The Chukchi Sea was sampled in August of 2011, a year of near-normal sea ice among recent years, and again in August 2012, a year of all time record low sea ice. We exploited this sampling to test the hypothesis that different sea ice conditions are associated with differences in abundances or species composition of microzooplankton through an examination of tintinnids and radiolarians. From 18 stations in 2011, and 19 stations in 2012, organisms were enumerated in plankton net tow material, and chlorophyll determinations made (total and ≤ 20 µm) from discrete depth samples. We found that the low sea ice conditions of 2012 were associated with higher chlorophyll concentrations (both total and the ≤ 20 µm size fraction), compared to 2011. However, tintinnid ciliates and radiolarians were much lower in concentration, by about an order of magnitude, compared to 2011. In both years the radiolarian assemblage was dominated by Amphiselma setosa. The species composition of the tintinnid ciliates was similar in the two years, but there were distinct differences in the relative abundances of certain species. The 2012, low sea ice assemblage, was dominated by small forms in contrast to 2011, when large species were the most abundant. We present these findings in detail and discuss possible explanations for the apparent differences in the microzooplankton communities associated with distinct sea ice conditions in the Chukchi Sea

Aerobic protozoa can maintain fully aerobic metabolic rates even at very low O₂-tensions; this is related to their small sizes. Many – or perhaps all – protozoa show particular preferences for a given range of O₂-tensions. The reasons for this and the role for their distribution in nature are discussed and examples of protozoan biota in O₂-gradients in aquatic systems are presented. Facultative anaerobes capable of both aerobic and anaerobic growth are probably common within several protozoan taxa. It is concluded that further progress in this area is contingent on physiological studies of phenotypes.

Analysing the spatio-temporal distribution of protistan microplankton has faced both conceptual and technical difficulties. However, recognition of a need to study planktonic patchiness, application of a major geology-based methodology (geostatistics) to ecology, and advances in computational technologies have widened the interest in this topic and made it more assessable. This review provides methodological and conceptual guidance on the application of geostatistics to microplankton analysis, using ciliates as example model organisms. Applying geostatistical analysis (and complementary methodologies) to the distribution of ciliate and phytoplankton reveals that attributes of their populations and assemblages (e.g. abundance, biomass, production, diversity) are patchily distributed at multiple spatial-scales in different aquatic environments, and these change over time. Data examined from several environments and scales exhibit distinct patterns of patches regarding their shape, density, and structure; these data can then be used to suggest a behavioural niche-separation of ciliates and the influence of patchiness on the rate processes of food webs. Throughout the review, basic guidance is provided for interpreting where, when, and why planktonic ciliate are so distributed, and directions for work on patchiness is offered, including a guide to the main literature on the topic. This should, therefore, be a useful stepping-stone for researchers interested in the impact of patchiness on protistan ecology, regardless of the environment.

Our best evidence is that life arose in the marine environment, and over many millennia of evolutionary proliferation, punctuated by occasional massive extinctions, marine protists have developed remarkably elegant and sometimes complex relationships with prokaryotic and eukaryotic symbionts. Current evidence of the range of marine protist taxa possessing symbionts, including their diversity and physiological functional relationships, is reviewed within an ecological context. Some perspectives are presented on potential opportunities for new avenues of research in unraveling the remarkable adaptive value of two or more genetically diverse marine unicellular organisms living in a close structural and physiological relationship.

Several dinoflagellates are known to practice acquired phototrophy by either hosting intact algal endosymbionts or retaining plastids. The acquisition of phototrophy in dinoflagellates appears to occur independently over a variety of orders, rather than being restricted to any specific order(s). While dinoflagellates with intact algal cells host endosymbionts of cyanobacteria, pelagophyte, prasinophyte or dictyochophyte, most organelle-retaining dinoflagellates acquire plastids from cryptophytes. In dinoflagellates with acquired phototrophy, the mechanism by which symbionts or plastids are obtained has not been well studied at sub-cellular or ultrastructural level, and thus little is known regarding their mechanism to sequester and maintain photosynthetic structures, except for three cases, Amphidinium poecilochroum, Gymnodinium aeruginosum, and Dinophysis caudata with peduncle feeding. Dinoflagellates with acquired phototrophy display different degrees of reduction of the retained endosymbiont and organelles, ranging from those which contain intact whole algal cells (e.g. green Noctiluca scintillans), to those which have retained almost a full complement of organelles (e.g., Amphidinium poecilochroum and Podolampas bipes), to those in which only the plastids remain (e.g., Amphidinium wigrense and Dinophysis spp.). A series of events leading to acquisition and subsequent degeneration of a whole-cell endosymbiont have been widely recognized as evolutionary pathway of the acquisition of plastids. However, recent work on D. caudata suggests that acquisition of phototrophy by predation (i.e. kleptoplastidy) may be a mechanism and evolutionary pathway through which plastids originated in dinoflagellates with ‘foreign’ plastids other than the ‘typical’ peridinin-type plastids. Most organelle-retaining dinoflagellates are facultative mixotrophs, with Dinophysis species and an undescribed Antarctic dinoflagellate being the only obligate mixotrophs known so far. The establishment of dinoflagellates with acquired phototrophy in cultures and careful research using the cultures would help improve our knowledge of the evolution of the dinoflagellate plastids and their ecophysiology.

Parasitism is an immensely successful mode of nutrition and parasitic organisms are abundant in most ecosystems. This is also the case for marine planktonic ecosystems in which a large variety of parasitic species are known. Most of these parasites are protists and they infect a wide range of hosts from the marine plankton, ranging from other protists to larger planktonic invertebrates. Parasites often have morphologies and life cycles that are highly specialized as compared to their free-living relatives. However, this does not mean that parasites are necessarily odd or rare phenomena; on the contrary parasites constitute numerically and ecologically important components of the ecosystem. This review gives an overview of the existing knowledge on the diversity and occurrence of parasitic protists in the marine plankton and examines the available information on the potential effects and role of parasitism in this ecosystem. Importance is given to the fact that prevalence and impact of parasitic organisms in marine planktonic systems appear to be overwhelmingly understudied.

Dinoflagellates (Alveolata, Dinophyceae) are protists with a truly remarkable diversity in lifestyles (free-living, parasites and mutualistic symbionts), habitats (marine, freshwater, plankton, benthos), and trophic modes (heterotrophic, plastid-containing). Here dinoflagellates are used to evaluate biases in the availability of molecular markers in relation to the variety of functional and ecological characteristics of protists. A large number of dinoflagellate sequences are available in GenBank, at least one for 56% of the 264 described genera. The most common marker is the small ribosomal subunit ribosomal DNA (49%). At the species level, SSU rDNA or the large subunit rDNA are available for 15% of the 2,386 described species. Availability of sequences of the internal transcribed spacers (ITS) and cytochrome oxidase I (COI) show a strong bias towards cultivable species. Relative to trophic mode, while about half of the known dinoflagellates are heterotrophic, only 12% of them have been sequenced compared to 29% of the plastid-containing species. For the COI marker availability is 10 times greater for plastid-containing compared to heterotrophic species. Freshwater species are underrepresented (13%) relative to the marine forms (22%). A high proportion of benthic species have been sequenced (46%) reflecting interest in Symbiodinium and harmful epiphytic taxa. Most of the relatively few described mutualistic species have been sequenced (> 80%). In contrast, only 17% of the described parasitic species have been sequenced, and most of the available sequences were not identified at the species level. In recent years, new species have been described mostly from coastal blooms or cultures. These studies are favored by the availability of abundant material for detailed studies of ultrastructure and multi-gene molecular phylogenies. Many methods are difficult to apply for the scarce specimens available from the open ocean. The requirement of these protocols, easy to apply with cultured species, is an obstacle in our knowledge of the open ocean diversity because it discourages studies based on sparse material. Consequently, in recent years descriptions of new species from the open ocean have declined considerably.

The evolution of the dominant marine plankton ciliates, the oligotrichids and choreotrichids, is analysed for morphologic and genetic convergences and apomorphies based on literature and our own data. These findings have taxonomic implications. Within the oligotrichid genus Parallelostrombidium two subgenera, Parallelostrombidium Agatha, 2004 nov. stat. and Asymptokinetum nov. subgen., are established, using the courses of the ventral and girdle kineties as a distinguishing feature. Likewise, a different arrangement of extrusome attachment sites is used for a split of the oligotrichid genus Novistrombidium into the subgenera Novistrombidium Song and Bradbury, 1998 nov. stat. and Propecingulum nov. subgen.; Novistrombidium (Propecingulum) ioanum (Lynn and Gilron, 1993) nov. comb. and Novistrombidium (Propecingulum) platum (Song and Packroff, 1997) nov. comb. are affiliated. Based on discrepancies in the somatic ciliary pattern and the presence of conspicuous argyrophilic inclusions, the aloricate choreotrichid species Pelagostrobilidium kimae nov. spec. is distinguished from P. conicum. The diagnosis for the tintinnid family Eutintinnidae Bachy et al., 2012 is improved by including cell features. The co-operation of taxonomists and molecular biologists is strongly recommended to prevent misinterpretations of gene trees due to incorrectly identified species and for better species circumscriptions.

Advances in sequencing technology and the environmental genomic approaches have brought attention to the vastness of protist biodiversity. While over much of the world’s oceans the species and phylotypes making up this diversity are assumed to be something previously hidden and now revealed, the recent rapid changes in the Arctic mean that such assumptions may be a simplification. Historical morphological species data can be used to validate new records provided that more of these species are identified using standard molecular markers. Environmental surveys can also go further by identifying species over regions, seasons and depths. High throughput sequencing and bioinformatics tools provide a means of monitoring and eventually predicting the consequences of change. We give an example of how microbial eukaryote communities differ over pan-arctic scales, emphasizing the need for additional sampling and the need for caution in extrapolating the results of one region to the entire Arctic.

The Chukchi Sea was sampled in August of 2011, a year of near-normal sea ice among recent years, and again in August 2012, a year of all time record low sea ice. We exploited this sampling to test the hypothesis that different sea ice conditions are associated with differences in abundances or species composition of microzooplankton through an examination of tintinnids and radiolarians. From 18 stations in 2011, and 19 stations in 2012, organisms were enumerated in plankton net tow material, and chlorophyll determinations made (total and ≤ 20 μm) from discrete depth samples. We found that the low sea ice conditions of 2012 were associated with higher chlorophyll concentrations (both total and the ≤ 20 μm size fraction), compared to 2011. However, tintinnid ciliates and radiolarians were much lower in concentration, by about an order of magnitude, compared to 2011. In both years the radiolarian assemblage was dominated by Amphiselma setosa. The species composition of the tintinnid ciliates was similar in the two years, but there were distinct differences in the relative abundances of certain species. The 2012, low sea ice assemblage, was dominated by small forms in contrast to 2011, when large species were the most abundant. We present these findings in detail and discuss possible explanations for the apparent differences in the microzooplankton communities associated with distinct sea ice conditions in the Chukchi Sea.

The ‘big new biology’ is a vision of a discipline transformed by a commitment to sharing data and with investigative practices that call on very large open pools of freely accessible data. As this datacentric world matures, biologists will be better able to manage the deluge of data arising from digitization programs, governmental mandates for data sharing, and increasing instrumentation of science. The big new biology will create new opportunities for research and will enable scientists to answer questions that require access to data on a scale not previously possible. Informatics will become the new genomics, and those not participating will become marginalized. If a traditional discipline like protistology is to benefit from this big data world, it must define, build, and populate an appropriate infrastructure. The infrastructure is likely to be modular, with modules focusing on needs within defined subject and makes it available in standard formats by an array of pathways. It is the responsibility of protistologists to build such nodes for their own discipline.

Protists are key components of marine microbial communities and hence of the biogeochemical mathematical models that are used to study the interaction between organisms, and the associated cycling of carbon and other nutrients. With increased computing power, models of microbial communities have markedly increased in complexity in the last 20 years, from relatively simple single nutrient currency, nutrient-phytoplankton-zooplankton-detritus (NPZD) models to plankton functional type (PFT) or trait based models of multiple organisms, or individual based models (IBMs) of specific organisms. However, our recognition, if not parameterisation, of the physiological processes that underpin both autotrophic and heterotrophic protist nutrition and growth arguably have increased faster than our modelling capability, generating a wealth of new modelling challenges. This paper therefore reviews historical development, current capability, and the future directions and challenges in protist based mathematical modelling.