Raphael M. Kudela

Raphael M. Kudela
University of California, Santa Cruz | UCSC · Department of Ocean Sciences

Ph.D.

About

331
Publications
98,718
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Introduction
I am a phytoplankton ecologist who wishes to understand the fundamental question: what controls phytoplankton growth and distribution in the ocean. More specifically, how do the multiple interactions of light, macro- and micronutrients and phytoplankton physiology determine the rates, processes, and patterns we observe in the marine environment?
Education
September 1989 - December 1995
University of Southern California
Field of study
  • Biological Science

Publications

Publications (331)
Article
Full-text available
Chemical signaling is ubiquitous in the marine environment. Plankton rely on chemical signals to find mates, hunt prey, and respond to threats, and these small‐scale interactions can propagate into community‐wide cascades and large‐scale ecological changes. The chemical signaling exchange in the open ocean is poorly understood, and fundamental info...
Article
In 2015, the largest recorded harmful algal bloom (HAB) occurred in the Northeast Pacific, causing nearly 100 million dollars in damages to fisheries and killing many protected marine mammals. Dominated by the toxic diatom Pseudo-nitzschia australis, this bloom produced high levels of the neurotoxin domoic acid (DA). Through molecular and transcrip...
Article
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Harmful algal blooms caused by toxin‐producing species of the diatom genus Pseudo‐nitzschia have been linked to anomalously warm ocean conditions in the Northern California Current System. This study compares summertime concentrations of Pseudo‐nitzschia spp. and the toxin they produce, domoic acid, during a marine heatwave year (2019) and a climat...
Article
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In marine ecosystems, most physiological, ecological, or physical processes are size dependent. These include metabolic rates, the uptake of carbon and other nutrients, swimming and sinking velocities, and trophic interactions, which eventually determine the stocks of commercial species, as well as biogeochemical cycles and carbon sequestration. As...
Article
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Ocean spring phytoplankton blooms are dynamic periods important to global primary production. We document vertical patterns of a diverse suite of eukaryotic algae, the prasinophytes, in the North Atlantic Subtropical Gyre with monthly sampling over four years at the Bermuda Atlantic Time-series Study site. Water column structure was used to delinea...
Article
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The launch of the NASA Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) and the Surface Biology and Geology (SBG) satellite sensors will provide increased spectral resolution compared to existing platforms. These new sensors will require robust calibration and validation datasets, but existing field-based instrumentation is limited in its availabil...
Article
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A massive bloom of the raphidophyte Heterosigma akashiwo occurred in summer 2022 in San Francisco Bay, causing widespread ecological impacts including events of low dissolved oxygen and mass fish kills. The rapidly evolving bloom required equally rapid management response, leading to the use of near-real-time image analysis of chlorophyll from the...
Article
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During 2018, a seabird mortality event occurred in central California, US, that affected Northern Fulmars (Fulmarus glacialis), Common Murres (Uria aalge), and Cassin's Auklets (Ptychoramphus aleuticus). An increase in beachcast birds were reported on standardized surveys in conjunction with an increased number of live-stranded birds admitted to re...
Preprint
In 2015, the largest recorded harmful algal bloom (HAB) occurred in the Northeast Pacific, causing nearly 100 million dollars in damages to fisheries and killing many protected marine mammals. Dominated by the toxic diatom Pseudo-nitzschia australis , this bloom produced high levels of the neurotoxin domoic acid (DA). Through molecular and transcri...
Article
Full-text available
The simultaneous remote estimation of biogeochemical parameters (BPs) and inherent optical properties (IOPs) from hyperspectral satellite imagery of globally distributed optically distinct inland and coastal waters is a complex, unsolved, non-unique inverse problem. To tackle this problem, we leverage a machine-learning model termed Mixture Density...
Article
Pseudo-nitzschia species with the ability to produce the neurotoxin domoic acid (DA) are the main cause of harmful algal blooms (HABs) along the U.S. West Coast, with major impacts on ecosystems, fisheries, and human health. While most Pseudo-nitzschia (PN) HAB studies to date have focused on their characteristics at specific sites, few cross-regio...
Article
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Kelp forests dominate autotrophic biomass and primary productivity of approximately 30,000 to 60,000 km of shallow temperate and Arctic rocky reef coastline globally and contribute significantly to carbon cycling in the coastal ocean. Rapid biomass turnover is driven by very high growth rates and seasonal environmental drivers. As a result, kelp bi...
Article
The Asian clam (Corbicula fluminea) and eastern oyster (Crassostrea virginica) are important resource bivalves found in and downstream of waterways afflicted with cyanobacterial harmful algae blooms (CHABs), respectively. This study examined the potential for C. fluminea and C. virginica to become vectors of the hepatotoxin, microcystin, from the C...
Article
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Many coastal states throughout the U.S. have observed negative effects in marine and estuarine environments due to cyanotoxins produced in inland waterbodies that were transported downstream or produced within the estuaries. Estuaries and other downstream receiving waters now face the dual risk of impacts from harmful algal blooms (HABs) that occur...
Article
NASA’s Student Airborne Research Program (SARP) has completed 13 years of airborne student research since its inception in 2009. The 8-week summer internship program provides students, typically rising undergraduate seniors, with an opportunity to get hands-on experience in making Earth system measurements using NASA’s airborne science platforms. S...
Article
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Offshore aquaculture has the potential to expand the macroalgal industry. However, moving into deeper waters requires suspended structures that will present novel farm-environment interactions. Here, we present a computational modeling framework, the Macroalgal Cultivation Modeling System (MACMODS), to explore within-farm modifications to light, se...
Article
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The hardware and software capabilities of the compact-profiling hybrid instrumentation for radiometry and ecology (C-PHIRE) instruments on an unmanned surface vessel (USV) are evaluated. Both the radiometers and USV are commercial-off-the-shelf (COTS) products, with the latter being only minimally modified to deploy the C-PHIRE instruments. The hyb...
Article
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Understanding spatial variability of water quality in estuary systems is important for making monitoring decisions and designing sampling strategies. In San Francisco Bay, the largest estuary system on the west coast of North America, tracking the concentration of suspended materials in water is largely limited to point measurements with the assump...
Article
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Maintaining healthy, productive ecosystems in the face of pervasive and accelerating human impacts including climate change requires globally coordinated and sustained observations of marine biodiversity. Global coordination is predicated on an understanding of the scope and capacity of existing monitoring programs, and the extent to which they use...
Article
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Increasing occurrence of harmful algal blooms across the land–water interface poses significant risks to coastal ecosystem structure and human health. Defining significant drivers and their interactive impacts on blooms allows for more effective analysis and identification of specific conditions supporting phytoplankton growth. A novel iterative Ra...
Conference Paper
The Global Harmful Algal Blooms (GlobalHAB, www.global hab.info) Program is aimed at fostering international cooperative research directed toward improving the prediction of harmful algal bloom (HAB) events in aquatic ecosystems, and providing sound knowledge for policy- and decision-making to manage and mitigate HAB impacts in a changing planet. G...
Article
Blooms of the diatom genus Pseudo-nitzschia occur annually in the Southern California Bight (SCB), and domoic acid (DA) associated with these events can contaminate fisheries, presenting both human and wildlife health risks. Recent studies have suggested that marine sediments may act as a reservoir for DA, extending the risk of food web contaminati...
Article
Full-text available
Next-generation satellite sensors such as the Ocean Color Instrument (OCI) aboard the NASA Plankton, Aerosols, Cloud and ocean Ecosystem (PACE) satellite and the proposed Surface Biology and Geology (SBG) sensor will provide hyperspectral measurements of water-leaving radiances. However, acquiring sufficiently accurate in situ validation data in co...
Article
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The marine biotoxin domoic acid (DA) is an analog of the neurotransmitter glutamate that exerts potent excitatory activity in the brain, heart, and other tissues. Produced by the diatom Pseudo-nitzschia spp., DA accumulates in marine invertebrates, fish, and sediment. Southern sea otters (Enhydra lutris nereis) feed primarily on invertebrates, incl...
Article
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Climate change is responsible for increased frequency, intensity, and duration of extreme events, such as marine heatwaves (MHWs). Within eastern boundary current systems, MHWs have profound impacts on temperature-nutrient dynamics that drive primary productivity. Bull kelp (Nereocystis luetkeana) forests, a vital nearshore habitat, experienced unp...
Article
The contamination of coastal ecosystems from a variety of toxins of marine algal origin is a common and well-documented situation along the coasts of the United States and globally. The occurrence of toxins originating from cyanobacteria along marine coastlines is much less studied, and little information exists on whether toxins from marine and fr...
Article
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Extending from central California to Alaska, bull kelp (Nereocystis luetkeana) forms seasonal kelp forests that are iconic coastal ecosystems in much of the eastern Pacific. Historical and ongoing field surveys and aerial imagery are used to provide biological data on kelp canopy cover and health, but satellite remote sensing provides the opportuni...
Article
The case-1 (optically simple) oceanic environment is described by a smoothly transitioning gradient in optical properties arising from the concentration of the primary algal photopigment, chlorophyll a, plus its covarying and optically relevant constituents. As such, the spectral transition that defines case-1 water types is captured by a single pr...
Article
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As harmful algal blooms (HABs) increase in magnitude and duration worldwide, they are becoming an expanding threat to marine wildlife. Over the past decade, blooms of algae that produce the neurotoxins domoic acid (DA) and saxitoxin (STX) and documented concurrent seabird mortality events have increased bicoastally in the United States. We conducte...
Article
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National Academies' Decadal Survey, Thriving on Our Changing Planet, recommended Surface Biology and Geology (SBG) as a "Designated Targeted Observable" (DO). The SBG DO is based on the need for capabilities to acquire global, high spatial resolution, visible to shortwave infrared (VSWIR; 380-2500 nm; ~30 m pixel resolution) hyperspectral (imaging...
Article
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The estimation of important carbon fluxes in a changing Arctic environment remains a challenge, one that could benefit from the development of biomarkers that distinguish between sympagic (ice-associated) and pelagic organic material. Products of 10S-DOX-like lipoxygenase and fatty acid cis-trans isomerase (CTI) activity of bacteria attached to sym...
Article
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The global proliferation of toxin producing cyanobacterial blooms has been attributed to a wide variety of environmental factors with nutrient pollution, increased temperatures, and drought being three of the most significant. The current study is the first formal assessment of cyanotoxins in two impaired lakes, Canyon Lake and Lake Elsinore, in so...
Article
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Harmful algal blooms produce toxins that bioaccumulate in the food web and adversely affect humans, animals, and entire marine ecosystems. Blooms of the diatom Pseudo-nitzschia can produce domoic acid (DA), a toxin that most commonly causes neurological disease in endothermic animals, with cardiovascular effects that were first recognized in southe...
Article
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A heatwave that blanketed the northeast Pacific Ocean in 2013–2015 had severe impacts on the marine ecosystem through altered species composition and survival. A direct result of this marine heatwave was a sustained, record-setting harmful algal bloom (HAB), caused by the toxigenic diatom, Pseudo-nitzschia , that led to an unprecedented delay in ha...
Article
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The optically active component of dissolved organic material in aquatic ecosystems, or colored dissolved organic matter (CDOM), is represented by the coefficient of absorption due to the dissolved aquatic constituents at 440 nm, aCDOM(440). Remote sensing of aCDOM(440) enables characterization of ecosystem processes and aids in retrieval of chlorop...
Article
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Present-day ocean color satellite sensors, which principally provide reliable data on chlorophyll, sediments, and colored dissolved organic material in the open ocean, are not well suited for coastal and inland water studies for a variety of reasons, including coarse spatial and spectral resolution plus challenges with atmospheric correction. Natio...
Article
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The California Current System (CCS) is a highly productive region because of wind-driven upwelling, which supplies nutrients to the euphotic zone. Numerous studies of the relationship between phytoplankton productivity and wind patterns suggest that an intermediate wind speed yields the most productivity on the shelf. However, few studies have cons...
Article
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Electromagnetic theory predicts spectral dependencies in extinction efficiency near a narrow absorption band for a particle with an index of refraction close to that of the medium in which it is immersed. These absorption band effects are anticipated in oceanographic beam-attenuation (beam-c) spectra, primarily due to the narrow red peak in absorpt...
Article
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In the last decade, the known biogeography of nitrogen fixation in the ocean has been expanded to colder and nitrogen‐rich coastal environments. The symbiotic nitrogen‐fixing cyanobacteria group A (UCYN‐A) has been revealed as one of the most abundant and widespread nitrogen‐fixers, and includes several sublineages that live associated with genetic...
Article
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Phytoplankton biomass in Monterey Bay, California is typically dominated by diatoms, but it shifted to dinoflagellates twice in the past 18 years (2004–2007, 2017–2018), which was associated with increased harmful algal blooms. Located within the central California Current System (CCS), Monterey Bay is strongly influenced by cycles of upwelling‐fav...
Article
Full-text available
This study establishes an optical inversion scheme for deriving the absorption coefficient of colored (or chromophoric, depending on the literature) dissolved organic material (CDOM) at the 440 nm wavelength, which can be applied to global water masses with near-equal efficacy. The approach uses a ratio of diffuse attenuation coefficient spectral e...
Article
Chlorophyll concentration in the ocean is a metric for phytoplankton biomass, which forms the base of most pelagic food webs and is a critical component of the planet's carbon cycle. Phytoplankton biomass has been designated an Essential Ocean Variable (EOV), but in situ chlorophyll measurements are challenging and expensive to obtain, especially i...
Article
The Publisher regrets that this article is an accidental duplication of an article that has already been published, https://doi.org/10.1016/j.marsys.2019.103266. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
Article
San Francisco Bay (SFB), California, USA is the largest estuary in the western United States and is home to more than 7 million people in nine counties and 101 cities. It is highly nutrient enriched and is directly connected to the Gulf of the Farallones and coastal Pacific ocean through the Golden Gate strait. The Gulf of the Farallones is one of...
Article
No PDF available ABSTRACT Monterey Bay National Marine Sanctuary, in the highly productive California Current System, is vital habitat for many marine mammal species. Passive acoustic monitoring (PAM) is an effective means to detect species’ presence and acoustic behavior. Using the infrastructure of a cabled observatory and detection and classific...
Article
Full-text available
Satellite estimation of oceanic chlorophyll-a content has enabled characterization of global phytoplankton stocks, but the quality of retrieval for many ocean color products (including chlorophyll-a) degrades with increasing phytoplankton biomass in eutrophic waters. Quality control of ocean color products is achieved primarily through the applicat...
Article
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This study examines the occurrence of humpback whale (Megaptera novaeangliae) song in the northeast Pacific from three years of continuous recordings off central California (36.713°N, 122.186°W). Song is prevalent in this feeding and migratory habitat, spanning nine months of the year (September–May), peaking in winter (November–January), and reach...
Article
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We compared the mean normalized water-leaving radiances ( [ L W ¯ ( λ ) ] N ) of two in-water optical profilers, a compact optical profiling system (C-OPS) and a HyperPro II Optical Profiler (HP2), with modeled [ L W ¯ ( λ ) ] N at five stations in Monterey Bay, California. Although C-OPS and HP2 [ L W ¯ ( λ ) ] N s were mostly within one standard...
Article
Full-text available
Presently, operational ocean color satellite sensors are designed with a legacy perspective for sampling the open ocean primarily in the visible domain, while high spatial resolution sensors such as Sentinel-2, Sentinel-3, and Landsat8 are increasingly used for observations of coastal and inland water quality. Next-generation satellites such as the...
Article
There is increasing concern that accelerating environmental change attributed to human-induced warming of the planet may substantially alter the patterns, distribution and intensity of Harmful Algal Blooms (HABs). Changes in temperature, ocean acidification, precipitation, nutrient stress or availability, and the physical structure of the water col...
Article
Full-text available
This study establishes an optical inversion scheme for deriving the absorption coefficient of colored (or chromophoric, depending on the literature) dissolved organic material (CDOM) at the 440 nm wavelength, which can be applied to global water masses with near-equal efficacy. The approach uses a ratio of diffuse attenuation coefficient spectral e...
Article
Full-text available
Development of global ocean observing capacity for the biological EOVs is on the cusp of a step-change. Current capacity to automate data collection and processing and to integrate the resulting data streams with complementary data, openly available as FAIR data, is certain to dramatically increase the amount and quality of information and knowledg...
Article
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Recurrent blooms of harmful algae and cyanobacteria (HABs) plague many coastal and inland waters throughout the United States and have significant socioeconomic impacts to the adjacent communities. Notable HAB events in recent years continue to underscore the many remaining gaps in knowledge and increased needs for technological advances leading to...
Article
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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...
Article
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Harmful algal blooms (HABs) produce local impacts in nearly all freshwater and marine systems. They are a problem that occurs globally requiring an integrated and coordinated scientific understanding, leading to regional responses and solutions. Given that these natural phenomena will never be completely eliminated, an improved scientific understan...
Article
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Impacts on growth rates from exposure to ammonium (NH4+) and nitrate (NO3-), at non-limiting concentrations, in combination with irradiances varying from 25 to 600 µmol photons m-2 s-1 were investigated in the pelagic diatom Thalassiosira weisflogii and the benthic diatom Entomoneis paludosa recently isolated from Suisun Bay in northern San Francis...
Article
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In this paper we review the technologies available to make globally quantitative observations of particles in general—and plankton in particular—in the world oceans, and for sizes varying from sub-microns to centimeters. Some of these technologies have been available for years while others have only recently emerged. Use of these technologies is cr...