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Book Chapter
Mitchell, BG, Bricaud A, Carder K, Cleveland J, Ferri GM, Gould RJ, Kahru M, Kishino M, Maske H, Moisan T, Moore L, Nelson NB, Phinney D, Reynolds RA, Sosik HM, Stramski D, Tassan S, Trees C, Weidemann A, Wieland JD, Vodacek A.  2000.  Determination of spectrl absorption coefficients of particles, dissolved material and phytoplankton for discrete water samples. Ocean optics protocols for satellite ocean color sensor validation, Revision 2, NASA Technical Memorandum 2000-209966m/cgaoer 12 m o. ( Fargion GS, Mueller JL, McClain CR, Eds.).:125-153., Greenbelt, Md.: National Aeronautics and Space Administration, Goddard Space Flight Center Abstract

"This document stipulates protocols for measuring bio-optical and radiometric data for the Senor Inter comparison and Merger for Biological and Interdisciplinary Oceanic Studies (SIMBIOS) Project activities and algorithm development. This document supersedes the earlier version published as Volume 25 in the SeaWiFS Technical report series ..."

O'Reilly, JE, Maritorena S, Siegel D, O'Brien MO, Toole D, Mitchell BG, Kahru M, Chavez F, Strutton PG, Cota GF, Hooker SB, McClain C, Carder K, Muller-Karger F, Harding L, Magnuson A, Phinney D, Moore G, Aiken J, Arrigo KR, Letelier RM, Culver M.  2000.  Ocean color chlorophyll a algorithms for SeaWiFS, OC2, and OC4: Version 4. SeaWiFS Postlaunch Calibration and Validation Analyses. 11( McClain CR, Ed.).:9-23., Greenbelt, Md.: Goddard Space Flight Center Abstract
Journal Article
Ohman, MD, Rudnick DL, Chekalyuk A, Davis RE, Feely RA, Kahru M, Kim HJ, Landry MR, Martz TR, Sabine CL, Send U.  2013.  Autonomous ocean measurements in the California Current ecosystem. Oceanography. 26:18-25. AbstractWebsite

Event-scale phenomena, of limited temporal duration or restricted spatial extent, often play a disproportionately large role in ecological processes occurring in the ocean water column. Nutrient and gas fluxes, upwelling and downwelling, transport of biogeochemically important elements, predator-prey interactions, and other processes may be markedly influenced by such events, which are inadequately resolved from infrequent ship surveys. The advent of autonomous instrumentation, including underwater gliders, profiling floats, surface drifters, enhanced moorings, coastal high-frequency radars, and satellite remote sensing, now provides the capability to resolve such phenomena and assess their role in structuring pelagic ecosystems. These methods are especially valuable when integrated together, and with shipboard calibration measurements and experimental programs.

Valente, A, Sathyendranath S, Brotas V, Groom S, Grant M, Taberner M, Antoine D, Arnone R, Balch WM, Barker K, Barlow R, Belanger S, Berthon JF, Besiktepe S, Brando V, Canuti E, Chavez F, Claustre H, Crout R, Frouin R, Garcia-Soto C, Gibb S, Gould R, Hooker S, Kahru M, Klein H, Kratzer S, Loisel H, McKee D, Mitchell BG, Moisan T, Muller-Karger F, O'Dowd L, Ondrusek M, Poulton AJ, Repecaud M, Smyth T, Sosik HM, Twardowski M, Voss K, Werdell J, Wernand M, Zibordi G.  2016.  A compilation of global bio-optical in situ data for ocean-colour satellite applications. Earth System Science Data. 8:235-252.   10.5194/essd-8-235-2016   AbstractWebsite

A compiled set of in situ data is important to evaluate the quality of ocean-colour satellite-data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT, GeP&CO), span between 1997 and 2012, and have a global distribution. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties and spectral diffuse attenuation coefficients. The data were from multi-project archives acquired via the open internet services or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenisation, quality control and merging of all data. No changes were made to the original data, other than averaging of observations that were close in time and space, elimination of some points after quality control and conversion to a standard format. The final result is a merged table designed for validation of satellite-derived ocean-colour products and available in text format. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) were preserved throughout the work and made available in the final table. Using all the data in a validation exercise increases the number of matchups and enhances the representativeness of different marine regimes. By making available the metadata, it is also possible to analyse each set of data separately. The compiled data are available at doi: 10.1594/PANGAEA.854832 (Valente et al., 2015).

Valente, A, Sathyendranath S, Brotas V, Groom S, Grant M, Taberner M, Antoine D, Arnone R, Balch WM, Barker K, Barlow R, Belanger S, Berthon JF, Besiktepe S, Borsheim Y, Bracher A, Brando V, Canuti E, Chavez F, Cianca A, Claustre H, Clementson L, Crout R, Frouin R, Garcia-Soto C, Gibb SW, Gould R, Hooker SB, Kahru M, Kampel M, Klein H, Kratzer S, Kudela R, Ledesma J, Loisel H, Matrai P, McKee D, Mitchell BG, Moisan T, Muller-Karger F, O'Dowd L, Ondrusek M, Platt T, Poulton AJ, Repecaud M, Schroeder T, Smythe T, Smythe-Wright D, Sosik HM, Twardowski M, Vellucci V, Voss K, Werdell J, Wernand M, Wright S, Zibordi G.  2019.  A compilation of global bio-optical in situ data for ocean-colour satellite applications - version two. Earth System Science Data. 11:1037-1068.   10.5194/essd-11-1037-2019   AbstractWebsite

A global compilation of in situ data is useful to evaluate the quality of ocean-colour satellite data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (including, inter alia, MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT and GeP&CO) and span the period from 1997 to 2018. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties, spectral diffuse attenuation coefficients and total suspended matter. The data were from multi-project archives acquired via open internet services or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenization, quality control and merging of all data. No changes were made to the original data, other than averaging of observations that were close in time and space, elimination of some points after quality control and conversion to a standard format. The final result is a merged table designed for validation of satellite-derived ocean-colour products and available in text format. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) was propagated throughout the work and made available in the final table. By making the metadata available, provenance is better documented, and it is also possible to analyse each set of data separately. This paper also describes the changes that were made to the compilation in relation to the previous version (Valente et al., 2016). The compiled data are available at (Valente et al., 2019).

Nevison, CD, Keeling RF, Kahru M, Manizza M, Mitchell BG, Cassar N.  2012.  Estimating net community production in the Southern Ocean based on atmospheric potential oxygen and satellite ocean color data. Global Biogeochemical Cycles. 26   10.1029/2011gb004040   AbstractWebsite

The seasonal cycle of atmospheric potential oxygen (APO similar to O-2 + 1.1 CO2) reflects three seasonally varying ocean processes: 1) thermal in- and outgassing, 2) mixed layer net community production (NCP) and 3) deep water ventilation. Previous studies have isolated the net biological seasonal signal (i.e., the sum of NCP and ventilation), after using air-sea heat flux data to estimate the thermal signal. In this study, we resolve all three components of the APO seasonal cycle using a methodology in which the ventilation signal is estimated based on atmospheric N2O data, the thermal signal is estimated based on heat flux or atmospheric Ar/N-2 data, and the production signal is inferred as a residual. The isolation of the NCP signal in APO allows for direct comparison to estimates of NCP based on satellite ocean color data, after translating the latter into an atmospheric signal using an atmospheric transport model. When applied to ocean color data using algorithms specially adapted to the Southern Ocean and APO data at three southern monitoring sites, these two independent methods converge on a similar phase and amplitude of the seasonal NCP signal in APO and yield an estimate of annual mean NCP south of 50 degrees S of 0.8-1.2 Pg C/yr, with corresponding annual mean NPP of similar to 3 Pg C/yr and a mean growing season f ratio of similar to 0.33. These results are supported by ocean biogeochemistry model simulations, in which air-sea O-2 and N2O fluxes are resolved into component thermal, ventilation and (for O-2) NCP contributions.

Lluch-Cota, SE, Aragon-Noriega EA, Arreguin-Sanchez F, Aurioles-Gamboa D, Bautista-Romero JJ, Brusca RC, Cervantes-Duarte R, Cortes-Altamirano R, Del-Monte-Luna P, Esquivel-Herrera A, Fernandez G, Hendrickx ME, Hernandez-Vazquez S, Herrera-Cervantes H, Kahru M, Lavin M, Lluch-Belda D, Lluch-Cota DB, Lopez-Martinez J, Marinone SG, Nevarez-Martinez MO, Ortega-Garcia S, Palacios-Castro E, Pares-Sierra A, Ponce-Diaz G, Ramirez-Rodriguez M, Salinas-Zavala CA, Schwartzlose RA, Sierra-Beltran AP.  2007.  The Gulf of California: Review of ecosystem status and sustainability challenges. Progress in Oceanography. 73:1-26.   10.1016/j.pocean.2007.01.013   AbstractWebsite

The Gulf of California is unique because of its geographical location and conformation. It hosts diverse ecosystems and important fisheries that support industry and provide livelihood to coastal settlements. It is also the site of interests and problems, and an intense interaction among managers, producers, and conservationists. In this report, we scrutinize the abiotic (hydrography, climate, ocean circulation, and chemistry) and biotic (phyto- and zooplankton, fish, invertebrates, marine mammals, birds, and turtles) components of the marine ecosystem, and some particular aspects of climate variability, endemisms, harmful algal blooms, oxygen minimum layer, and pollution. We also review the current conditions and conflicts around the main fisheries (shrimp, small and large pelagic fishes, squid, artisanal and sportfishing), the most important human activity in the Gulf of California. We cover some aspects of management and conservation of fisheries, especially the claimed overexploitation of fish resources and the ecosystems, and review proposals for creating networks of marine protected areas. We conclude by identifying main needs for information and research, particularly the integration of data bases, the implementation of models and paleoreconstructions, establishment of monitoring programs, and the evaluation of fishing impacts and management actions. (c) 2007 Elsevier Ltd. All rights reserved.

Cloern, JE, Abreu PC, Carstensen J, Chauvaud L, Elmgren R, Grall J, Greening H, Johansson JOR, Kahru M, Sherwood ET, Xu J, Yin KD.  2016.  Human activities and climate variability drive fast-paced change across the world's estuarine-coastal ecosystems. Global Change Biology. 22:513-529.   10.1111/gcb.13059   AbstractWebsite

Time series of environmental measurements are essential for detecting, measuring and understanding changes in the Earth system and its biological communities. Observational series have accumulated over the past 2-5 decades from measurements across the world's estuaries, bays, lagoons, inland seas and shelf waters influenced by runoff. We synthesize information contained in these time series to develop a global view of changes occurring in marine systems influenced by connectivity to land. Our review is organized around four themes: (i) human activities as drivers of change; (ii) variability of the climate system as a driver of change; (iii) successes, disappointments and challenges of managing change at the sea-land interface; and (iv) discoveries made from observations over time. Multidecadal time series reveal that many of the world's estuarine-coastal ecosystems are in a continuing state of change, and the pace of change is faster than we could have imagined a decade ago. Some have been transformed into novel ecosystems with habitats, biogeochemistry and biological communities outside the natural range of variability. Change takes many forms including linear and nonlinear trends, abrupt state changes and oscillations. The challenge of managing change is daunting in the coastal zone where diverse human pressures are concentrated and intersect with different responses to climate variability over land and over ocean basins. The pace of change in estuarine-coastal ecosystems will likely accelerate as the human population and economies continue to grow and as global climate change accelerates. Wise stewardship of the resources upon which we depend is critically dependent upon a continuing flow of information from observations to measure, understand and anticipate future changes along the world's coastlines.

Anderson, CR, Kudela RM, Kahru M, Chao Y, Rosenfeld LK, Bahr FL, Anderson DM, Norris TA.  2016.  Initial skill assessment of the California Harmful Algae Risk Mapping (C-HARM) system. Harmful Algae. 59:1-18.   10.1016/j.hal.2016.08.006   AbstractWebsite

Toxic algal events are an annual burden on aquaculture and coastal ecosystems of California. The threat of domoic acid (DA) toxicity to human and wildlife health is the dominant harmful algal bloom (HAB) concern for the region, leading to a strong focus on prediction and mitigation of these blooms and their toxic effects. This paper describes the initial development of the California Harmful Algae Risk Mapping (C-HARM) system that predicts the spatial likelihood of blooms and dangerous levels of DA using a unique blend of numerical models, ecological forecast models of the target group, Pseudo-nitzschia, and satellite ocean color imagery. Data interpolating empirical orthogonal functions (DINEOF) are applied to ocean color imagery to fill in missing data and then used in a multivariate mode with other modeled variables to forecast biogeochemical parameters. Daily predictions (nowcast and forecast maps) are run routinely at the Central and Northern California Ocean Observing System (CeNCOOS) and posted on its public website. Skill assessment of model output for the nowcast data is restricted to nearshore pixels that overlap with routine pier monitoring of HABs in California from 2014 to 2015. Model lead times are best correlated with DA measured with solid phase adsorption toxin tracking (SPATI') and marine mammal strandings from DA toxicosis, suggesting long-term benefits of the HAB predictions to decision making. Over the next three years, the C-HARM application system will be incorporated into the NOAA operational HAB forecasting system and HAB Bulletin. (C) 2016 Elsevier B.V. All rights reserved.

Maiti, K, Charette MA, Buesseler KO, Kahru M.  2013.  An inverse relationship between production and export efficiency in the Southern Ocean. Geophysical Research Letters. 40:1557-1561.   10.1002/grl.50219   AbstractWebsite

In the past two decades, a number of studies have been carried out in the Southern Ocean to look at export production using drifting sediment traps and thorium-234 based measurements, which allows us to reexamine the validity of using the existing relationships between production, export efficiency, and temperature to derive satellite-based carbon export estimates in this region. Comparisons of in situ export rates with modeled rates indicate a two to fourfold overestimation of export production by existing models. Comprehensive analysis of in situ data indicates two major reasons for this difference: (i) in situ data indicate a trend of decreasing export efficiency with increasing production which is contrary to existing export models and (ii) the export efficiencies appear to be less sensitive to temperature in this region compared to the global estimates used in the existing models. The most important implication of these observations is that the simplest models of export, which predict increase in carbon flux with increasing surface productivity, may require additional parameters, different weighing of existing parameters, or separate algorithms for different oceanic regimes.

McQuatters-Gollop, A, Reid PC, Edwards M, Burkill PH, Castellani C, Batten S, Gieskes W, Beare D, Bidigare RR, Head E, Johnson R, Kahru M, Koslow JA, Pena A.  2011.  Is there a decline in marine phytoplankton? Nature. 472:E6-E7.   10.1038/nature09950   AbstractWebsite

Phytoplankton account for approximately 50% of global primary production, form the trophic base of nearly all marine ecosystems, are fundamental in trophic energy transfer and have key roles in climate regulation, carbon sequestration and oxygen production. Boyce et al. compiled a chlorophyll index by combining in situ chlorophyll and Secchi disk depth measurements that spanned a more than 100-year time period and showed a decrease in marine phytoplankton biomass of approximately 1% of the global median per year over the past century. Eight decades of data on phytoplankton biomass collected in the North Atlantic by the Continuous Plankton Recorder (CPR) survey, however, show an increase in an index of chlorophyll (Phytoplankton Colour Index) in both the Northeast and Northwest Atlantic basinsFig. 1), and other long-term time series, including the Hawaii Ocean Time-series (HOT)8, the Bermuda Atlantic Time Series (BATS)8 and the California Cooperative Oceanic Fisheries Investigations (CalCOFI)9 also indicate increased phytoplankton biomass over the last 20–50 years. These findings, which were not discussed by Boyce et al.1, are not in accordance with their conclusions and illustrate the importance of using consistent observations when estimating long-term trends.

Melville, WK, Lenain L, Cayan DR, Kahru M, Kleissl JP, Linden PF, Statom NM.  2016.  The Modular Aerial Sensing System. Journal of Atmospheric and Oceanic Technology. 33:1169-1184.   10.1175/jtech-d-15-0067.1   AbstractWebsite

Satellite remote sensing has enabled remarkable progress in the ocean, earth, atmospheric, and environmental sciences through its ability to provide global coverage with ever-increasing spatial resolution. While exceptions exist for geostationary ocean color satellites, the temporal coverage of low-Earth-orbiting satellites is not optimal for oceanographic processes that evolve over time scales of hours to days. In hydrology, time scales can range from hours for flash floods, to days for snowfall, to months for the snowmelt into river systems. On even smaller scales, remote sensing of the built environment requires a building-resolving resolution of a few meters or better. For this broad range of phenomena, satellite data need to be supplemented with higher-resolution airborne data that are not tied to the strict schedule of a satellite orbit. To address some of these needs, a novel, portable, high-resolution airborne topographic lidar with video, infrared, and hyperspectral imaging systems was integrated. The system is coupled to a highly accurate GPS-aided inertial measurement unit (GPS IMU), permitting airborne measurements of the sea surface displacement, temperature, and kinematics with swath widths of up to 800 m under the aircraft, and horizontal spatial resolution as low as 0.2 m. These data are used to measure ocean waves, currents, Stokes drift, sea surface height (SSH), ocean transport and dispersion, and biological activity. Hydrological and terrestrial applications include measurements of snow cover and the built environment. This paper describes the system, its performance, and present results from recent oceanographic, hydrological, and terrestrial measurements.

O'Reilly, JE, Maritorena S, Mitchell BG, Siegel DA, Carder KL, Garver SA, Kahru M, McClain C.  1998.  Ocean color chlorophyll algorithms for SeaWiFS. Journal of Geophysical Research-Oceans. 103:24937-24953.   10.1029/98jc02160   AbstractWebsite

A large data set containing coincident in situ chlorophyll and remote sensing reflectance measurements was used to evaluate the accuracy, precision, and suitability of a wide variety of ocean color chlorophyll algorithms for use by SeaWiFS (Sea-viewing Wide Field-of-view Sensor). The radiance-chlorophyll data were assembled from various sources during the SeaWiFS Bio-optical Algorithm Mini-Workshop (SeaBAM) and is composed of 919 stations encompassing chlorophyll concentrations between 0.019 and 32.79 mu g L(-1). Most of the observations are from Case I nonpolar waters, and similar to 20 observations are from more turbid coastal waters. A variety of statistical and graphical criteria were used to evaluate the performances of 2 semianalytic and 15 empirical chlorophyll/pigment algorithms subjected to the SeaBAM data. The empirical algorithms generally performed better than the semianalytic. Cubic polynomial formulations were generally superior to other kinds of equations. Empirical algorithms with increasing complexity (number of coefficients and wavebands), were calibrated to the SeaBAM data, and evaluated to illustrate the relative merits of different formulations. The ocean chlorophyll 2 algorithm (OC2), a modified cubic polynomial (MCP) function which uses Rrs490/Rrs555, well simulates the sigmoidal pattern evident between log-transformed radiance ratios and chlorophyll, and has been chosen as the at-launch SeaWiFS operational chlorophyll a algorithm. Improved performance was obtained using the ocean chlorophyll 4 algorithm (OC4), a four-band (443, 490, 510, 555 nm), maximum band ratio formulation. This maximum band ratio (MBR) is a new approach in empirical ocean color algorithms and has the potential advantage of maintaining the highest possible satellite sensor signal:noise ratio over a 3-orders-of-magnitude range in chlorophyll concentration.

Cape, MR, Vernet M, Kahru M, Spreen G.  2014.  Polynya dynamics drive primary production in the Larsen A and B embayments following ice shelf collapse. Journal of Geophysical Research-Oceans. 119:572-594.   10.1002/2013jc009441   AbstractWebsite

The climate-driven collapses of the Larsen A and B ice shelves have opened up new regions of the coastal Antarctic to the influence of sea ice resulting in increases in seasonal primary production. In this study, passive microwave remote sensing of sea ice concentration and satellite imagery of ocean color are employed to quantify the magnitude of and variability in open water area and net primary productivity (NPP) in the Larsen embayments between 1997 and 2011. Numerical model output provides context to analyze atmospheric forcing on the coastal ocean. Following ice shelf disintegration the embayments function as coastal, sensible heat polynyas. The Larsen A and B are as productive as other Antarctic shelf regions, with seasonally averaged daily NPP rates reaching 1232 and 1127 mg C m(-2) d(-1) and annual rates reaching 200 and 184 g C m(-2) yr(-1), respectively. A persistent cross-shelf gradient in NPP is present with higher productivity rates offshore, contrasting with patterns observed along the West Antarctic Peninsula. Embayment productivity is intimately tied to sea ice dynamics, with large interannual variability in NPP rates driven by open water area and the timing of embayment opening. Opening of the embayment is linked to periods of positive Southern Annular Mode and stronger westerlies, which lead to the vertical deflection of warm, maritime air over the peninsula and down the leeward side causing increases in surface air temperature and wind velocity. High productivity in these new polynyas is likely to have ramifications for organic matter export and marine ecosystem evolution. Key Points Primary production and sea ice dynamics after ice shelf disintegration Larsen embayments function as productive coastal sensible heat polynyas High sea ice interannual variability affects total production

Leising, AW, Schroeder ID, Bograd SJ, Bjorkstedt EP, Field J, Sakuma K, Abell J, Robertson RR, Tyburczy J, Peterson WT, Brodeur R, Barcelo C, Auth TD, Daly EA, Campbell GS, Hildebrand JA, Suryan RM, Gladics AJ, Horton CA, Kahru M, Manzano-Sarabia M, McClatchie S, Weber ED, Watson W, Santora JA, Sydeman WJ, Melin SR, DeLong RL, Largier J, Kim SY, Chavez FP, Golightly RT, Schneider SR, Warzybok P, Bradley R, Jahncke J, Fisher J, Peterson J.  2014.  State of the California Current 2013-14: El Nino looming. California Cooperative Oceanic Fisheries Investigations Reports. 55:51-87. AbstractWebsite

In 2013, the California current was dominated by strong coastal upwelling and high productivity. Indices of total cumulative upwelling for particular coastal locations reached some of the highest values on record. Chlorophyll a levels were high throughout spring and summer. Catches of upwelling-related fish species were also high. After a moderate drop in upwelling during fall 2013, the California current system underwent a major change in phase. Three major basin-scale indicators, the PDO, the NPGO, and the ENSO-MEI, all changed phase at some point during the winter of 2013/14. The PDO changed to positive values, indicative of warmer waters in the North Pacific; the NPGO to negative values, indicative of lower productivity along the coast; and the MEI to positive values, indicative of an oncoming El Nino. Whereas the majority of the California Current system appears to have transitioned to an El Nino state by August 2014, based on decreases in upwelling and chlorophyll a concentration, and increases in SST, there still remained pockets of moderate upwelling, cold water, and high chlorophyll a biomass at various central coast locations, unlike patterns seen during the more major El Ninos (e.g., the 97-98 event). Catches of rockfish, market squid, euphausiids, and juvenile sanddab remained high along the central coast, whereas catches of sardine and anchovy were low throughout the CCS. 2014 appears to be heading towards a moderate El Nino state, with some remaining patchy regions of upwelling-driven productivity along the coast. Superimposed on this pattern, three major regions have experienced possibly non-El Nino-related warming since winter: the Bering Sea, the Gulf of Alaska, and offshore of southern California. It is unclear how this warming may interact with the predicted El Nino, but the result will likely be reduced growth or reproduction for many key fisheries species.

McClatchie, S, Goericke R, Koslow JA, Schwing FB, Bograd SJ, Charter R, Lo WWN, Hill K, Gottschalck J, L'Heureux M, Xue Y, Peterson WT, Emmett R, Collins C, Gaxiola-Castro G, Durazo R, Kahru M, Mitchell BG, Hyrenbach KD, Sydeman WJ, Bradley RW, Warzybok P, Bjorkstedt E.  2008.  THE STATE OF THE CALIFORNIA CURRENT, 2007-2008: LA NINA CONDITIONS AND THEIR EFFECTS ON THE ECOSYSTEM. California Cooperative Oceanic Fisheries Investigations Reports. 49:39-76. AbstractWebsite

The state of the California Current system (CCS) between Oregon and Baja California is summarized in this report, covering spring of 2007 to winter/spring 2008. The 2006-07 period began with moderate El Nino conditions which decayed rapidly in early 2007. By summer 2007, a moderate-to-strong La Nina had developed. The North Pacific sea surface temperature (SST) anomalies displayed a negative pattern of Pacific Decadal Oscillation with below-normal SSTs in the California Current and Gulf of Alaska consistent with this pattern. The region experienced anomalously strong southward coastal winds, leading to positive anomalies of the West Coast upwelling index, in Strong contrast with 2005. The 2007 upwelling season also began early (in contrast to delayed onset in 2005 and 2006) and remained unseasonably strong through May. The cumulative upwelling for the 2007 season was greater than normal in the southern portion of the California Current system. Despite the La Nina conditions, nitrate and chlorophyll concentrations off Oregon were about average in 2007. On the other hand, copepod biomass rebounded strongly in 2006 after the exceptionally low biomass in 2005, and copepod species richness in 2006 was low, also indicating transport Of sub-arctic water into the northern California Current in 2006-07, which is relatively productive but low in diversity. Anomalously high salinities at 200 in depth were also observed during CalCOFI and IMECOCAL cruises off Southern and Baja California. In the CalCOFI area, where there has been a general trend toward a deepening mixed layer, the mixed layer responded to this year's La Nina conditions by shoaling. Nitrate (but not silicate and phosphate) concentrations in the mixed layer were anomalously high, but chlorophyll concentrations were about average, except for spring 2007, which was one of the lowest values on record. Spring chlorophyll a concentrations are notably variable during La Ninas. In the northern California Current, forage fish and predatory fish abundance remained low in 2007. In the southern California Current, Pacific sardine (Sardinops sagax) larval abundance was relatively high and distributed in relation to the inner edge of the California Current and the edge of an eddy. Northern anchovy (Engraulis mordax) larvae were relatively low in abundance, apparently related to a large downwelling feature. Reproductive success of all six seabirds monitored on Farallon Island was recovering slowly this year, following the previous two disastrous seasons. However, cluster analysis indicated that reproductive success is still relatively low. The cold-water planktivorous auklets (Ptychoramphus aleuticus) continued to be found at high densities in Southern waters. Overall, the transition in 2007 to La Nina conditions appeared to contribute to average to above average productivity in the California Current, but the physical, chemical, and biological (phytoplankton, zooplankton, Fish, and seabird) indices of productivity were far from consistent.

McClatchie, S, Charter R, Watson W, Lo N, Hill K, Manzano-Sarabia M, Goericke R, Collins C, Bjorkstedt E, Schwing FB, Bograd SJ, Kahru M, Mitchell BG, Koslow JA, Ralston S, Field J, Peterson WT, Emmett R, Gomez-Valdes J, Lavaniegos BE, Caxiola-Castro G, Rogers-Bennet L, Gottschalck J, Heureux ML, Xue Y, Munger L, Campbell G, Merkens K, Camacho D, Havron A, Douglas A, Hildebrand J.  2009.  The state of the California Current, Spring 2008-2009: Cold conditions drive regional differences in coastal production. California Cooperative Oceanic Fisheries Investigations Reports. 50:43-68. AbstractWebsite

This report describes the state of the California Current system (CCS) between the springs of 2008 and 2009 based on observations taken along the west coast of North America The dominant forcing on the CCS during this time period were La Nina-type conditions that prevailed from the summer of 2007 through early 2009, transitioning to neutral El Nino-Southern Oscillation conditions in the spring of 2009 The Pacific Decadal Oscillation index was negative during this time period and its values had not returned to normal by the spring of 2009 The general effects on the California Current system were stronger thin normal southward winds and upwelling as well as generally colder than normal SST and shallow nitraclines, however, there were repot-ill differences Off alp California sea surface temperatures did not respond to the La Nina conditions, however, concentrations of chlorophyll a (Chl a) were significantly above normal, probably due to the anomalously high upwelling off Baja during most of the year Off southern California there was no clear evidence of increased primary or secondary production, despite observations that previous La Nina conditions affected mixed layer depth, temperatures, nutrients, and nitracline depths In both central and northern California and Oregon, stronger than normal upwelling increased primary production and prevented potential spawning of sardine north of San Francisco In central California the midwater fish community resembled that of recent cool years, and cover by kelp was much reduced along the coast Off Oregon there was evidence of increased abundance of boreal copepods, although the neritic boreal species did not appear to extend as far south is central California Current predictions are for cooler conditions to change to El Nino conditions by the end of 2009, these are expected to last through the Northern Hemisphere wintet of 2009-10

Schwarz, JN, Kowalczuk P, Kaczmarek S, Cota GF, Mitchell BG, Kahru M, Chavez FP, Cunningham A, McKee D, Gege P, Kishino T, Phinney DA, Raine R.  2002.  Two models for absorption by coloured dissolved organic matter (CDOM). Oceanologia. 44:209-241. AbstractWebsite

The standard exponential model for CDOM absorption has been applied to data from diverse waters. Absorption at 440 nm (a(g)440) ranged between close to zero and 10 m(-1), and the slope of the semilogarithmic absorption spectrum over a minimum range of 400 to 440 nm (s440) ranged between < 0.01 and 0.04 nm(-1). NO relationship was found between a(g)440 or s440 and salinity. Except in the southern Baltic, s440 was found to have abroad distribution (0.0165 +/- 0.0035), suggesting that it should be introduced as an additional variable in bio-optical models when a(g)440 is large. An alternative model for CDOM absorption was applied to available high quality UV-visible absorption spectra from the Wisla river (Poland). This model assumes that, the CDOM absorption spectrum comprises distinct Gaussian absorption bands in the UV, similar to those of benzene. Five bands were fit to the data. The mean central energy of all hands was higher in early summer (E &SIM;7.2, 6.6, 6.4, 6.2 and 5.5 eV or 172, 188, 194, 200 and 226 nm)) than in winter. The higher energy bands were found to decay in both height and width with increasing salinity, while lower energy bands broadened with increasing salinity. 8440 was found to be correlated with shape parameters of the bands centred at 6.4 and 5.5 eV. While the exponential model is convenient for optical modelling and remote sensing applications, these results suggest that the Gaussian model offers a deeper understanding of chemical interactions affecting CDOM molecular structure.

Murakami, H, Sasaoka K, Hosoda K, Fukushima H, Toratani M, Frouin R, Mitchell BG, Kahru M, Deschamps PY, Clark D, Flora S, Kishino M, Saitoh S, Asanuma I, Tanaka A, Sasaki H, Yokouchi K, Kiyomoto Y, Saito H, Dupouy C, Siripong A, Matsumura S, Ishizaka J.  2006.  Validation of ADEOS-II GLI ocean color products using in-situ observations. Journal of Oceanography. 62:373-393.   10.1007/s10872-006-0062-6   AbstractWebsite

The Global Imager (GLI) aboard the Advanced Earth Observing Satellite-II (ADEOS-II) made global observations from 2 April 2003 to 24 October 2003. In cooperation with several institutes and scientists, we obtained quality controlled match-ups between GLI products and in-situ data, 116 for chlorophyll-a concentration (CHLA), 249 for normalized water-leaving radiance (nLw) at 443 nm, and 201 for aerosol optical thickness at 865 nm (Tau_865) and Angstrom exponent between 520 and 865 nm (Angstrom). We evaluated the GLI ocean color products and investigated the causes of errors using the match-ups. The median absolute percentage differences (MedPD) between GLI and in-situ data were 14.1-35.7% for nLws at 380-565 nm 52.5-74.8% nLws at 625-680 nm, 47.6% for Tau_865, 46.2% for Angstrom, and 46.6% for CHLA, values that are comparable to the ocean-color products of other sensors. We found that some errors in GLI products are correlated with observational conditions; nLw values were underestimated when nLw at 680 nm was high, CHLA was underestimated in absorptive aerosol conditions, and Tau_865 was overestimated in sunglint regions. The error correlations indicate that we need to improve the retrievals of the optical properties of absorptive aerosols and seawater and sea surface reflection for further applications, including coastal monitoring and the combined use of products from multiple sensors.

Neal, BP, Condit C, Liu G, dos Santos S, Kahru M, Mitchell BG, Kline DI.  2014.  When depth is no refuge: cumulative thermal stress increases with depth in Bocas del Toro, Panama. Coral Reefs. 33:193-205.   10.1007/s00338-013-1081-6   AbstractWebsite

Coral reefs are increasingly affected by high-temperature stress events and associated bleaching. Monitoring and predicting these events have largely utilized sea surface temperature data, due to the convenience of using large-scale remotely sensed satellite measurements. However, coral bleaching has been observed to vary in severity throughout the water column, and variations in coral thermal stress across depths have not yet been well investigated. In this study, in situ water temperature data from 1999 to 2011 from three depths were used to calculate thermal stress on a coral reef in Bahia Almirante, Bocas del Toro, Panama, which was compared to satellite surface temperature data and thermal stress calculations for the same area and time period from the National Oceanic and Atmospheric Administration Coral Reef Watch Satellite Bleaching Alert system. The results show similar total cumulative annual thermal stress for both the surface and depth-stratified data, but with a striking difference in the distribution of that stress among the depth strata during different high-temperature events, with the greatest thermal stress unusually recorded at the deepest measured depth during the most severe bleaching event in 2005. Temperature records indicate that a strong density-driven temperature inversion may have formed in this location in that year, contributing to the persistence and intensity of bleaching disturbance at depth. These results indicate that depth may not provide a stress refuge from high water temperature events in some situations, and in this case, the water properties at depth appear to have contributed to greater coral bleaching at depth compared to near-surface locations. This case study demonstrates the importance of incorporating depth-stratified temperature monitoring and small-scale oceanographic and hydrologic data for understanding and predicting local reef responses to elevated water temperature events.