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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.

© 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.

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.

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.

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.

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.

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.

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.