-change-induced phenological shifts will exceed background natural variability by the end of the twenty-first century, which may impact energy flow in the marine food webs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{clements2022constraining,

title = {Constraining the particle size distribution of large marine particles in the global ocean with in situ optical observations and supervised learning},

author = {DJ Clements and S Yang and T Weber and AMP McDonnell and R Kiko and L Stemmann and D Bianchi},

url = {https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2021GB007276},

year  = {2022},

date = {2022-01-01},

journal = {Global Biogeochemical Cycles},

pages = {e2021GB007276},

publisher = {Wiley Online Library},

abstract = {The abundance and size distribution of marine particles control a range of biogeochemical and ecological processes in the ocean, including carbon sequestration. These quantities are the result of complex physical-biological interactions that are difficult to observe, and their spatial and temporal patterns remain uncertain. Here, we present a novel analysis of particle size distributions (PSDs) from a global compilation of in situ Underwater Vision Profiler 5 (UVP5) optical measurements. Using a machine learning algorithm, we extrapolate sparse UVP5 observations to the global ocean from well-sampled oceanographic variables. We reconstruct global maps of PSD parameters (biovolume [BV] and slope) for particles at the base of the euphotic zone. These reconstructions reveal consistent global patterns, with high chlorophyll regions generally characterized by high particle BV and flatter PSD slope, that is, a high relative abundance of large versus small particles. The resulting negative correlations between particle BV and slope further suggests synergistic effects on size-dependent processes such as sinking particle fluxes. Our approach and estimates provide a baseline for an improved understanding of particle cycles in the ocean, and pave the way to global, three-dimensional reconstructions of PSD and sinking particle fluxes from the growing body of UVP5 observations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{patra2022forward,

title = {Forward and Inverse Modelling of Atmospheric Nitrous Oxide Using MIROC4-Atmospheric Chemistry-Transport Model},

author = {Prabir K Patra and Edward J Dlugokencky and James W Elkins and Geoff S Dutton and Yasunori Tohjima and Motoki Sasakawa and Akihiko Ito and Ray F Weiss and Manfredi Manizza and Paul B Krummel and others},

url = {https://www.jstage.jst.go.jp/article/jmsj/advpub/0/advpub_2022-018/_article/-char/ja/},

year  = {2022},

date = {2022-01-01},

journal = {Journal of the Meteorological Society of Japan. Ser. II},

publisher = {Meteorological Society of Japan},

abstract = {Atmospheric nitrous oxide (N2O) contributes to global warming and stratospheric ozone depletion, so reducing uncertainty in estimates of emissions from different sources is important for climate policy. Here, we simulate atmospheric N2O using an atmospheric chemistry-transport model (ACTM), and the results are first compared with the in situ measurements. Five combinations of known (a priori) N2O emissions due to natural soil, agricultural land, other human activities and sea-air exchange are used. The N2O lifetime is 127.6 ± 4.0 yr in the control ACTM simulation (range indicate interannual variability). Regional N2O emissions are optimised by Bayesian inverse modelling for 84 partitions of the globe at monthly intervals, using measurements at 42 sites around the world covering 1997-2019. The best estimate global land and ocean emissions are 12.99 ± 0.22 and 2.74 ± 0.27 TgN yr-1, respectively, for 2000-2009, and 14.30 ± 0.20 and 2.91 ± 0.27 TgN yr-1, respectively, for 2010-2019. On regional scales, we find that the most recent ocean emission estimation, with lower emissions in the Southern Ocean regions, fits better with that predicted by the inversions. Marginally higher (lower) emissions than the inventory/model for the tropical (extra-tropical) land regions is estimated and validated using independent aircraft observations. Global land and ocean emission variabilities show statistically significant correlation with El Niño Southern Oscillation (ENSO). Analysis of regional land emissions shows increases over America (Temperate North, Central, Tropical), Central Africa, and Asia (South, East and Southeast) between the 2000s and 2010s. Only Europe as a whole recorded a slight decrease in N2O emissions due to chemical industry. Our inversions suggest revisions to seasonal emission variations for 3 of the 15 land regions (East Asia, Temperate North America and Central Africa), and the Southern Ocean region. The terrestrial ecosystem model (VISIT) is able to simulate annual total emissions in agreement with the observed N2O growth rate since 1978, but the lag-time scales of N2O emissions from nitrogen fertiliser application may need to be revised.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cram2022slow,

title = {Slow particle remineralization, rather than suppressed disaggregation, drives efficient flux transfer through the Eastern Tropical North Pacific Oxygen Deficient Zone},

author = {Jacob A Cram and Clara A Fuchsman and Megan E Duffy and Jessica L Pretty and Rachel M Lekanoff and Jacquelyn A Neibauer and Shirley W Leung and Klaus B Huebert and Thomas S Weber and Daniele Bianchi and others},

url = {https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2021GB007080},

year  = {2022},

date = {2022-01-01},

journal = {Global Biogeochemical Cycles},

volume = {36},

number = {1},

pages = {e2021GB007080},

publisher = {Wiley Online Library},

abstract = {Models and observations suggest that particle flux attenuation is lower across the mesopelagic zone of anoxic environments compared to oxic environments. Flux attenuation is controlled by microbial metabolism as well as aggregation and disaggregation by zooplankton, all of which shape the relative abundance of differently sized particles. Observing and modeling particle spectra can provide information about the contributions of these processes. We measured particle size spectrum profiles at one station in the oligotrophic Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ) using an underwater vision profiler (UVP), a high-resolution camera that counts and sizes particles. Measurements were taken at different times of day, over the course of a week. Comparing these data to particle flux measurements from sediment traps collected over the same time-period allowed us to constrain the particle size to flux relationship, and to generate highly resolved depth and time estimates of particle flux rates. We found that particle flux attenuated very little throughout the anoxic water column, and at some time points appeared to increase. Comparing our observations to model predictions suggested that particles of all sizes remineralize more slowly in the ODZ than in oxic waters, and that large particles disaggregate into smaller particles, primarily between the base of the photic zone and 500 m. Acoustic measurements of multiple size classes of organisms suggested that many organisms migrated, during the day, to the region with high particle disaggregation. Our data suggest that diel-migrating organisms both actively transport biomass and disaggregate particles in the ODZ core.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{guiet2022movement,

title = {Movement shapes the structure of fish communities along a cross-shore section in the California Current},

author = {Jérôme Guiet and Daniele Bianchi and Olivier Maury and Nicolas Barrier and Fayçal Kessouri},

url = {https://www.frontiersin.org/articles/10.3389/fmars.2022.785282/full},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Marine Science},

volume = {9},

publisher = {Frontiers Media SA},

abstract = {Pelagic fish communities are shaped by bottom-up and top-down processes, transport by currents, and active swimming. However, the interaction of these processes remains poorly understood. Here, we use a regional implementation of the APex ECOSystem Model (APECOSM), a mechanistic model of the pelagic food web, to investigate these processes in the California Current, a highly productive upwelling system characterized by vigorous mesoscale circulation. The model is coupled with an eddy-resolving representation of ocean currents and lower trophic levels, and is tuned to reproduce observed fish biomass from fisheries independent trawls. Several emergent properties of the model compare realistically with observations. First, the epipelagic community accounts for one order of magnitude less biomass than the vertically migratory community, and is composed by smaller species. Second, the abundance of small fish decreases from the coast to the open ocean, while the abundance of large fish remains relatively uniform. This in turn leads to flattening of biomass size-spectra away from the coast for both communities. Third, the model reproduces a cross-shore succession of small to large sizes moving offshore, consistent with observations of species occurrence. These cross-shore variations emerge in the model from a combination of: (1) passive offshore advection by the mean current, (2) active swimming toward coastal productive regions to counterbalance this transport, and (3) mesoscale heterogeneity that reduces the ability of organisms to return to coastal waters. Our results highlight the importance of passive and active movement in structuring the pelagic food web, and suggest that a representation of these processes can help to improve the realism in simulations with marine ecosystem models.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bianchi2021estimating,

title = {Estimating global biomass and biogeochemical cycling of marine fish with and without fishing},

author = {Daniele Bianchi and David A Carozza and Eric D Galbraith and Jérôme Guiet and Timothy DeVries},

url = {https://www.science.org/doi/full/10.1126/sciadv.abd7554},

year  = {2021},

date = {2021-10-01},

journal = {Science advances},

volume = {7},

number = {41},

pages = {eabd7554},

publisher = {American Association for the Advancement of Science},

abstract = {The biomass and biogeochemical roles of fish in the ocean are ecologically important but poorly known. Here, we use a data-constrained marine ecosystem model to provide a first-order estimate of the historical reduction of fish biomass due to fishing and the associated change in biogeochemical cycling rates. The pre-exploitation global biomass of exploited fish (10 g to 100 kg) was 3.3 ± 0.5 Gt, cycling roughly 2% of global primary production (9.4 ± 1.6 Gt year-1) and producing 10% of surface biological export. Particulate organic matter produced by exploited fish drove roughly 10% of the oxygen consumption and biological carbon storage at depth. By the 1990s, biomass and cycling rates had been reduced by nearly half, suggesting that the biogeochemical impact of fisheries has been comparable to that of anthropogenic climate change. Our results highlight the importance of developing a better mechanistic understanding of how fish alter ocean biogeochemistry.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{le2021global,

title = {Global nutrient cycling by commercially-targeted marine fish},

author = {Priscilla Le Mézo and Jérôme Guiet and Kim Scherrer and Daniele Bianchi and Eric Galbraith},

year  = {2021},

date = {2021-01-01},

journal = {Biogeosciences Discussions},

pages = {1–37},

publisher = {Copernicus GmbH},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{tittensor2021next,

title = {Next-generation ensemble projections reveal higher climate risks for marine ecosystems},

author = {Derek P Tittensor and Camilla Novaglio and Cheryl S Harrison and Ryan F Heneghan and Nicolas Barrier and Daniele Bianchi and Laurent Bopp and Andrea Bryndum-Buchholz and Gregory L Britten and Matthias Büchner and others},

url = {https://www.nature.com/articles/s41558-021-01173-9},

year  = {2021},

date = {2021-01-01},

journal = {Nature climate change},

volume = {11},

number = {11},

pages = {973–981},

publisher = {Nature Publishing Group},

abstract = {Projections of climate change impacts on marine ecosystems have revealed long-term declines in global marine animal biomass and unevenly distributed impacts on fisheries. Here we apply an enhanced suite of global marine ecosystem models from the Fisheries and Marine Ecosystem Model Intercomparison Project (Fish-MIP), forced by new-generation Earth system model outputs from Phase 6 of the Coupled Model Intercomparison Project (CMIP6), to provide insights into how projected climate change will affect future ocean ecosystems. Compared with the previous generation CMIP5-forced Fish-MIP ensemble, the new ensemble ecosystem simulations show a greater decline in mean global ocean animal biomass under both strong-mitigation and high-emissions scenarios due to elevated warming, despite greater uncertainty in net primary production in the high-emissions scenario. Regional shifts in the direction of biomass changes highlight the continued and urgent need to reduce uncertainty in the projected responses of marine ecosystems to climate change to help support adaptation planning.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kessouri2021configuration,

title = {Configuration and validation of an oceanic physical and biogeochemical model to investigate coastal eutrophication in the Southern California Bight},

author = {Fayçal Kessouri and Karen McLaughlin and Martha Sutula and Daniele Bianchi and Minna Ho and James C McWilliams and Lionel Renault and Jeroen Molemaker and Curtis Deutsch and Anita Leinweber},

year  = {2021},

date = {2021-01-01},

journal = {Journal of Advances in Modeling Earth Systems},

volume = {13},

number = {12},

pages = {e2020MS002296},

publisher = {Wiley Online Library},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2282,

title = {A new estimate of Global Ocean Carbon Flux from In Situ Optical Observations and Supervised Learning.},

author = {Daniel J Clements and Simon Yang and Thomas S Weber and Andrew MP McDonnell and Rainer Kiko and Lars Stemmann and Daniele Bianchi},

url = {https://www.essoar.org/doi/10.1002/essoar.10507104.1},

year  = {2021},

date = {2021-01-01},

journal = {Earth and Space Science Open Archive ESSOAr},

publisher = {American Geophysical Union},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2280,

title = {A baseline of terrestrial freshwater and nitrogen fluxes to the southern california bight, usa},

author = {Martha Sutula and Minna Ho and Ashmita Sengupta and Fayçal Kessouri and Karen McLaughlin and Kenny McCune and Daniele Bianchi},

url = {https://www.sciencedirect.com/science/article/pii/S0025326X21007037},

isbn = {0025-326X},

year  = {2021},

date = {2021-01-01},

journal = {Marine Pollution Bulletin},

volume = {170},

pages = {112669},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2279,

title = {Coastal eutrophication drives acidification, oxygen loss, and ecosystem change in a major oceanic upwelling system},

author = {Faycal Kessouri and James C McWilliams and Daniele Bianchi and Martha Sutula and Lionel Renault and Curtis Deutsch and Richard A Feely and Karen McLaughlin and Minna Ho and Evan M Howard},

url = {https://www.pnas.org/content/118/21/e2018856118.short},

isbn = {0027-8424},

year  = {2021},

date = {2021-01-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {118},

number = {21},

publisher = {National Acad Sciences},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2278,

title = {Biogeochemical variability in the California Current system},

author = {Curtis Deutsch and Hartmut Frenzel and James C McWilliams and Lionel Renault and Faycal Kessouri and Evan Howard and Jun-Hong Liang and Daniele Bianchi and Simon Yang},

url = {https://www.sciencedirect.com/science/article/pii/S0079661121000525},

isbn = {0079-6611},

year  = {2021},

date = {2021-01-01},

journal = {Progress in Oceanography},

pages = {102565},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gmd-14-763-2021,

title = {The Meridionally Averaged Model of Eastern Boundary Upwelling Systems (MAMEBUSv1.0)},

author = {J. E. Moscoso and A. L. Stewart and D. Bianchi and J. C. McWilliams},

url = {https://gmd.copernicus.org/articles/14/763/2021/},

doi = {10.5194/gmd-14-763-2021},

year  = {2021},

date = {2021-01-01},

journal = {Geoscientific Model Development},

volume = {14},

number = {2},

pages = {763–794},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SUTULA2021106802,

title = {Dataset of Terrestrial Fluxes of Freshwater, Nutrients, Carbon, and Iron to the Southern California Bight, U.S.A.},

author = {Martha Sutula and Minna Ho and Ashmita Sengupta and Fayçal Kessouri and Karen McLaughlin and Kenny McCune and Daniele Bianchi},

url = {https://www.sciencedirect.com/science/article/pii/S235234092100086X},

doi = {https://doi.org/10.1016/j.dib.2021.106802},

issn = {2352-3409},

year  = {2021},

date = {2021-01-01},

journal = {Data in Brief},

pages = {106802},

abstract = {The Southern California Bight (SCB) is an upwelling-dominated, open embayment on the U.S. West Coast and receives discharges of anthropogenically-enhanced freshwater, nutrients, carbon, and other materials. These inputs include direct point sources discharged from wastewater treatment (WWT) plants via ocean outfalls and point, non-point, and natural sources discharged via coastal rivers. We assembled a daily time series over 1971-2017 of discharges from large WWT plants >= 50 million gallon per day (MGD) and 1997-2017 from small WWT plants and coastal rivers. Constituents include nitrogen, phosphorus, organic carbon, alkalinity, iron, and silica. Data from research studies, several government and non-government agency databases containing discharge monitoring reports, river flow gauges, and other collateral information were compiled to produce this dataset. Predictive models and expert analysis addressed unmonitored sources and data gaps. The time series of terrestrial discharge and fluxes are provided with location of coastal discharge point or tributary. The data are deposited in a repository found in Sutula et~al. [1].},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2281,

title = {Configuration and validation of an oceanic physical and biogeochemical model to investigate coastal eutrophication: case study in the Southern California Bight},

author = {Faycal Kessouri and Karen McLaughlin and Martha A Sutula and Daniele Bianchi and Minna Ho and James C McWilliams and Lionel Renault and Jeroen Molemaker and Curtis A Deutsch and Anita Leinweber},

url = {https://www.essoar.org/doi/abs/10.1002/essoar.10504012.3},

year  = {2020},

date = {2020-01-01},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.3389/feart.2020.00376,

title = {Efficient Particle Transfer to Depth in Oxygen Minimum Zones of the Pacific and Indian Oceans},

author = {Thomas Weber and Daniele Bianchi},

url = {https://www.frontiersin.org/article/10.3389/feart.2020.00376},

doi = {10.3389/feart.2020.00376},

issn = {2296-6463},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in Earth Science},

volume = {8},

pages = {376},

abstract = {The remineralization depth of sinking organic particles controls the efficiency of the biological carbon pump by setting the sequestration timescale of remineralized carbon in the ocean interior. Oxygen minimum zones (OMZs) have been identified as regions of elevated particle transfer and efficient carbon sequestration at depth, but direct measurements remain sparse in these regions and only provide snapshots of the particle flux. Here, we use remineralization tracers to reconstruct time-mean particle flux profiles in the OMZs of the Eastern Tropical Pacific and the Arabian Sea. Compared to the surrounding tropical waters, both OMZs exhibit slow flux attenuation between 100 and 1000 m where suboxic waters reside, and sequester carbon beneath 1000 m more than twice as efficiently. Using a mechanistic model of particle sinking, remineralization, and disaggregation, we show that three different mechanisms might explain the shape of the OMZ flux profiles: (i) a significant slow-down of remineralization when carbon oxidation transitions from aerobic to anaerobic respiration (e.g., denitrification); (ii) the exclusion of zooplankton that mediate disaggregation of large particles from suboxic waters, and (iii) the limitation of remineralization by the diffusive supply of oxidants (oxygen and nitrate) into large particles. We show that each mechanism leaves a unique signature in the size distribution of particles, suggesting that observations with optical instruments such as Underwater Vision Profilers hold great promise for understanding the drivers of efficient carbon transfer though suboxic water columns. In turn, this will allow more accurate prediction of future changes in carbon sequestration as the ocean loses oxygen in a warming climate.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1029/2020GB006646,

title = {Attributing Causes of Future Climate Change in the California Current System With Multimodel Downscaling},

author = {Evan M. Howard and Hartmut Frenzel and Fayçal Kessouri and Lionel Renault and Daniele Bianchi and James C. McWilliams and Curtis Deutsch},

url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020GB006646},

doi = {https://doi.org/10.1029/2020GB006646},

year  = {2020},

date = {2020-01-01},

journal = {Global Biogeochemical Cycles},

volume = {34},

number = {11},

pages = {e2020GB006646},

abstract = {Abstract Coastal winds in the California Current System (CCS) are credited with the high productivity of its planktonic ecosystem and the shallow hypoxic and corrosive waters that structure diverse macrofaunal habitats. These winds thus are considered a leading mediator of climate change impacts in the CCS and other Eastern Boundary Upwelling systems. We use an eddy-permitting regional model to downscale the response of the CCS to three of the major distinct climate changes commonly projected by global Earth System Models: regional winds, ocean warming and stratification, and remote water chemical properties. An increase in alongshore winds intensifies spring upwelling across the CCS, but this response is muted by increased stratification, especially during summer. Despite the seasonal shift in regional wind-driven upwelling, basin-scale changes are the decisive factor in the response of marine ecosystem properties including temperature, nutrients, productivity, and oxygen. Downscaled temperature increases and dissolved oxygen decreases are broadly consistent with coarse resolution Earth System Models, and these projected changes are large and well constrained across the models, whereas nutrient and productivity changes are small compared to the intermodel spread. These results imply that global models with poor resolution of coastal processes nevertheless yield important information about the dominant climate impacts on coastal ecosystems.},

note = {e2020GB006646 2020GB006646},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{MCCOY2020102452,

title = {Global observations of submesoscale coherent vortices in the ocean},

author = {Daniel McCoy and Daniele Bianchi and Andrew L. Stewart},

url = {http://www.sciencedirect.com/science/article/pii/S0079661120301890},

doi = {https://doi.org/10.1016/j.pocean.2020.102452},

issn = {0079-6611},

year  = {2020},

date = {2020-01-01},

journal = {Progress in Oceanography},

volume = {189},

pages = {102452},

abstract = {Subsurface-intensified anticyclones are ubiquitous in the ocean, yet their impact on the large-scale transport of heat, salt and chemical tracers is poorly understood. These submesoscale coherent vortices (SCVs) can trap and advect waters thousands of kilometers away from the formation region, providing a transport pathway that is unresolved by low-resolution Earth System Models. However, knowledge of the importance of these eddies for the large scale circulation is hindered by the lack of systematic observations. Here, we take advantage of the global network of Argo floats to identify occurrences of these eddies, which appear as weakly stratified anomalous water masses with Gaussian-shaped vertical structures. We develop a general algorithm to detect subsurface eddies that have propagated away from their source region, and apply it to the database of Argo float profiles, resulting in roughly 4000 detections from more than 20 years of observations. We further group detections into regional populations to identify hot-spots of generation and mechanisms of formation. Analysis of regional SCV statistics reveals important sites of SCV generation in Eastern Boundary Upwelling Systems, marginal sea overflows, and mode water formation regions along major open-ocean fronts. Because of the heat and salt anomaly contained within their cores, SCV could leave a significant imprint on the hydrographic properties of water masses in regions of high SCV density.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1029/2020GB006578,

title = {Submesoscale Currents Modulate the Seasonal Cycle of Nutrients and Productivity in the California Current System},

author = {Fayçal Kessouri and Daniele Bianchi and Lionel Renault and James C. McWilliams and Hartmut Frenzel and Curtis A. Deutsch},

url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020GB006578},

doi = {https://doi.org/10.1029/2020GB006578},

year  = {2020},

date = {2020-01-01},

journal = {Global Biogeochemical Cycles},

volume = {34},

number = {10},

pages = {e2020GB006578},

abstract = {In the California Current, subduction by mesoscale eddies removes nutrients from the coastal surface layer, counteracting upwelling and quenching productivity. Submesoscale eddies are also ubiquitous in the California Current, but their biogeochemical role has not been quantified yet in the region. Here, we present results from a physical-biogeochemical model of the California Current run at a resolution of 1 km, sufficient to represent submesoscale dynamics. By comparing it with a coarser simulation run at 4 km resolution, we demonstrate the importance of submesoscale currents for the seasonal cycles of nutrients and organic matter and highlight the existence of different regimes along a cross-shore gradient. In the productive coastal region, submesoscale currents intensify quenching and reduce productivity, further counteracting wind-driven upwelling. In the offshore oligotrophic region, submesoscale currents enhance the upward transport of nutrients, fueling a dramatic increase in new production. These effects are modulated by seasonality, strengthening near the coast during upwelling and offshore in wintertime. The intensification of the transport by submesoscale eddies drives an adjustment of the planktonic ecosystem, with a reduction of plankton biomass, productivity, and size near the coast and an increase offshore. In contrast, organic matter export by sinking particles and subduction of detritus and living cells are enhanced nearly everywhere. Similar processes are likely important in other regions characterized by seasonal upwelling, for example, other eastern boundary upwelling systems.},

note = {e2020GB006578 10.1029/2020GB006578},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wilson2020ideas,

title = {Ideas and perspectives: A strategic assessment of methane and nitrous oxide measurements in the marine environment},

author = {Samuel T Wilson and Alia N Al-Haj and Annie Bourbonnais and Claudia Frey and Robinson W Fulweiler and John D Kessler and Hannah K Marchant and Jana Milucka and Nicholas E Ray and Parv Suntharalingham and others},

url = {https://bg.copernicus.org/articles/17/5809/2020/},

year  = {2020},

date = {2020-01-01},

journal = {Biogeosciences},

volume = {17},

number = {22},

pages = {5809–5828},

publisher = {Copernicus GmbH},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{yang2020global,

title = {Global reconstruction reduces the uncertainty of oceanic nitrous oxide emissions and reveals a vigorous seasonal cycle},

author = {Simon Yang and Bonnie X Chang and Mark J Warner and Thomas S Weber and Annie M Bourbonnais and Alyson E Santoro and Annette Kock and Rolf E Sonnerup and John L Bullister and Samuel T Wilson and others},

year  = {2020},

date = {2020-01-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {117},

number = {22},

pages = {11954–11960},

publisher = {National Acad Sciences},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bryndum2020climate,

title = {Climate-change impacts and fisheries management challenges in the North Atlantic Ocean},

author = {Andrea Bryndum-Buchholz and Daniel G Boyce and Derek P Tittensor and Villy Christensen and Daniele Bianchi and Heike K Lotze},

year  = {2020},

date = {2020-01-01},

journal = {Marine Ecology Progress Series},

volume = {648},

pages = {1–17},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{guiet2020bioenergetic,

title = {Bioenergetic influence on the historical development and decline of industrial fisheries},

author = {J Guiet and ED Galbraith and D Bianchi and WWL Cheung},

year  = {2020},

date = {2020-01-01},

journal = {ICES Journal of Marine Science},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{howard2020climate,

title = {Climate-driven aerobic habitat loss in the California Current System},

author = {Evan M Howard and Justin L Penn and Hartmut Frenzel and Brad A Seibel and Daniele Bianchi and Lionel Renault and Fayçal Kessouri and Martha A Sutula and James C McWilliams and Curtis Deutsch},

year  = {2020},

date = {2020-01-01},

journal = {Science Advances},

volume = {6},

number = {20},

pages = {eaay3188},

publisher = {American Association for the Advancement of Science},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{palter2019sidebar,

title = {SIDEBAR. Acoustic Backscatter Patterns},

author = {Jaime Palter and Lauren Cook and Afonso Gonçalves Neto and Sarah Nickford and Daniele Bianchi},

year  = {2019},

date = {2019-01-01},

journal = {Oceanography},

volume = {32},

number = {3},

pages = {140–141},

publisher = {JSTOR},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.3389/fmars.2019.00509,

title = {Growth Limitation of Marine Fish by Low Iron Availability in the Open Ocean},

author = {Eric D. Galbraith and Priscilla Le Mézo and Gerard Solanes Hernandez and Daniele Bianchi and David Kroodsma},

url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00509},

doi = {10.3389/fmars.2019.00509},

issn = {2296-7745},

year  = {2019},

date = {2019-01-01},

journal = {Frontiers in Marine Science},

volume = {6},

pages = {509},

abstract = {It is well-established that phytoplankton growth can be limited by the vanishingly low concentrations of dissolved iron found in large areas of the open ocean. However, the availability of iron is not typically considered an important factor in the ecology of marine animals, including fish. Here we compile observations to show that the iron contents of lower trophic level organisms in iron-limited regions can be an order of magnitude less than the iron contents of most fish. Although this shortfall could theoretically be overcome if iron assimilation rates were very high in fish, observations suggest this is not the case, consistent with the high recommended iron contents for mariculture feed. In addition, we highlight two occurrences among fish living in iron-poor regions that would conceivably be beneficial given iron scarcity: the absence of hemoglobin in Antarctic icefish, and the anadromous life history of salmon. Based on these multiple lines of evidence, we suggest that the iron content of lower trophic level organisms can be insufficient to support many fish species throughout their life cycles in iron-poor oceanic regions. We then use a global satellite-based estimate of fishing effort to show that relatively little fishing activity occurs in High Nitrate Low Chlorophyll (HNLC) regions, the most readily-identified iron-poor domains of the ocean, particularly when compared to satellite-based estimates of primary production and the observed mesozooplankton biomass in those waters. The low fishing effort is consistent with a low abundance of epipelagic fish in iron-limited regions, though other factors are likely to contribute as well. Our results imply that the importance of iron nutrition extends well beyond plankton and plays a role in the ecology of large marine animals.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1956,

title = {Global ensemble projections reveal trophicamplification of ocean biomass declineswith climate change},

author = {Heike K. Lotze and Derek P. Tittensor and Andrea Bryndum-Buchholz and William W. L. Cheung and Eric D. Galbraith and Manuel Barange and Nicolas Barrier and Daniele Bianchi and Julia L. Blanchard and Laurent Bopp and Matthias Büchner and Catherine M. Bulman and David A. Carozza and Villy Christensen and Marta Coll and John P. Dunne and Elizabeth A. Fulton and Simon Jennings and Miranda C. Jones and Steve Mackinson and Olivier Maury and Susa Niiranen and Ricardo Oliveros-Ramos and Tilla Roy and José A. Fernandes and Jacob Schewe and Yunne-Jai Shin and Tiago A. M. Silva and Jeroen Steenbeek and Charles A. Stock and Philippe Verley and Jan Volkholz and Nicola D. Walker and Boris Worm},

url = {https://www.pnas.org/content/116/26/12907},

year  = {2019},

date = {2019-01-01},

journal = {Proceedings of the National Academy of Sciences},

abstract = {While the physical dimensions of climate change are now routinely assessed through multimodel intercomparisons, projected impacts on the global ocean ecosystem generally rely on individual models with a specific set of assumptions. To address these single-model limitations, we present standardized ensemble projections from six global marine ecosystem models forced with two Earth system models and four emis- sion scenarios with and without fishing. We derive average biomass trends and associated uncertainties across the marine food web. Without fishing, mean global animal biomass decreased by 5% (±4% SD) under low emissions and 17% (±11% SD) under high emissions by 2100, with an average 5% decline for every 1 °C of warming. Projected biomass declines were primarily driven by increasing temperature and decreasing primary production, and were more pronounced at higher trophic levels, a process known as trophic amplification. Fishing did not substantially alter the effects of climate change. Considerable regional variation featured strong biomass increases at high latitudes and de- creases at middle to low latitudes, with good model agreement on the direction of change but variable magnitude. Uncertainties due to vari- ations in marine ecosystem and Earth system models were similar. Ensemble projections performed well compared with empirical data, emphasizing the benefits of multimodel inference to project future outcomes. Our results indicate that global ocean animal biomass con- sistently declines with climate change, and that these impacts are am- plified at higher trophic levels. Next steps for model development include dynamic scenarios of fishing, cumulative human impacts, and the effects of management measures on future ocean biomass trends.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1346,

title = {Global niche of marine anaerobic metabolisms expanded by particle microenvironments},

author = {Daniele Bianchi and Thomas S Weber and Rainer Kiko and Curtis Deutsch},

url = {https://www.nature.com/articles/s41561-018-0081-0},

isbn = {1752-0908},

year  = {2018},

date = {2018-03-01},

journal = {Nature Geoscience},

publisher = {Nature Publishing Group},

abstract = {In ocean waters, anaerobic microbial respiration should be confined to the anoxic waters found in coastal regions and tropical oxygen minimum zones, where it is energetically favourable. However, recent molecular and geochemical evidence has pointed to a much broader distribution of denitrifying and sulfate-reducing microbes. Anaerobic metabolisms are thought to thrive in microenvironments that develop inside sinking organic aggregates, but the global distribution and geochemical significance of these microenvironments is poorly understood. Here, we develop a new size-resolved particle model to predict anaerobic respiration from aggregate properties and seawater chemistry. Constrained by observations of the size spectrum of sinking particles, the model predicts that denitrification and sulfate reduction can be sustained throughout vast, hypoxic expanses of the ocean, and could explain the trace metal enrichment observed in particles due to sulfide precipitation. Globally, the expansion of the anaerobic niche due to particle microenvironments doubles the rate of water column denitrification compared with estimates based on anoxic zones alone, and changes the sensitivity of the marine nitrogen cycle to deoxygenation in a warming climate.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carozzametabolic,

title = {Metabolic impacts of climate change on marine ecosystems: Implications for fish communities and fisheries},

author = {David A Carozza and Daniele Bianchi and Eric D Galbraith},

url = {DOI: 10.1111/geb.12832},

year  = {2018},

date = {2018-01-01},

journal = {Global Ecology and Biogeography},

publisher = {Wiley Online Library},

abstract = {Aim: Climate change will reshape marine ecosystems over the 21st century through diverse and complex mechanisms that are difficult to assess quantitatively. Here, we characterize expectations for how marine community biomass will respond to the energetic consequences of changes in primary production and temperature-depend- ent metabolic rates, under a range of fishing/conservation scenarios. 

	  

	Location: Global ocean. 

	  

	Time period: 1950–2100. 

	  

	Major taxa studied: Commercially harvested marine ectotherms (‘fish’). 

	  

	Methods: We use a size-structured macroecological model of the marine ecosystem, coupled with a catch model that allows for calibration with global historical data and simulation of fishing. We examine the four energetic mechanisms that, within the model framework, determine the community response to climate change: net pri- mary production, phytoplankton cell size, and the temperature dependencies of growth and natural mortality. 

	  

	Results: Climate change decreases the modelled global fish community biomass by as much as 30% by 2100. This results from a diminished energy supply to upper trophic levels as photosynthesis becomes more nutrient limited and phytoplankton cells shrink, and from a temperature-driven increase of natural mortality that, together, overwhelm the effect of accelerated somatic growth rates. Ocean circulation changes drive regional variations of primary production, producing patterns of winners and los- ers that largely compensate each other when averaged globally, whereas decreasing phytoplankton size drives weaker but more uniformly negative changes. The climate impacts are similar across the range of conservation scenarios but are slightly amplified in the strong conservation scenarios owing to the greater role of natural mortality. Main conclusions: The spatial pattern of climate impacts is mostly determined by changes in primary production. The overall decline of community biomass is attributed to a temperature-driven increase of natural mortality, alongside an overall decrease in phytoplankton size, despite faster somatic growth. Our results highlight the importance of the competition between accelerated growth and mortality in a warming ocean.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1677,

title = {Roles of the ocean mesoscale in the horizontal supply of mass, heat, carbon and nutrients to the Northern Hemisphere subtropical gyres},

author = {Ayako Yamamoto and Jaime B Palter and Carolina O Dufour and Stephen M Griffies and Daniele Bianchi and Mariona Claret and John P Dunne and Ivy Frenger and Eric D Galbraith},

url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JC013969},

isbn = {2169-9275},

year  = {2018},

date = {2018-01-01},

journal = {Journal of Geophysical Research: Oceans},

publisher = {Wiley Online Library},

abstract = {Horizontal transport at the boundaries of the subtropical gyres plays a crucial role in providing the nutrients that fuel gyre primary productivity, the heat that helps restratify the surface mixed layer, and the dissolved inorganic carbon that influences air-sea carbon exchange. Mesoscale eddies may be an important component of these horizontal transports; however, previous studies have not quantified the horizontal tracer transport due to eddies across the subtropical gyre boundaries. Here we assess the physical mechanisms that control the horizontal transport of mass, heat, nutrients, and carbon across the North Pacific and North Atlantic subtropical gyre boundaries using the eddy-rich ocean component of a climate model (Geophysical Fluid Dynamics Laboratory Climate Model version 2.6) coupled to a simple biogeochemical model (mini-BLING). Our results suggest that horizontal transport across the gyre boundaries supplies a substantial amount of mass and tracers to the ventilated layer of both Northern Hemisphere subtropical gyres, with the Kuroshio and Gulf Stream acting as main exchange gateways. Mass, heat, and dissolved inorganic carbon supply is principally driven by the time-mean circulation, whereas nutrient transport differs markedly from the other tracers, as nutrients are mainly supplied to both subtropical gyres by downgradient eddy mixing across gyre boundaries. A budget analysis further reveals that the horizontal nutrient transport, combining the roles of both mean and eddy components, is responsible for more than three quarters of the total nutrient supply into the subtropical gyres, surpassing a recent estimate based on a coarse-resolution model and thus further highlighting the importance of horizontal nutrient transport.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1676,

title = {Rapid coastal deoxygenation due to ocean circulation shift in the northwest Atlantic},

author = {Mariona Claret and Eric D Galbraith and Jaime B Palter and Daniele Bianchi and Katja Fennel and Denis Gilbert and John P Dunne},

url = {https://www.nature.com/articles/s41558-018-0263-1},

isbn = {1758-6798},

year  = {2018},

date = {2018-01-01},

journal = {Nature Climate Change},

pages = {1},

publisher = {Nature Publishing Group},

abstract = {Global observations show that the ocean lost approximately 2% of its oxygen inventory over the past five decades, with important implications for marine ecosystems. The rate of change varies regionally, with northwest Atlantic coastal waters showing a long-term drop that vastly outpaces the global and North Atlantic basin mean deoxygenation rates. However, past work has been unable to differentiate the role of large-scale climate forcing from that of local processes. Here, we use hydrographic evidence to show that a Labrador Current retreat is playing a key role in the deoxygenation on the northwest Atlantic shelf. A high-resolution global coupled climate–biogeochemistry model reproduces the observed decline of saturation oxygen concentrations in the region, driven by a retreat of the equatorward-flowing Labrador Current and an associated shift towards more oxygen-poor subtropical waters on the shelf. The dynamical changes underlying the shift in shelf water properties are correlated with a slowdown in the simulated Atlantic Meridional Overturning Circulation (AMOC). Our results provide strong evidence that a major, centennial-scale change of the Labrador Current is underway, and highlight the potential for ocean dynamics to impact coastal deoxygenation over the coming century.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1284,

title = {Biogeochemical role of subsurface coherent eddies in the ocean: Tracer cannonballs, hypoxic storms, and microbial stewpots?},

author = {Ivy Frenger and Daniele Bianchi and Carolin Stührenberg and Andreas Oschlies and John Dunne and Curtis Deutsch and Eric Galbraith and Florian Schütte},

url = {http://onlinelibrary.wiley.com/doi/10.1002/2017GB005743/full},

year  = {2018},

date = {2018-01-01},

journal = {Global Biogeochemical Cycles},

volume = {32},

number = {2},

pages = {226-249},

abstract = {Subsurface coherent eddies are well-known features of ocean circulation, but the sparsity of observations prevents an assessment of their importance for biogeochemistry. Here, we use a global eddying (0.1° ) ocean-biogeochemical model to carry out a census of subsurface coherent eddies originating from eastern boundary upwelling systems (EBUS), and quantify their biogeochemical effects as they propagate westward into the subtropical gyres. While most eddies exist for a few months, moving over distances of 100s of km, a small fraction (< 5%) of long-lived eddies propagates over distances greater than 1000km, carrying the oxygen-poor and nutrient-rich signature of EBUS into the gyre interiors. In the Pacific, transport by subsurface coherent eddies accounts for roughly 10% of the offshore transport of oxygen and nutrients in pycnocline waters. This "leakage" of subsurface waters can be a significant fraction of the transport by nutrient-rich poleward undercurrents, and may contribute to the well-known reduction of productivity by eddies in EBUS. Furthermore, at the density layer of their cores, eddies decrease climatological oxygen locally by close to 10%, thereby expanding oxygen minimum zones. Finally, eddies represent low-oxygen extreme events in otherwise oxygenated waters, increasing the area of hypoxic waters by several percent and producing dramatic short-term changes that may play an important ecological role. Capturing these non-local effects in global climate models, which typically include non-eddying oceans, would require dedicated parameterizations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{galbraith2017coupled,

title = {A coupled human-Earth model perspective on long-term trends in the global marine fishery},

author = {ED Galbraith and DA Carozza and D Bianchi},

url = {https://www.nature.com/articles/ncomms14884},

year  = {2017},

date = {2017-01-01},

journal = {Nature Communications},

volume = {8},

pages = {14884},

publisher = {Nature Publishing Group},

abstract = {The global wild marine fish harvest increased fourfold between 1950 and a peak value near the end of the 20th century, reflecting interactions between anthropogenic and ecological forces. Here, we examine these interactions in a bio-energetically constrained, spatially and temporally resolved model of global fisheries. We conduct historical hindcasts with the model, which suggest that technological progress can explain most of the 20th century increase of fish harvest. In contrast, projections extending this rate of technological progress into the future under open access suggest a long-term decrease in harvest due to over-fishing. Climate change is predicted to gradually decrease the global fish production capacity, though our model suggests that this is of secondary importance to social and economic factors. Our study represents a novel way to integrate human-ecological interactions within a single model framework for long-term simulations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carozza2017formulation,

title = {Formulation, General Features and Global Calibration of a Bioenergetically-Constrained Fishery Model},

author = {David A Carozza and Daniele Bianchi and Eric D Galbraith},

url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0169763},

year  = {2017},

date = {2017-01-01},

journal = {PloS one},

volume = {12},

number = {1},

pages = {e0169763},

publisher = {Public Library of Science},

abstract = {Human exploitation of marine resources is profoundly altering marine ecosystems, while climate change is expected to further impact commercially-harvested fish and other species. Although the global fishery is a highly complex system with many unpredictable aspects, the bioenergetic limits on fish production and the response of fishing effort to profit are both relatively tractable, and are sure to play important roles. Here we describe a generalized, coupled biological-economic model of the global marine fishery that represents both of these aspects in a unified framework, the BiOeconomic mArine Trophic Size-spectrum (BOATS) model. BOATS predicts fish production according to size spectra as a function of net primary production and temperature, and dynamically determines harvest spectra from the biomass density and interactive, prognostic fishing effort. Within this framework, the equilibrium fish biomass is determined by the economic forcings of catchability, ex-vessel price and cost per unit effort, while the peak harvest depends on the ecosystem parameters. Comparison of a large ensemble of idealized simulations with observational databases, focusing on historical biomass and peak harvests, allows us to narrow the range of several uncertain ecosystem parameters, rule out most parameter combinations, and select an optimal ensemble of model variants. Compared to the prior distributions, model variants with lower values of the mortality rate, trophic efficiency, and allometric constant agree better with observations. For most acceptable parameter combinations, natural mortality rates are more strongly affected by temperature than growth rates, suggesting different sensitivities of these processes to climate change. These results highlight the utility of adopting large-scale, aggregated data constraints to reduce model parameter uncertainties and to better predict the response of fisheries to human behaviour and climate change.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Holzer2017305,

title = {Objective estimates of mantle 3He in the ocean and implications for constraining the deep ocean circulation},

author = {Mark Holzer and Timothy DeVries and Daniele Bianchi and Robert Newton and Peter Schlosser and Gisela Winckler},

url = {//www.sciencedirect.com/science/article/pii/S0012821X16306197},

doi = {http://dx.doi.org/10.1016/j.epsl.2016.10.054},

issn = {0012-821X},

year  = {2017},

date = {2017-01-01},

journal = {Earth and Planetary Science Letters},

volume = {458},

pages = {305 - 314},

abstract = {Abstract Hydrothermal vents along the ocean’s tectonic ridge systems inject superheated water and large amounts of dissolved metals that impact the deep ocean circulation and the oceanic cycling of trace metals. The hydrothermal fluid contains dissolved mantle helium that is enriched in 3He relative to the atmosphere, providing an isotopic tracer of the ocean’s deep circulation and a marker of hydrothermal sources. This work investigates the potential for the 3He/4He isotope ratio to constrain the ocean’s mantle 3He source and to provide constraints on the ocean’s deep circulation. We use an ensemble of 11 data-assimilated steady-state ocean circulation models and a mantle helium source based on geographically varying sea-floor spreading rates. The global source distribution is partitioned into 6 regions, and the vertical profile and source amplitude of each region are varied independently to determine the optimal 3He source distribution that minimizes the mismatch between modeled and observed δ3He. In this way, we are able to fit the observed δ3He distribution to within a relative error of ~15%, with a global 3He source that ranges from 640 to 850 mol yr-1, depending on circulation. The fit captures the vertical and interbasin gradients of the δ3He distribution very well and reproduces its jet-sheared saddle point in the deep equatorial Pacific. This demonstrates that the data-assimilated models have much greater fidelity to the deep ocean circulation than other coarse-resolution ocean models. Nonetheless, the modelled δ3He distributions still display some systematic biases, especially in the deep North Pacific where δ3He is overpredicted by our models, and in the southeastern tropical Pacific, where observed westward-spreading δ3He plumes are not well captured. Sources inferred by the data-assimilated transport with and without isopycnally aligned eddy diffusivity differ widely in the Southern Ocean, in spite of the ability to match the observed distributions of CFCs and radiocarbon for either eddy parameterization.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carozza2016ecological,

title = {The ecological module of BOATS-1.0: a bioenergetically constrained model of marine upper trophic levels suitable for studies of fisheries and ocean biogeochemistry},

author = {David Anthony Carozza and Daniele Bianchi and Eric Douglas Galbraith},

year  = {2016},

date = {2016-01-01},

journal = {Geoscientific Model Development},

volume = {9},

number = {4},

pages = {1545–1565},

publisher = {Copernicus GmbH},

abstract = {Environmental change and the exploitation of marine resources have had profound impacts on marine communities, with potential implications for ocean biogeochemistry and food security. In order to study such global-scale problems, it is helpful to have computationally efficient numerical models that predict the first-order features of fish biomass production as a function of the environment, based on empirical and mechanistic understandings of marine ecosystems. Here we describe the ecological module of the BiOeconomic mArine Trophic Size-spectrum (BOATS) model, which takes an Earth-system approach to modelling fish biomass at the global scale. The ecological model is designed to be used on an Earth-system model grid, and determines size spectra of fish biomass by explicitly resolving life history as a function of local temperature and net primary production. Biomass production is limited by the availability of photosynthetic energy to upper trophic levels, following empirical trophic efficiency scalings, and by well-established empirical temperature-dependent growth rates. Natural mortality is calculated using an empirical size-based relationship, while reproduction and recruitment depend on both the food availability to larvae from net primary production and the production of eggs by mature adult fish. We describe predicted biomass spectra and compare them to observations, and conduct a sensitivity study to determine how they change as a function of net primary production and temperature. The model relies on a limited number of parameters compared to similar modelling efforts, while retaining reasonably realistic representations of biological and ecological processes, and is computationally efficient, allowing extensive parameter-space analyses even when implemented globally. As such, it enables the exploration of the linkages between ocean biogeochemistry, climate, and upper trophic levels at the global scale, as well as a representation of fish biomass for idealized studies of fisheries.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bianchi2016global,

title = {Global patterns of diel vertical migration times and velocities from acoustic data},

author = {Daniele Bianchi and KAS Mislan},

url = {http://onlinelibrary.wiley.com/doi/10.1002/lno.10219/abstract},

year  = {2016},

date = {2016-01-01},

journal = {Limnology and Oceanography},

volume = {61},

number = {1},

pages = {353–364},

publisher = {Wiley Online Library},

abstract = {Diel vertical migrations (DVM) of zooplankton and micronekton are observed throughout the world ocean, where they influence ecological interactions and biogeochemical cycles. Despite their common occurrence, descriptions of the characteristics of these migrations are currently limited at the large scale. We analyze trajectories of migrations from a global dataset of acoustic backscatter to identify the large-scale patterns of the timing and speed of DVM. Sound scattering layers (SSL) leave the surface 21 ± 20 min before sunrise, and return to it 17 ± 23 min after sunset, while changes in bulk surface backscatter appear to be nearly synchronous to sunrise and sunset. Mean downward migrations (7.6 ± 3.6 cm s-1) are significantly faster than mean upward migrations (6.5 ± 3.5 cm s-1). Furthermore, coherent and predictable variations of migration properties at the scale of ocean basins are evident. These variations appear to be related to the depths of migration, such that deeper migrations, observed for example in the subtropical gyres, the western tropical Pacific and the Southern Ocean, show earlier departures and later arrivals than shallower migrations. Vertical velocities peak in the tropical and subtropical regions, and decline towards the poles, with the strongest declines observed in the North Pacific. Migration velocities are also correlated to migration depths, with deeper migrations being faster than shallow migrations. These new constraints on the characteristics of migrating SSL could help shed light on the physiological, ecological, and environmental controls that regulate DVM behavior.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cartapanis2016global,

title = {Global pulses of organic carbon burial in deep-sea sediments during glacial maxima},

author = {Olivier Cartapanis and Daniele Bianchi and Samuel L Jaccard and Eric D Galbraith},

url = {http://www.nature.com/articles/ncomms10796},

year  = {2016},

date = {2016-01-01},

journal = {Nature communications},

volume = {7},

publisher = {Nature Publishing Group},

abstract = {The burial of organic carbon in marine sediments removes carbon dioxide from the ocean–atmosphere pool, provides energy to the deep biosphere, and on geological timescales drives the oxygenation of the atmosphere. Here we quantify natural variations in the burial of organic carbon in deep-sea sediments over the last glacial cycle. Using a new data compilation of hundreds of sediment cores, we show that the accumulation rate of organic carbon in the deep sea was consistently higher (50%) during glacial maxima than during interglacials. The spatial pattern and temporal progression of the changes suggest that enhanced nutrient supply to parts of the surface ocean contributed to the glacial burial pulses, with likely additional contributions from more efficient transfer of organic matter to the deep sea and better preservation of organic matter due to reduced oxygen exposure. These results demonstrate a pronounced climate sensitivity for this global carbon cycle sink.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{galbraith2015complex,

title = {Complex functionality with minimal computation: Promise and pitfalls of reduced-tracer ocean biogeochemistry models},

author = {Eric D Galbraith and John P Dunne and Anand Gnanadesikan and Richard D Slater and Jorge L Sarmiento and Carolina O Dufour and Gregory F Souza and Daniele Bianchi and Mariona Claret and Keith B Rodgers and others},

url = {http://onlinelibrary.wiley.com/doi/10.1002/2015MS000463/full},

year  = {2015},

date = {2015-01-01},

journal = {Journal of Advances in Modeling Earth Systems},

volume = {7},

number = {4},

pages = {2012–2028},

publisher = {Wiley Online Library},

abstract = {Earth System Models increasingly include ocean biogeochemistry models in order to predict changes in ocean carbon storage, hypoxia, and biological productivity under climate change. However, state-of-the-art ocean biogeochemical models include many advected tracers, that significantly increase the computational resources required, forcing a trade-off with spatial resolution. Here, we compare a state-of-the art model with 30 prognostic tracers (TOPAZ) with two reduced-tracer models, one with 6 tracers (BLING), and the other with 3 tracers (miniBLING). The reduced-tracer models employ parameterized, implicit biological functions, which nonetheless capture many of the most important processes resolved by TOPAZ. All three are embedded in the same coupled climate model. Despite the large difference in tracer number, the absence of tracers for living organic matter is shown to have a minimal impact on the transport of nutrient elements, and the three models produce similar mean annual preindustrial distributions of macronutrients, oxygen, and carbon. Significant differences do exist among the models, in particular the seasonal cycle of biomass and export production, but it does not appear that these are necessary consequences of the reduced tracer number. With increasing CO2, changes in dissolved oxygen and anthropogenic carbon uptake are very similar across the different models. Thus, while the reduced-tracer models do not explicitly resolve the diversity and internal dynamics of marine ecosystems, we demonstrate that such models are applicable to a broad suite of major biogeochemical concerns, including anthropogenic change. These results are very promising for the further development and application of reduced-tracer biogeochemical models that incorporate “sub-ecosystem-scale” parameterizations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{galbraith2015impact,

title = {The impact of atmospheric pCO2 on carbon isotope ratios of the atmosphere and ocean},

author = {Eric D Galbraith and Eun Young Kwon and Daniele Bianchi and Mathis P Hain and Jorge L Sarmiento},

url = {http://onlinelibrary.wiley.com/doi/10.1002/2014GB004929/abstract},

year  = {2015},

date = {2015-01-01},

journal = {Global Biogeochemical Cycles},

volume = {29},

number = {3},

pages = {307–324},

publisher = {Wiley Online Library},

abstract = {It is well known that the equilibration timescale for the isotopic ratios 13C/12C and 14C/12C in the ocean mixed layer is on the order of a decade, 2 orders of magnitude slower than for oxygen. Less widely appreciated is the fact that the equilibration timescale is quite sensitive to the speciation of dissolved inorganic carbon (DIC) in the mixed layer, scaling linearly with the ratio DIC/CO2, which varies inversely with atmospheric pCO2. Although this effect is included in models that resolve the role of carbon speciation in air-sea exchange, its role is often unrecognized, and it is not commonly considered in the interpretation of carbon isotope observations. Here we use a global three-dimensional ocean model to estimate the redistribution of the carbon isotopic ratios between the atmosphere and ocean due solely to variations in atmospheric pCO2. Under Last Glacial Maximum (LGM) pCO2, atmospheric Δ14C is increased by ≈30‰ due to the speciation change, all else being equal, raising the surface reservoir age by about 250 years throughout most of the ocean. For 13C, enhanced surface disequilibrium under LGM pCO2 causes the upper ocean, atmosphere, and North Atlantic Deep Water δ13C to become at least 0.2‰ higher relative to deep waters ventilated by the Southern Ocean. Conversely, under high pCO2, rapid equilibration greatly decreases isotopic disequilibrium. As a result, during geological periods of high pCO2, vertical δ13C gradients may have been greatly weakened as a direct chemical consequence of the high pCO2, masquerading as very well ventilated or biologically dead Strangelove Oceans. The ongoing anthropogenic rise of pCO2 is accelerating the equilibration of the carbon isotopes in the ocean, lowering atmospheric Δ14C and weakening δ13C gradients within the ocean to a degree that is similar to the traditional fossil fuel “Suess” effect.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cabre2015oxygen,

title = {Oxygen minimum zones in the tropical Pacific across CMIP5 models: mean state differences and climate change trends},

author = {A Cabré and I Marinov and R Bernardello and D Bianchi},

url = {http://www.biogeosciences.net/12/5429/2015/},

year  = {2015},

date = {2015-01-01},

journal = {Biogeosciences Discussions},

volume = {12},

number = {8},

abstract = { We analyse simulations of the Pacific Ocean oxygen minimum zones (OMZs) from 11 Earth system model contributions to the Coupled Model Intercomparison Project Phase 5, focusing on the mean state and climate change projections. The simulations tend to overestimate the volume of the OMZs, especially in the tropics and Southern Hemisphere. Compared to observations, five models introduce incorrect meridional asymmetries in the distribution of oxygen including larger southern OMZ and weaker northern OMZ, due to interhemispheric biases in intermediate water mass ventilation. Seven models show too deep an extent of the tropical hypoxia compared to observations, stemming from a deficient equatorial ventilation in the upper ocean, combined with too large a biologically driven downward flux of particulate organic carbon at depth, caused by particle export from the euphotic layer that is too high and remineralization in the upper ocean that is too weak.  At interannual timescales, the dynamics of oxygen in the eastern tropical Pacific OMZ is dominated by biological consumption and linked to natural variability in the Walker circulation. However, under the climate change scenario RCP8.5, all simulations yield small and discrepant changes in oxygen concentration at mid depths in the tropical Pacific by the end of the 21st century due to an almost perfect compensation between warming-related decrease in oxygen saturation and decrease in biological oxygen utilization. Climate change projections are at odds with recent observations that show decreasing oxygen levels at mid depths in the tropical Pacific. Out of the OMZs, all the CMIP5 models predict a decrease of oxygen over most of the surface and deep ocean at low latitudes and over all depths at high latitudes due to an overall slow-down of ventilation and increased temperature.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{babbin2015rapid,

title = {Rapid nitrous oxide cycling in the suboxic ocean},

author = {Andrew R Babbin and Daniele Bianchi and Amal Jayakumar and Bess B Ward},

url = {http://science.sciencemag.org/content/348/6239/1127},

year  = {2015},

date = {2015-01-01},

journal = {Science},

volume = {348},

number = {6239},

pages = {1127–1129},

publisher = {American Association for the Advancement of Science},

abstract = {Nitrous oxide (N2O) is a powerful greenhouse gas and a major cause of stratospheric ozone depletion, yet its sources and sinks remain poorly quantified in the oceans. We used isotope tracers to directly measure N2O reduction rates in the eastern tropical North Pacific. Because of incomplete denitrification, N2O cycling rates are an order of magnitude higher than predicted by current models in suboxic regions, and the spatial distribution suggests strong dependence on both organic carbon and dissolved oxygen concentrations. Furthermore, N2O turnover is 20 times higher than the net atmospheric efflux. The rapid rate of this cycling coupled to an expected expansion of suboxic ocean waters implies future increases in N2O emissions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bianchi2014enhancement,

title = {Enhancement of anammox by the excretion of diel vertical migrators},

author = {Daniele Bianchi and Andrew R Babbin and Eric D Galbraith},

url = {http://www.pnas.org/content/111/44/15653.abstract},

year  = {2014},

date = {2014-01-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {111},

number = {44},

pages = {15653–15658},

publisher = {National Acad Sciences},

abstract = {Measurements show that anaerobic ammonium oxidation with nitrite (anammox) is a major pathway of fixed nitrogen removal in the anoxic zones of the open ocean. Anammox requires a source of ammonium, which under anoxic conditions could be supplied by the breakdown of sinking organic matter via heterotrophic denitrification. However, at many locations where anammox is measured, denitrification rates are small or undetectable. Alternative sources of ammonium have been proposed to explain this paradox, for example through dissimilatory reduction of nitrate to ammonium and transport from anoxic sediments. However, the relevance of these sources in open-ocean anoxic zones is debated. Here, we bring to attention an additional source of ammonium, namely, the daytime excretion by zooplankton and micronekton migrating from the surface to anoxic waters. We use a synthesis of acoustic data to show that, where anoxic waters occur within the water column, most migrators spend the daytime within them. Although migrators export only a small fraction of primary production from the surface, they focus excretion within a confined depth range of anoxic water where particle input is small. Using a simple biogeochemical model, we suggest that, at those depths, the source of ammonium from organisms undergoing diel vertical migrations could exceed the release from particle remineralization, enhancing in situ anammox rates. The contribution of this previously overlooked process, and the numerous uncertainties surrounding it, call for further efforts to evaluate the role of animals in oxygen minimum zone biogeochemistry.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{galbraith2013acceleration,

title = {The acceleration of oceanic denitrification during deglacial warming},

author = {Eric D Galbraith and Markus Kienast and others},

url = {http://www.nature.com/ngeo/journal/v6/n7/full/ngeo1832.html},

year  = {2013},

date = {2013-01-01},

journal = {Nature Geoscience},

volume = {6},

number = {7},

pages = {579–584},

publisher = {Nature Publishing Group},

abstract = {Over much of the ocean’s surface, productivity and growth are limited by a scarcity of bioavailable nitrogen. Sedimentary δ15N records spanning the last deglaciation suggest marked shifts in the nitrogen cycle during this time, but the quantification of these changes has been hindered by the complexity of nitrogen isotope cycling. Here we present a database of δ15N in sediments throughout the world’s oceans, including 2,329 modern seafloor samples, and 76 timeseries spanning the past 30,000 years. We show that the δ15N values of modern seafloor sediments are consistent with values predicted by our knowledge of nitrogen cycling in the water column. Despite many local deglacial changes, the globally averaged δ15N values of sinking organic matter were similar during the Last Glacial Maximum and Early Holocene. Considering the global isotopic mass balance, we explain these observations with the following deglacial history of nitrogen inventory processes. During the Last Glacial Maximum, the nitrogen cycle was near steady state. During the deglaciation, denitrification in the pelagic water column accelerated. The flooding of continental shelves subsequently increased denitrification at the seafloor, and denitrification reached near steady-state conditions again in the Early Holocene. We use a recent parameterization of seafloor denitrification to estimate a 30–120% increase in benthic denitrification between 15,000 and 8,000 years ago. Based on the similarity of globally averaged δ15N values during the Last Glacial Maximum and Early Holocene, we infer that pelagic denitrification must have increased by a similar amount between the two steady states.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gnanadesikan2013critical,

title = {Critical role for mesoscale eddy diffusion in supplying oxygen to hypoxic ocean waters},

author = {Anand Gnanadesikan and Daniele Bianchi and Marie-Aude Pradal},

url = {http://onlinelibrary.wiley.com/doi/10.1002/grl.50998/abstract},

year  = {2013},

date = {2013-01-01},

journal = {Geophysical Research Letters},

volume = {40},

number = {19},

pages = {5194–5198},

publisher = {Wiley Online Library},

abstract = {Estimates of the oceanic lateral eddy diffusion coefficient Aredi vary by more than an order of magnitude, ranging from less than a few hundred m2/s to thousands of m2/s. This uncertainty has first-order implications for the intensity of oceanic hypoxia, which is poorly simulated by the current generation of Earth System Models. Using satellite-based estimate of oxygen consumption in hypoxic waters to estimate the required diffusion coefficient for these waters gives a value of order 1000 m2/s. Varying Aredi across a suite of Earth System Models yields a broadly consistent result given a thermocline diapycnal diffusion coefficient of 1 × 10-5 m2/s.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bianchi2013diel,

title = {Diel vertical migration: Ecological controls and impacts on the biological pump in a one-dimensional ocean model},

author = {Daniele Bianchi and Charles Stock and Eric D Galbraith and Jorge L Sarmiento},

url = {http://onlinelibrary.wiley.com/doi/10.1002/gbc.20031/abstract},

year  = {2013},

date = {2013-01-01},

journal = {Global Biogeochemical Cycles},

volume = {27},

number = {2},

pages = {478–491},

publisher = {Wiley Online Library},

abstract = {Diel vertical migration (DVM) of zooplankton and micronekton is widespread in the ocean and forms a fundamental component of the biological pump, but is generally overlooked in global models of the Earth system. We develop a parameterization of DVM in the ocean and integrate it with a size-structured NPZD model. We assess the model’s ability to recreate ecosystem and DVM patterns at three well-observed Pacific sites, ALOHA, K2, and EQPAC, and use it to estimate the impact of DVM on marine ecosystems and biogeochemical dynamics. Our model includes the following: (1) a representation of migration dynamics in response to food availability and light intensity; (2) a representation of the digestive and metabolic processes that decouple zooplankton feeding from excretion, egestion, and respiration; and (3) a light-dependent parameterization of visual predation on zooplankton. The model captures the first-order patterns in plankton biomass and productivity across the biomes, including the biomass of migrating organisms. We estimate that realistic migratory populations sustain active fluxes to the mesopelagic zone equivalent to between 15% and 40% of the particle export and contribute up to half of the total respiration within the layers affected by migration. The localized active transport has important consequences for the cycling of oxygen, nutrients, and carbon. We highlight the importance of decoupling zooplankton feeding and respiration and excretion with depth for capturing the impact of migration on the redistribution of carbon and nutrients in the upper ocean.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bianchi2013intensification,

title = {Intensification of open-ocean oxygen depletion by vertically migrating animals},

author = {Daniele Bianchi and Eric D Galbraith and David A Carozza and KAS Mislan and Charles A Stock},

url = {http://www.nature.com/ngeo/journal/v6/n7/full/ngeo1837.html},

year  = {2013},

date = {2013-01-01},

journal = {Nature Geoscience},

volume = {6},

number = {7},

pages = {545–548},

publisher = {Nature Publishing Group},

abstract = {Throughout the ocean, countless small animals swim to depth in the daytime, presumably to seek refuge from large predators1, 2. These animals return to the surface at night to feed1, 2. This substantial diel vertical migration can result in the transfer of significant amounts of carbon and nutrients from the surface to depth3, 4, 5, 6, 7. However, its consequences on ocean chemistry at the global scale have remained uncertain8, 9. Here, we determine the depths of these diel migrations in the global ocean using a global array of backscatter data from acoustic Doppler current profilers, collected between 1990 and 2011. We show that the depth of diel migration follows coherent large-scale patterns. We find that migration depth is greater where subsurface oxygen concentrations are high, such that seawater oxygen concentration is the best single predictor of migration depth at the global scale. In oxygen minimum zone areas, migratory animals generally descend as far as the upper margins of the low-oxygen waters. Using an ocean biogeochemical model coupled to a general circulation model, we show that by focusing oxygen consumption in poorly ventilated regions of the upper ocean, diel vertical migration intensifies oxygen depletion in the upper margin of oxygen minimum zones. We suggest that future changes in the extent of oxygen minimum zones could alter the migratory depths of marine organisms, with consequences for marine biogeochemistry, food webs and fisheries.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}