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Tropical cyclones drive coastal ecosystem dynamics, and their frequency, intensity, and spatial distribution are predicted to shift with climate change. Patterns of resistance and resilience were synthesized for 4138 ecosystem time series from n = 26 storms occurring between 1985 and 2018 in the Northern Hemisphere to predict how coastal ecosystems will respond to future disturbance regimes. Data were grouped by ecosystems (fresh water, salt water, terrestrial, and wetland) and response categories (biogeochemistry, hydrography, mobile biota, sedentary fauna, and vascular plants). We observed a repeated pattern of trade-offs between resistance and resilience across analyses. These patterns are likely the outcomes of evolutionary adaptation, they conform to disturbance theories, and they indicate that consistent rules may govern ecosystem susceptibility to tropical cyclones.

Schnetzer,Associate Professor and Associate DepartmentHead in Marine, Earthand Atmospheric Sciences, discussed harmful algal blooms and its impact on food webs. Schentzer explainedhow harmful algal blooms have beenincreasing in frequency, magnitude, and geographic extent over the past two decades, creating water contamination and toxins in food webs. Schnetzer concluded by discussing additional consequences of harmful algal blooms, including human health risks, socioeconomic impacts, property values, ecosystem regime shifts, fish kills, and pet deaths.

Coastal acidification in southeastern U.S. estuaries and coastal waters is influenced by biological activity, run-off from the land, and increasing carbon dioxide in the atmosphere. Acidification can negatively impact coastal resources such as shellfish, finfish, and coral reefs, and the communities that rely on them. Organismal responses for species located in the U.S. Southeast document large negative impacts of acidification, especially in larval stages. For example, the toxicity of pesticides increases under acidified conditions and the combination of acidification and low oxygen has profoundly negative influences on genes regulating oxygen consumption. In corals, the rate of calcification decreases with acidification and processes such as wound recovery, reproduction, and recruitment are negatively impacted. Minimizing the changes in global ocean chemistry will ultimately depend on the reduction of carbon dioxide emissions, but adaptation to these changes and mitigation of the local stressors that exacerbate global acidification can be addressed locally. The evolution of our knowledge of acidification, from basic understanding of the problem to the emergence of applied research and monitoring, has been facilitated by the development of regional Coastal Acidification Networks (CANs) across the United States. This synthesis is a product of the Southeast Coastal and Ocean Acidification Network (SOCAN). SOCAN was established to better understand acidification in the coastal waters of the U.S. Southeast and to foster communication among scientists, resource managers, businesses, and governments in the region. Here we review acidification issues in the U.S. Southeast, including the regional mechanisms of acidification and their potential impacts on biological resources and coastal communities. We recommend research and monitoring priorities and discuss the role SOCAN has in advancing acidification research and mitigation of and adaptation to these changes.

Blooms of the marine diatom genus Pseudo-nitzschia that produce the neurotoxin domoic acid have been documented with regularity along the coast of southern California since 2003, with the occurrence of the toxin in shellfish tissue predating information on domoic acid in the particulate fraction in this region. Domoic acid concentrations in the phytoplankton inhabiting waters off southern California during 2003, 2006, 2007, 2011 and 2017 were comparable to some of the highest values that have been recorded in the literature. Blooms of Pseudo-nitzschia have exhibited strong seasonality, with toxin appearing predominantly in the spring. Year-to-year variability of particulate toxin has been considerable, and observations during 2003, 2006, 2007, 2011 and again in 2017 linked domoic acid in the diets of marine mammals and seabirds to mass mortality events among these animals. This work reviews information collected during the past 15 years documenting the phenology and magnitude of Pseudo-nitzschia abundances and domoic acid within the Southern California Bight. The general oceanographic factors leading to blooms of Pseudo-nitzschia and outbreaks of domoic acid in this region are clear, but subtle factors controlling spatial and interannual variability in bloom magnitude and toxin production remain elusive.

The formation of marine snow (MS) by the toxic diatom Pseudo-nitschia australis was simulated using a roller table experiment. Concentrations of particulate and dissolved domoic acid (pDA and dDA) differed significantly among exponential phase and MS formation under simulated near surface conditions (16 °C/12:12-dark:light cycle) and also differed compared to subsequent particle decomposition at 4 °C in the dark, mimicking conditions in deeper waters. Particulate DA was first detected at the onset of exponential growth, reached maximum levels associated with MS aggregates (1.21 ± 0.24 ng mL−1) and declined at an average loss rate of ∼1.2% pDA day−1 during particle decomposition. Dissolved DA concentrations increased throughout the experiment and reached a maximum of ∼20 ng mL−1 at final sampling on day 88. The succession by P. australis from active growth to aggregation resulted in increasing MS toxicity and based on DA loading of particles and known in situ sinking speeds, a significant amount of toxin could have easily reached the deeper ocean or seafloor. MS formation was further associated with significant dDA accumulation at a ratio of pDA: dDA: cumulative dDA of approximately 1:10:100. Overall, this study confirms that MS functions as a major vector for toxin flux to depth, that Pseudo-nitzschia-derived aggregates should be considered ‘toxic snow’ for MS-associated organisms, and that effects of MS toxicity on interactions with aggregate-associated microbes and zooplankton consumers warrant further consideration.

The eutrophication of waterways has led to a rise in cyanobacterial, harmful algal blooms (CyanoHABs) worldwide. The deterioration of water quality due to excess algal biomass in lakes has been well documented (e.g., water clarity, hypoxic conditions), but health risks associated with cyanotoxins remain largely unexplored in the absence of toxin information. This study is the first to document the presence of dissolved microcystin, anatoxin-a, cylindrospermopsin, and β-N-methylamino-l-alanine in Jordan Lake, a major drinking water reservoir in North Carolina. Saxitoxin presence was not confirmed. Multiple toxins were detected at 86% of the tested sites and during 44% of the sampling events between 2014 and 2016. Although concentrations were low, continued exposure of organisms to multiple toxins raises some concerns. A combination of discrete sampling and in-situ tracking (Solid Phase Adsorption Toxin Tracking [SPATT]) revealed that microcystin and anatoxin were the most pervasive year-round. Between 2011 and 2016, summer and fall blooms were dominated by the same cyanobacterial genera, all of which are suggested producers of single or multiple cyanotoxins. The study’s findings provide further evidence of the ubiquitous nature of cyanotoxins, and the challenges involved in linking CyanoHAB dynamics to specific environmental forcing factors are discussed.

Organic matter produced and released by phytoplankton during growth is processed by heterotrophic bacterial communities that transform dissolved organic matter into biomass and recycle inorganic nutrients, fueling microbial food web interactions. Bacterial transformation of phytoplankton-derived organic matter also plays a poorly known role in the formation of chromophoric dissolved organic matter (CDOM) which is ubiquitous in the ocean. Despite the importance of organic matter cycling, growth of phytoplankton and activities of heterotrophic bacterial communities are rarely measured in concert. To investigate CDOM formation mediated by microbial processing of phytoplankton-derived aggregates, we conducted growth experiments with non-axenic monocultures of three diatoms (Skeletonema grethae, Leptocylindrus hargravesii, Coscinodiscus sp.) and one haptophyte (Phaeocystis globosa). Phytoplankton biomass, carbon concentrations, CDOM and base-extracted particulate organic matter (BEPOM) fluorescence, along with bacterial abundance and hydrolytic enzyme activities (α-glucosidase, β-glucosidase, leucine-aminopeptidase) were measured during exponential growth and stationary phase (~3-6 weeks) and following six weeks of POM degradation. Incubations were performed in rotating glass bottles to keep cells suspended, promoting cell coagulation and, thus, formation of macroscopic aggregates (marine snow), more similar to surface ocean processes. Maximum carbon concentrations, enzyme activities, and BEPOM fluorescence occurred during stationary phase. Net DOC concentrations (0.19-0.46 mg C L-1) increased on the same order as open ocean concentrations. CDOM fluorescence was dominated by protein-like signals that increased throughout growth and degradation becoming increasingly humic-like, implying the production of more complex molecules from planktonic-precursors mediated by microbial processing. Our experimental results suggest that at least a portion of open-ocean CDOM is produced by autochthonous processes and aggregation likely facilitates microbial reprocessing of organic matter into refractory DOM.

© 2015, The Oceanography Society. All rights reserved. Ocean acidification (OA) research seeks to understand how marine ecosystems and global elemental cycles will respond to changes in seawater carbonate chemistry in combination with other environmental perturbations such as warming, eutrophication, and deoxygenation. Here, we discuss the effectiveness and limitations of current research approaches used to address this goal. A diverse combination of approaches is essential to decipher the consequences of OA to marine organisms, communities, and ecosystems. Consequently, the benefits and limitations of each approach must be considered carefully. Major research challenges involve experimentally addressing the effects of OA in the context of large natural variability in seawater carbonate system parameters and other interactive variables, integrating the results from different research approaches, and scaling results across different temporal and spatial scales.

The production and transformation of marine chromophoric dissolved organic matter (CDOM) provides a window into the marine biological pump as it is present at all depths and can be measured both in the field and via satellite. However, outside of lignin for terrestrial DOM, few studies have linked marine CDOM characteristics with biomarker indices. In this study, we quantified five fluorescent components of marine CDOM and base-extractable particulate organic matter (BEPOM) in a growth and degradation experiment using a natural plankton assemblage, and compared those results to bacterial abundances, hydrolytic enzyme activities , and amino acid concentrations and associated diagenetic indices. Rotating glass bottles containing plankton were sampled initially (day 0), during the mid-exponential (day 13) and stationary (day 20) growth phases, and again following a dark degradation period that lasted 42 days. Protein-like fluorescence (tryptophan-like and tyrosine-like) was correlated with the total amino acid concentrations for both the DOM and BEPOM through all phases of the incubation. However, tryptophan-like fluorescence showed a stronger correlation for aromatic amino acids . The concentration of particulate organic carbon changed significantly during each phase of the experiment and this substrate correlated with hydrolytic enzyme activities and bacterial abundance. This heterotrophy diagenetically altered the POM during the stationary phase and ultimately resulted in the increased production of more humic-like CDOM after degradation in the dark. Results from this study indicate that CDOM formation and cycling may play a prominent role in the ocean's nitrogen cycle.

Small-scale spatial and temporal variabiliy in protistan community composition was investigated at the USC San Pedro Ocean Time-series (SPOT) station and contrasted with a 10 yr (2000 to 2010) dataset of samples collected at approximately monthly intervals from the same station. Surface seawater samples were collected for 12 consecutive days at the SPOT station, and an addi- tional 17 stations (16 within a grid surrounding the SPOT station and 1 outlying station; 2 to 21 km apart) were sam- pled during 1 of the 12 sampling days, to investigate the small-scale temporal and spatial variability, respectively. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the 18S rRNA gene was used to gen- erate DNA fingerprints of the protistan community, which were used for the calculation of pair-wise Bray-Curtis and Jaccard similarity values at different spatial and temporal scales. Temperature, salinity, pH, wind, and upwelling did not appear to have any significant effect on commu- nity composition, and distance had a weak correlation with the similarity indices generated from spatial sam- ples. Communities separated by the smallest spatial scales (0 to 2 km) had significantly higher average similar- ity than communities separated by small temporal scales (1 to 9 d). Comparisons with a 10 yr dataset of monthly samples revealed significantly lower average similarity values among communities separated by time periods ≥ 1 mo (45 to 52%) compared to communities separated by the smallest spatial (0 to 2 km; 67 to 71%) and temporal (1 d; 64%) scales. Our results indicate that small-scale spatial and day-to-day variability of protistan communi- ties was overshadowed by monthly, seasonal, and inter- annual variabilities.

Harmful algal blooms dominated by the diatom Pseudo-nitzschia spp. have become a perennial but variable event within surface waters near the greater Los Angeles area. Toxic blooms during spring seasons from 2005 to 2007 varied strongly in their overall toxicity and duration. Differences in bloom dynamics were linked to differences in storm-induced river discharge following episodic rain events and coastal upwelling, both major coastal processes that led to the injection of nutrients into coastal surface waters. Heavy river runoff during early 2005, a record-rainfall year, favored a phytoplankton community mainly comprised of algal taxa other than Pseudo-nitzschia. The spring bloom during 2005 was associated with low domoic acid surface concentrations and minor contributions of (mainly) P. delicatissima to the diatom assemblage. In contrast, highly toxic P. australis-dominated blooms during spring seasons of 2006 and 2007 were linked to strong upwelling events. River discharge quotas in 2006 and 2007, in contrast to 2005, fell well below annual averages for the region. Surface toxin levels were linked to colder, more saline (i.e. upwelled) water over the 3-year study, but no such consistent relationship between domoic acid levels and other physiochemical parameters, such as macronutrient concentrations or nutrient ratios, was observed.

Harmful blooms formed by species of the dinoflagellate Cochlodinium have caused massive fish kills and substantial economic losses in the Pacific Ocean. Recently, prominent blooms of Cochlodinium have occurred in central and southern California (2004-2008), and Cochlodinium cells are now routinely observed in microscopical analysis of algal assemblages from Californian coastal waters. The first documented economic loss due to a Cochlodinium bloom in California occurred in Monterey Bay and resulted in the mortality of commercially farmed abalone. Increasing occurrences of Cochlodinium blooms, the fact that these cells preserve poorly using standard techniques, and the difficulty of identifying preserved specimens using morphological criteria make Cochlodinium species prime candidates for the development of a quantitative real-time polymerase chain reaction (qPCR) approach. The 18S rDNA gene sequenced from Cochlodinium cells obtained from California coastal waters, as well as GenBank sequences of Cochlodinium, were used to design and test a Molecular Beacon(®) approach. The qPCR method developed in this study is species specific, sensitive for the detection of C. fulvescens that has given rise to the recent blooms in the eastern Pacific Ocean, and spans a dynamic abundance range of seven orders of magnitude. Initial application of the method to archived field samples collected during blooms in Monterey Bay revealed no statistically significant correlations between gene copy number and environmental parameters. However, the onset of Cochlodinium blooms in central California was consistent with previously reported findings of correlations to decreased surface temperature and increased inputs of nitrogenous nutrients.

The occurrence and intensity of harmful algal blooms (HABs) have been increasing globally during the past few decades. The impact of these events on seawater desalination facilities has become an important topic in recent years due to enhanced societal interest and reliance on this technology for augmenting world water supplies. A variety of harmful bloom-forming species of microalgae occur in southern California, as well as many other locations throughout the world, and several of these species are known to produce potent neurotoxins. These algal toxins can cause a myriad of human health issues, including death, when ingested via contaminated seafood. This study was designed to investigate the impact that algal toxin presence may have on both the intake and reverse osmosis (RO) desalination process; most importantly, whether or not the naturally occurring algal toxins can pass through the RO membrane and into the desalination product. Bench-scale RO experiments were conducted to explore the potential of extracellular algal toxins contaminating the RO product. Concentrations exceeding maximal values previously reported during natural blooms were used in the laboratory experiments, with treatments comprised of 50 μg/L of domoic acid (DA), 2 μg/L of saxitoxin (STX) and 20 μg/L of brevetoxin (PbTx). None of the algal toxins used in the bench-scale experiments were detectable in the desalinated product water. Monitoring for intracellular and extracellular concentrations of DA, STX, PbTx and okadaic acid (OA) within the intake and desalinated water from a pilot RO desalination plant in El Segundo, CA, was conducted from 2005 to 2009. During the five-year monitoring period, DA and STX were detected sporadically in the intake waters but never in the desalinated water. PbTx and OA were not detected in either the intake or desalinated water. The results of this study demonstrate the potential for HAB toxins to be inducted into coastal RO intake facilities, and the ability of typical RO operations to effectively remove these toxins.

Mass mortality events are ephemeral phenomena in marine ecosystems resulting from anthropogenically enhanced and natural processes. A fish kill in King Harbor, Redondo Beach, California, USA, in March 2011 killed ~1.54 × 10 5 kg of fish and garnered international attention as a marine system out of balance. Here, we present data collected prior to, during, and following the event that describe the oceanographic conditions preceding the event, spatial extent of hypoxia (dissolved oxygen 10 d following the event. Initial recovery of dissolved oxygen in the harbor was facilitated by storm-mediated mixing. No connection was apparent between increased algal biomass or phycotoxins within the harbor and the mortality event, although the fish showed evidence of prior exposure to the algal neurotoxin domoic acid. Our findings underscore the essential role of ocean observing and rapid response in the study of these events and the role that oceanographic processes play in hypoxia-driven fish mortalities. Alterations in upwelling regimes as a consequence of climate change are likely to further increase the frequency and magnitude of upwelling-driven hypoxia and mortality events.

Fish mortality and hypoxic events occur in many coastal and inland systems and may result from natural or anthropogenically mediated processes. The effects of consequent changes in water biogeochemistry have been investigated for communities of benthic invertebrates and pelagic metazoans. The responses of micro-plankton assemblages, however, have remained largely unstudied. The northern basin of King Harbor, a small embayment within Santa Monica Bay, CA, USA, suffered a massive fish kill in March 2011 as a consequence of acute hypoxia. Dissolved oxygen concentrations < 0.1 ml l−1 were measured in the northern basin of the harbor for several days following the mortality event, and a strong spatial gradient of oxygen was observed from the northern basin to waters outside the harbor. The microplankton community within King Harbor differed significantly from a diatom-dominated community present in neighboring Santa Monica Bay. The latter region appeared unaffected by physicochemical changes, induced by the fish kill, that were observed within the harbor. A trophic shift was observed throughout King Harbor from a photoautotrophic-dominated assemblage to one of heterotrophic forms, with relative abundances of bacterivorous ciliates increasing by more than 80 % in the most impacted part of the harbor. Significant changes in community structure were observed together with dramatically reduced photosynthetic yield of the remaining phytoplankton, indicating severe physiological stress during the extreme hypoxia.

Harmful blooms formed by species of the dinoflagellate Cochlodinium have caused massive fish kills and substantial economic losses in the Pacific Ocean. Recently, prominent blooms of Cochlodinium have occurred in central and southern California (2004-2008), and Cochlodinium cells are now routinely observed in microscopical analysis of algal assemblages from Californian coastal waters. The first documented economic loss due to a Cochlodinium bloom in California occurred in Monterey Bay and resulted in the mortality of commercially farmed abalone. Increasing occurrences of Cochlodinium blooms, the fact that these cells preserve poorly using standard techniques, and the difficulty of identifying preserved specimens using morphological criteria make Cochlodinium species prime candidates for the development of a quantitative real-time polymerase chain reaction (qPCR) approach. The 18S rDNA gene sequenced from Cochlodinium cells obtained from California coastal waters, as well as GenBank sequences of Cochlodinium, were used to design and test a Molecular Beacon(®) approach. The qPCR method developed in this study is species specific, sensitive for the detection of C. fulvescens that has given rise to the recent blooms in the eastern Pacific Ocean, and spans a dynamic abundance range of seven orders of magnitude. Initial application of the method to archived field samples collected during blooms in Monterey Bay revealed no statistically significant correlations between gene copy number and environmental parameters. However, the onset of Cochlodinium blooms in central California was consistent with previously reported findings of correlations to decreased surface temperature and increased inputs of nitrogenous nutrients.

The presence of neurotoxic species within the genus Alexandrium along the U.S. coastline has raised concern of potential poisoning through the consumption of contaminated seafood. Paralytic shellfish toxins (PSTs) detected in shellfish provide evidence that these harmful events have increased in frequency and severity along the California coast during the past 25 years, but the timing and location of these occurrences have been highly variable. We conducted a 4-year survey in King Harbor, CA, to investigate the seasonal dynamics of Alexandrium catenella and the presence of a particulate saxitoxin (STX), the parent compound of the PSTs. A quantitative PCR (qPCR) assay was developed for quantifying A. catenella in environmental microbial assemblages. This approach allowed for the detection of abundances as low as 12 cells liter 1 , 2 orders of magnitude below threshold abundances that can impact food webs. A. catenella was found repeatedly during the study, particularly in spring, when cells were detected in 38% of the samples (27 to 5,680 cells liter 1 ). This peak in cell abundances was observed in 2006 and corresponded to a particulate STX concentration of 12 ng liter 1 , whereas the maximum STX concentration of 26 ng liter 1 occurred in April 2008. Total cell abundances and toxin levels varied strongly throughout each year, but A. catenella was less abundant during summer, fall, and winter, when only 2 to 11% of the samples yielded positive qPCR results. The qPCR method developed here provides a useful tool for investigating the ecology of A. catenella at subbloom and bloom abundances. Many estuaries and coastal ecosystems are sites of occasional or recurrent algal blooms formed by species capable of producing noxious or toxic compounds that adversely affect ecosystem structure and function. These harmful algal blooms (HABs) often occur in coastal areas impacted by urbanization or agricultural activity, where their effects can cascade through food webs to negatively impact marine fauna and fishery activities and pose risks to human health (62, 74). A major concern regarding these events is that their frequency and distribution appear to be increasing in coastal environments throughout the world (3, 25, 27–29, 72) including the North American west coast (31, 38, 57, 76). Paralytic shellfish toxins (PSTs) constitute a suite of harmful neurotoxins commonly produced in marine ecosystems by several species of dinoflagellates within the genus Alexandrium (51). Transfer and accumulation of PSTs through marine food webs have been implicated in instances of mass mortality of fish, birds, and marine mammals (12, 24, 55, 59). In humans, PST poisoning manifests itself as paralytic shellfish poisoning (PSP) through the consumption of contaminated seafood. The PSTs are guanidine-based alkaloids, and over 30 analogues have been identified in nature. The parent compound, saxitoxin (STX), is the most potent marine toxin identified at

Protistan community structure was examined from 6 depths (1.5, 20, 42, 150, 500, 880 m) at a coastal ocean site in the San Pedro Channel, California. A total of 856 partial length 18S rDNA protistan sequences from the six clone libraries were analyzed to characterize diversity present at each depth. The sequences were grouped into a total of 259 Operational Taxonomic Units (OTUs) that were inferred using an automated OTU calling program that formed OTUs with approximately species-level distinction (95% sequence similarity). Most OTUs (194 out of 259) were observed at only one specific depth, and only two were present in clone libraries from all depths. OTUs were obtained from 21 major protistan taxonomic groups determined by their closest BLAST matches to identified protists in the NCBI database. Approximately 74% of the detected OTUs belonged to the Chromalveolates, with Group II alveolates making up the largest single group. Protistan assemblages at euphotic depths (1.5, 20 and 42 m) were characterized by the presence of clades that contained phototrophic species (stramenopiles, chlorophytes and haptophytes) as well as consumers (especially ciliates). Assemblages in the lower water column (150, 500 and 800 m) were distinct from communities at shallow depths because of strong contributions from taxa belonging to euglenozoans, acantharians, polycystines and Taxopodida ( Sticholonche spp. and close relatives). Species richness (Chao I estimate) and diversity (Shannon index) were highest within the euphotic zone and at 150 m, and lowest for protistan assemblages located in the oxygen minimum zone (500 and 880 m). Multivariate analyses (Bray–Curtis coefficient) confirmed that protistan assemblage composition differed significantly when samples were grouped into shallow (≤150 m) and deep water assemblages (≥150 m).

The structure and genetic diversity of marine protistan assemblages were investigated in the upper 500 m of the water column at a Pacific Ocean time-series station off the coast of Southern California. Deoxyribonucleic acid sequence-based microbial eukaryote diversity was examined in January, April, July, and October of 2001 at four depths (5 m, chlorophyll maximum [CM], 150 m, and 500 m). A total of 2956 partial 18S ribosomal ribonucleic acid gene sequences yielded representatives from most of the major eukaryotic lineages. Notable among the taxonomic groups were recently described lineages of stramenopiles, alveolates, and euglenozoa. A large number of polycystine and acantharean sequences were observed at depth. Pairwise sequence analysis was performed to establish operational taxonomic units (OTUs) that were then used to estimate the unsampled protistan diversity by parametric and nonparametric techniques. A total of 2246 protistan sequences grouped into 377 distinct OTUs, with remaining sequences attributed to metazoa. Protistan richness estimates ranged from , 600 to 1500 OTUs when all depths and seasons were combined into a single data set. Seasonal and depth-related trends in the observed protistan diversity were apparent from comparisons of univariate and multivariate analyses. Cluster analysis combined with nonmetric multidimensional scaling and analysis of similarity testing identified distinct protistan assemblages at the shallowest depths (5 m and CM) for each season, which were significantly different (p , 0.03) from assemblages at the two deepest depths (150 and 500 m) where seasonal changes in the protistan assemblage were not apparent.

Incomplete knowledge of acantharian life cycles has hampered their study and limited our understanding of their role in the vertical flux of carbon and strontium. Molecular tools can help identify enigmatic life stages and offer insights into aspects of acantharian biology and evolution. We inferred the phylogenetic position of acantharian sequences from shallow water, as well as acantharian-like clone sequences from 500 and 880 m in the San Pedro Channel, California. The analyses included validated acantharian and polycystine sequences from public databases with environmental clone sequences related to acantharia and used Bayesian inference methods. Our analysis demonstrated strong support for two branches of unidentified organisms that are closely related to, but possibly distinct from the Acantharea. We also found evidence of acantharian sequences from mesopelagic environments branching within the chaunacanthid clade, although the morphology of these organisms is presently unknown. HRP-conjugated probes were developed to target Acantharea and phylotypes from Unidentified Clade 1 using Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) on samples collected at 500 m. Our CARD-FISH experiments targeting phylotypes from an unidentified clade offer preliminary glimpses into the morphology of these protists, while a morphology for the aphotic acantharian lineages remains unknown at this time.

More than 70% of our earth is covered by water, yet we have explored less than 5% of the aquatic environment. Aquatic robots, such as autonomous underwater vehicles (AUVs), and their supporting infrastructure play a major role in the collection of oceanographic data. To make new discoveries and improve our overall understanding of the ocean, scientists must make use of these platforms by implementing effective monitoring and sampling techniques to study ocean upwelling, tidal mixing, and other ocean processes. Effective observation and continual monitoring of a dynamic system as complex as the ocean cannot be done with one instrument in a fixed location. A more practical approach is to deploy a collection of static and mobile sensors, where the information gleaned from the acquired data is distributed across the network. Additionally, orchestrating a multisensor, long-term deployment with a high volume of distributed data involves a robust, rapid, and cost-effective communication network. Connecting all of these components, which form an aquatic robotic system, in synchronous operation can greatly assist the scientists in improving our overall understanding of the complex ocean environment.

Quantitative polymerase chain reaction (qPCR) for the identification and quantification of microbes has become a common tool for the study of harmful algal blooms (HABs). We developed a qPCR method for the diatom genus Pseudo-nitzschia. Several species of this genus form toxic blooms through the production of the neurotoxin domoic acid (DA). Outbreaks of toxicity attributed to DA along the US west coast have caused sickness and death of marine mammals and seabirds through food web contamination. The method developed here quantifies Pseudo-nitzschia spp. at low abundances in natural samples, thereby, providing a method to improve our understanding of the environmental conditions leading to blooms of these species. This has been accomplished previously by techniques for identification and quantification that are slow and laborious compared to qPCR. The approach was successfully tested and validated using eight species of Pseudo-nitzschia and 33 non-target organisms and employed to follow local bloom dynamics.

Seawater desalination by reverse osmosis (RO) is a reliable method for augmenting drinking water supplies. In recent years, the number and size of these water projects have increased dramatically. As freshwater resources become limited due to global climate change, rising demand, and exhausted local water supplies, seawater desalination will play an important role in the world's future water supply, reaching far beyond its deep roots in the Middle East. Emerging contaminants have been widely discussed with respect to wastewater and freshwater sources, but also must be considered for seawater desalination facilities to ensure the long-term safety and suitability of this emerging water supply. Harmful algal blooms, frequently referred to as 'red tides' due to their vibrant colors, are a concern for desalination plants due to the high biomass of microalgae present in ocean waters during these events, and a variety of substances that some of these algae produce. These compounds range from noxious substances to powerful neurotoxins that constitute significant public health risks if they are not effectively and completely removed by the RO membranes. Algal blooms can cause significant operational issues that result in increased chemical consumption, increased membrane fouling rates, and in extreme cases, a plant to be taken off-line. Early algal bloom detection by desalination facilities is essential so that operational adjustments can be made to ensure that production capacity remains unaffected. This review identifies the toxic substances, their known producers, and our present state of knowledge regarding the causes of toxic episodes, with a special focus on the Southern California Bight.

DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.

The diatom Pseudo-nitzschia produces the neurotoxin domoic acid, known to cause illness and death in marine mammals and humans. Measurements of surface- and deep-water domoic acid concentrations off the coast of California suggest that this toxin is rapidly transported to depth following diatom blooms.

Protistan assemblages of aquatic ecosystems are the focus of extensive research in aquatic ecology. One stimulus for this work has been the long-standing recognition that phototrophic protists (the unicellular algae) constitute a major fraction of the primary productivity within aquatic ecosystems. We have learned a great deal about the taxonomic composition and trophic structure of aquatic protistan communities through the application of traditional approaches of morphological analysis and culture. Nevertheless, the tremendous diversity of protistan assemblages and the varied methods required for identifying protistan species and their abundances, biomass, and trophic activity continue to hamper in-depth understanding of the structure and function of these communities. The success of using molecular (genetic/immunological) signatures for assessing the community structure of natural protistan assemblages will ultimately depend on linking these signatures to classical (morphological) species descriptions and to the physiological abilities of protistan phylotypes. Ultimately, molecular approaches, in combination with classical methods, will provide new tools for studying the emergent physiological, ecological, and biogeochemical processes that are created and/or affected by protistan community structure. Probably the most distinct difference between freshwater and marine protistan communities is the restriction of the larger sarcodines (acantharia, radiolaria, and foraminifera) to brackish and marine ecosystems. Modern molecular biological approaches have revealed unexpected, and as yet largely uncharacterized, protistan diversity in a wide variety of ecosystems.

In August 2002 and March 2003 the trophic structure of the microbial assemblage from the San Pedro Channel, California was studied following the experimental alteration of the number of copepods. Changes in the abundance/biomass of microorganisms 80 μm, (ii) the presence of natural abundances of metazoa and (iii) the presence of an elevated number of copepods. Prokaryotes and small-sized eukaryotes (

The feeding preferences of three common diel vertically migrating zooplankton were investigated from December 1999 to October 2000 at the U.S. JGOFS Bermuda Atlantic Time-Series Study (BATS) station in the Sargasso Sea. Gut content analysis of the copepods Pleuromamma xiphias (Giesbrecht) and Euchirella messinensis (Claus) and of the euphausiid Thysanopoda aequalis (Hansen) indicated that all three species fed on a wide variety of phytoplankton, zooplankton, and detrital material. Diet changes generally reflected seasonal trends in phytoplankton community structure. However, species-specific feeding preferences and differences in feeding selectivity among the three species were evident, and in general agreement with feeding habits predicted from the analysis of mouthpart morphology. The euphausiid T. aequalis fed equally on more different food types compared to both copepod species. The copepod P. xiphias consumed a diverse assemblage of phytoplankton from late winter through the summer (78–93% of gut items, by number, were phytoplankton) and based its diet more strongly on carnivorous feeding in autumn and early winter (31% and 61% of gut items were phytoplankton, respectively). E. messinensis showed the greatest feeding specialization, with a strong preference for pennate diatoms in winter and spring and for coccolithophorids during late summer and fall (constituting 67–93% of gut items by number). All three species consumed diatoms more than other phytoplankton taxa, even though diatoms form only a small fraction of the phytoplankton biomass in the Sargasso Sea. Although the majority of gut items identified were phytoplankton cells, the relative biomass contribution of these small cells may be lower than that of zooplankton and detritus. Zooplankton on which the three species primarily preyed were protozoans and crustaceans, but also included other metazoans such as chaetognaths and cnidarians. Marine snow was also an important component of the diet in all three species, with typically >50% and rarely 4 µm in diameter) found in guts were also likely consumed with marine snow. The species-specific differences in the diets of these three migrating species suggest that an individual species approach is important in determining how feeding habits affect the structure of pelagic food webs and carbon cycling in the sea. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00227-002-0815-8.

Diel vertically migrating zooplankton can contribute significantly to dissolved carbon and nutrient export by respiring and excreting surface-ingested particulate organic matter below the mixed layer. Active export of particulate organic carbon (POC) and particulate organic nitrogen (PON) due to defecation at depth has rarely been considered in export budgets. We measured the gut passage time (GPT) of common migrant species at the Bermuda Atlantic Time-series Study (BATS) site, using the gut fluorescence method, to determine whether GPT is slow enough to allow active export of POC and PON to depth. Mean GPT for the copepods Pleuromamma xiphias and Euchirella messinensis was 191 and 114 min, respectively, and for the euphausiids Thysanopoda aequalis and Euphausia brevis (analyzed together) was 41 min, exceeding previously reported GPT for non- migrating zooplankton by a factor of 6. Between 18 and 81% of the initial gut pigment was retained in zooplankton guts upon descent below a mixed layer of 150 m. By comparing pigment ingestion rates (gut fluorescence technique) with total ingestion rates (CHN analysis of fecal material), we esti- mated that 71 to 85% of the migrant diet originated from non-plant material, which we included in our estimates of active POC/PON export. We applied the mean weight-specific active POC/PON export rate for the species examined to the total migratory zooplankton biomass using data from the BATS zooplankton time-series. Mean active POC (PON) flux at BATS was 0.94 mg C m -2 d -1 (0.18 mg N m -2 d -1 ) and the maximum was 5.27 mg C m -2 d -1 (1.02 mg N m -2 d -1 ), corresponding to a mean of 3% (4%) and a maximum of 18% (20%) of the mean gravitational POC (PON) flux measured by sediment traps at 150 m. Migrants also contributed significantly to passive flux via production of sinking fecal pellets during the night in surface waters. This passive flux exceeded active POC flux by ~10-fold. Freshly released feces by migrators at depth could be a valuable food source for mesopelagic organisms, in contrast to feces produced in surface waters which decompose while settling through the water column.

Ocean acidification and greenhouse warming will interactively influence competitive success of key phytoplankton groups such as diatoms, but how long-term responses to global change will affect community structure is unknown. We incubated a mixed natural diatom community from coastal New Zealand waters in a short-term (two-week) incubation experiment using a factorial matrix of warming and/or elevated p CO 2 and measured effects on community structure. We then isolated the dominant diatoms in clonal cultures and conditioned them for 1 year under the same temperature and p CO 2 conditions from which they were isolated, in order to allow for extended selection or acclimation by these abiotic environmental change factors in the absence of interspecific interactions. These conditioned isolates were then recombined into ‘artificial’ communities modelled after the original natural assemblage and allowed to compete under conditions identical to those in the short-term natural community experiment. In general, the resulting structure of both the unconditioned natural community and conditioned ‘artificial’ community experiments was similar, despite differences such as the loss of two species in the latter. p CO 2 and temperature had both individual and interactive effects on community structure, but temperature was more influential, as warming significantly reduced species richness. In this case, our short-term manipulative experiment with a mixed natural assemblage spanning weeks served as a reasonable proxy to predict the effects of global change forcing on diatom community structure after the component species were conditioned in isolation over an extended timescale. Future studies will be required to assess whether or not this is also the case for other types of algal communities from other marine regimes.

Increasing pCO2 (partial pressure of CO2 ) in an "acidified" ocean will affect phytoplankton community structure, but manipulation experiments with assemblages briefly acclimated to simulated future conditions may not accurately predict the long-term evolutionary shifts that could affect inter-specific competitive success. We assessed community structure changes in a natural mixed dinoflagellate bloom incubated at three pCO2 levels (230, 433, and 765 ppm) in a short-term experiment (2 weeks). The four dominant species were then isolated from each treatment into clonal cultures, and maintained at all three pCO2 levels for approximately 1 year. Periodically (4, 8, and 12 months), these pCO2 -conditioned clones were recombined into artificial communities, and allowed to compete at their conditioning pCO2 level or at higher and lower levels. The dominant species in these artificial communities of CO2 -conditioned clones differed from those in the original short-term experiment, but individual species relative abundance trends across pCO2 treatments were often similar. Specific growth rates showed no strong evidence for fitness increases attributable to conditioning pCO2 level. Although pCO2 significantly structured our experimental communities, conditioning time and biotic interactions like mixotrophy also had major roles in determining competitive outcomes. New methods of carrying out extended mixed species experiments are needed to accurately predict future long-term phytoplankton community responses to changing pCO2 .

The monthly, seasonal and interannual variability of microbial eukaryote assemblages were examined at 5 m, the deep chlorophyll maximum, 150 m and 500 m at the San Pedro Ocean Time-series station (eastern North Pacific). The depths spanned transitions in temperature, light, nutrients and oxygen, and included a persistently hypoxic environment at 500 m. Terminal restriction fragment length polymorphism was used for the analysis of 237 samples that were collected between September 2000 and December 2010. Spatiotemporal variability patterns of microeukaryote assemblages indicated the presence of distinct shallow and deep communities at the SPOT station, presumably reflecting taxa that were specifically adapted for the conditions in those environments. Community similarity values between assemblages collected 1 month apart at each depth ranged between ∼20% and ∼84% (averages were ∼50–59%). The assemblage at 5 m was temporally more dynamic than deeper assemblages and also displayed substantial interannual variability during the first ∼3 years of the study. Evidence of seasonality was detected for the microbial eukaryote assemblage at 5 m between January 2008 and December 2010 and at 150 m between September 2000 and December 2003. Seasonality was not detected for assemblages at the deep chlorophyll a maximum, which varied in depth seasonally, or at 500 m. Microbial eukaryote assemblages exhibited cyclical patterns in at least 1 year at each depth, implying an annual resetting of communities. Substantial interannual variability was detected for assemblages at all depths and represented the largest source of temporal variability in this temperate coastal ecosystem.

Protists have fascinated microbiologists since their discovery nearly 350 years ago. These single-celled, eukaryotic species span an incredible range of sizes, forms, and functions and, despite their generally diminutive size, constitute much of the genetic diversity within the domain Eukarya. Protists in marine ecosystems play fundamental ecological roles as primary producers, consumers, decomposers, and trophic links in aquatic food webs. Much of our knowledge regarding the diversity and ecological activities of these species has been obtained during the past half century, and only within the past few decades have hypotheses depicting the evolutionary relationships among the major clades of protists attained some degree of consensus. This recent progress is attributable to the development of genetic approaches, which have revealed an unexpectedly large diversity of protists, including cryptic species and previously undescribed clades of protists. New genetic tools now exist for identifying protistan species of interest and for reexamining long-standing debates regarding the biogeography of protists. Studies of protistan diversity provide insight regarding how species richness and community composition contribute to ecosystem function. These activities support the development of predictive models that describe how microbial communities will respond to natural or anthropogenically mediated changes in environmental conditions.

Domoic acid (DA) is a potent toxin produced by bloom-forming phytoplankton in the genus Pseudo-nitzschia, which is responsible for causing amnesic shellfish poisoning (ASP) in humans. ASP symptoms include vomiting, diarrhea, and in more severe cases confusion, loss of memory, disorientation, and even coma or death. This paper describes the development and validation of a rapid, sensitive, enzyme linked immunosorbent assay test kit for detecting DA using a monoclonal antibody. The assay gives equivalent results to those obtained using standard high performance liquid chromatography, fluorenylmethox- ycarbonyl high performance liquid chromatography, or liquid chromatography—mass spectrometry methods. It has a linear range from 0.1-3 ppb and was used successfully to measure DA in razor clams, mussels, scallops, and phytoplankton. The assay requires approximately 1.5 h to complete and has a standard 96-well format where each strip of eight wells is removable and can be stored at 4� C until needed. The first two wells of each strip serve as an internal control eliminating the need to run a standard curve. This allows as few as 3 or as many as 36 duplicate samples to be run at a time enabling real-time sample processing and limiting degradation of DA, which can occur during storage. There was minimal cross-reactivity in this assay with glutamine, glutamic acid, kainic acid, epi- or iso-DA. This accurate, rapid, cost-effective, assay offers environmental managers and public health officials an effective tool for monitoring DA concentrations in environment samples.

Abundances of Pseudo-nitzschia spp. and concentrations of particulate domoic acid (DA) were determined in the Southern California Bight (SCB) along the coasts of Los Angeles and Orange Counties during spring and summer of 2003 and 2004. At least 1500 km2 were affected by a toxic event in May/June of 2003 when some of the highest particulate DA concentrations reported for US coastal waters were measured inside the Los Angeles harbor (12.7 μg DA L−1). Particulate DA levels were an order of magnitude lower in spring of 2004 (February and March), but DA concentrations per cell at several sampling stations during 2004 exceeded previously reported maxima for natural populations of Pseudo-nitzschia (mean = 24 pg DA cell−1, range = 0–117 pg DA cell−1). Pseudo-nitzschia australis dominated the Pseudo-nitzschia assemblage in spring 2004. Overall, DA-poisoning was implicated in >1400 mammal stranding incidents within the SCB during 2003 and 2004. Ancillary physical and chemical data obtained during our regional surveys in 2004 revealed that Pseudo-nitzschia abundances, particulate DA and cellular DA concentrations were inversely correlated with concentrations of silicic acid, nitrogen and phosphate, and to specific nutrient ratios. Particulate DA was detected in sediment traps deployed at 550 and 800 m depth during spring of 2004 (0.29–7.6 μg DA (g sediment dry weight)−1). The highest DA concentration in the traps was measured within 1 week of dramatic decreases in the abundances of Pseudo-nitzschia in surface waters. To our knowledge these are the deepest sediment trap collections from which DA has been detected. Sinking of the spring Pseudo-nitzschia bloom may constitute a potentially important link between DA production in surface waters and benthic communities in the coastal ocean near Los Angeles. Our study indicates that toxic blooms of Pseudo-nitzschia are a recurring phenomenon along one of the most densely populated coastal stretches of the SCB and that the severity and magnitude of these events can be comparable to or greater than these events in other geographical regions affected by domoic acid.

Summary form only given. Protists are unicellular, eukaryotic organisms that exhibit phototrophic (microalgae), heterotrophic (protozoa) or mixotrophic nutrition. These species play essential roles in planktonic food webs as primary producers and consumers. Protistan species have traditionally been identified based on morphological and ultrastructural features, and the techniques used to identify these species have often been varied or taxon-specific. While morphological features have proven useful for taxonomists and evolutionists, they have not proven helpful to ecologists studying complex natural communities of protists where biodiversity may be high and phylogenetic breadth may be great. For this reason, ecological studies have rapidly incorporated new approaches from molecular biology and immunology for assessing protistan species diversity, species identification and quantification of taxa of ecological interest. Surprisingly, analyses of protistan biodiversity by sequencing DNA taken from environmental samples have indicated a significant protistan assemblage that has gone undetected until recently by traditional, microscopical analyses. In this presentation, information supporting this finding will be presented and studies being undertaken to describe and isolate these species will be discussed.