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Global warming is rapidly altering physicochemical attributes of Arctic waters. These changes are predicted to alter microbial networks, potentially perturbing wider community functions including parasite infections and saprotrophic recycling of biogeochemical compounds. Specifically, the interaction between autotrophic phytoplankton and heterotrophic fungi e.g. chytrids (fungi with swimming tails) requires further analysis. Here, we investigate the diversity and distribution patterns of fungi in relation to abiotic variables during one record sea ice minimum in 2012 and explore co-occurrence of chytrids with diatoms, key primary producers in these changing environments. We show that chytrid fungi are primarily encountered at sites influenced by sea ice melt. Furthermore, chytrid representation positively correlates with sea ice-associated diatoms such as Fragilariopsis or Nitzschia. Our findings identify a potential future scenario where chytrid representation within these communities increases as a consequence of ice retreat, further altering community structure through perturbation of parasitic or saprotrophic interaction networks., Estelle. S. Kilias et al. show that chytrid fungi exhibiting swimming tales are primarily encountered at sites influenced by sea ice melt and that its representation positively correlates with sea ice-associated diatoms. This study predicts that chytrid representation within its Arctic communities may increase as ice retreats further.

Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland. We have sought consensus from a wide range of scientists across taxonomic domains to determine the minimal set of metadata that we collectively deem as critically important to accompany each sequenced specimen. These metadata are made available throughout the subsequent laboratory processes, and once collected, need to be adequately managed to fulfil the requirements of good data management practice. Due to the size and scale of management required, software tools are needed. These tools need to implement rigorous development pathways and change management procedures to ensure that effective research data management of key project and sample metadata is maintained. Tracking of sample properties through the sequencing process is handled by Lab Information Management Systems (LIMS), so publication of the sequenced data is achieved via technical integration of LIMS and data management tools. Discussions with community members on how metadata standards need to be managed within large-scale programmes is a priority in the planning process. Here we report on the standards we developed with respect to a robust and reusable mechanism of metadata collection, in the hopes that other projects forthcoming or underway will adopt these practices for metadata.

Next-generation sequencing is a common method for analysing microbial community diversity and composition. Configuring an appropriate sequence processing strategy within the variety of tools and methods is a nontrivial task and can considerably influence the resulting community characteristics. We analysed the V4 region of 18S rRNA gene sequences of marine samples by 454-pyrosequencing. Along this process, we generated several data sets with QIIME, mothur, and a custom-made pipeline based on DNAStar and the phylogenetic tree-based PhyloAssigner. For all processing strategies, default parameter settings and punctual variations were used. Our results revealed strong differences in total number of operational taxonomic units (OTUs), indicating that sequence preprocessing and clustering had a major impact on protist diversity estimates. However, diversity estimates of the abundant biosphere (abundance of ≥1%) were reproducible for all conducted processing pipeline versions. A qualitative comparison of diatom genera emphasized strong differences between the pipelines in which phylogenetic placement of sequences came closest to light microscopy-based diatom identification. We conclude that diversity studies using different sequence processing strategies are comparable if the focus is on higher taxonomic levels, and if abundance thresholds are used to filter out OTUs of the rare biosphere.

Exposing a microbial community to alternating absence and presence of carbon substrate in aerobic conditions is an effective strategy for enrichment of storage polymers (polyhydroxybutyrate, PHB) producing microorganisms. In this work we investigate to which extent intermediate storage polymer production is a temperature independent microbial competition determining factor. Eight parallel bioreactors were operated in the temperature range of 20-40 °C, but intermediate storage polymer production was only obtained at 25-35 °C. Besides PHB production and consumption, cell decay and subsequent cryptic growth on lysis products was found to determine process properties and the microbial community structure at all operational temperatures. At 40 °C decay processes cannot be overcome with additional energy from storage polymers, and fast-growing microorganisms dominate the system. At 20 °C, highly competitive communities with ambiguous storage properties were enriched. The results described here demonstrate that a rigorous experimental approach could aid in the understanding of competitive strategies in microbial communities.

In the ongoing discussion of the distribution of protists, whether they are globally distributed or endemic to one or both of the polar regions is the subject of heated debate. In this study, we compared next-generation sequencing data from the Arctic and the Southern oceans to reveal the extent of similarities and dissimilarities between the protist communities in the polar regions. We found a total overlap of operational taxonomic units (OTUs) between the two regions of 11.2%. On closer inspection of different taxonomic groups, the overlap ranged between 5.5% (haptophytes) and 14.5% (alveolates). Within the different groups, the proportion of OTUs occurring in both regions greatly differed between the polar regions. On the one hand, the overlap between these two regions is remarkable, given the geographical distance between them. On the other hand, one could expect a greater overlap of OTUs between these regions on account of the similar environmental conditions. The overlap suggests a connection between the polar regions for at least certain species or that the evolutionary divergence has been slow, relative to the timescales of isolation. The different proportions of common OTUs among the groups or regions may be a result of different life cycle strategies or environmental adaptations. Keywords: 18S rDNA; bipolar; next-generation sequencing; phytoplankton; polar regions; protist distribution. (Published: 18 May 2015) Citation: Polar Research 2015, 34 , 23225, http://dx.doi.org/10.3402/polar.v34.23225 To access the supplementary material for this article, please see supplementary files under Article Tools.

Investigation of marine eukaryotic picoplankton composition is limited by missing morphological features for appropriate identification. Consequently, molecular methods are required. In this study, we used 454-pyrosequencing to study picoplankton communities at four stations in the West Spitsbergen Current (WSC; Fram Strait). High abundances of Micromonas pusilla were detected in the station situated closest to Spitsbergen, as seen in surveys of picoplankton assemblages in the Beaufort Sea. At the other three stations, other phylotypes, affiliating with Phaeocystis pouchetii and Syndiniales in the phylogenetic tree, were present in high numbers, dominating most of them. The picoplankton community structures at three of the stations, all with similar salinity and temperature, were alike. At the fourth station, the influence of the East Spitsbergen Current (ESC), transporting cold water from the Barents Sea around Spitsbergen, causes different abiotic parameters that result in a significantly different picoeukaryote community composition, which is dominated by Micromonas pusilla. This observation is particularly interesting in regard to ongoing environmental changes in the Arctic. Ongoing warming of the WSC could convey a new picoplankton assemblage into the Arctic Ocean, which may come to affect the dominance of Micromonas pusilla.

The protist assemblage in the central Arctic Ocean is scarcely surveyed despite them being the major primary producers. Elucidating their response to changing environmental variables requires an a priori analysis of their current diversity, including abundant and rare species. In late summer 2011, samples were collected during the ARK-XXVI/3 expedition (RV Polarstern) to study Arctic protist community structures, by implementation of automated ribosomal intergenic spacer analysis (ARISA) and 454-pyrosequencing. Protist assemblages were related to the hydrology and environmental variables (temperature, salinity, ice coverage, nitrate, phosphate, and silicate). The abundant (a parts per thousand yen1 %) biosphere and rare (< 1 %) biosphere were considered separately in the diversity analysis in order to reveal their mutual relationships. A relation between hydrology and protist community structure was highly supported by ARISA and partially by 454-pyrosequencing. Sea ice showed a stronger influence on the local community structure than nutrient availability, making statements on the water mass influence more difficult. Dinoflagellates (Syndiniales), chlorophytes (Micromonas spp.), and haptophytes (Phaeocystis spp.) were important contributors to the abundant biosphere, while other dinoflagellates and stramenopiles dominated the rare biosphere. No significant correlation was found between the abundant and rare biosphere. However, relative contributions of major taxonomic groups revealed an unexpected stable community structure within the rare biosphere, indicating a potential constant protist reservoir. This study provides a first molecular survey of protist diversity in the central Arctic Ocean, focusing on the diversity and distribution of abundant and rare protists according to the environmental conditions, and can serve as baseline for future analysis.

In this study we present the first comprehensive analyses of the diversity and distribution of marine protist (micro- nano- and picoeukaryotes) in the Western Fram Strait, using 454-pyrosequencing and high-pressure liquid chromatography (HPLC) at five stations in summer 2010. Three stations (T1; T5; T7) were influenced by Polar Water, characterized by cold water with lower salinity (

Information on recent photosynthetic biomass distribution and biogeography of Arctic marine pico-eukaryotes (0.2–3 μm) is needed to better understand consequences of environmental change for Arctic marine ecosystems. We analysed pico-eukaryote biomass and community composition in Fram Strait and large parts of the Central Arctic Ocean (Nansen Basin, Amundsen Basin) using chlorophyll a (Chl a) measurements, automated ribosomal intergenic spacer analysis (ARISA) and 454-pyrosequencing. Samples were collected during summer 2012, the year with the most recent record sea ice minimum. Chl a concentrations were highest in eastern Fram Strait and pico-plankton accounted for 60–90% of Chl a biomass during the observation period. ARISA-patterns and 454-pyrosequencing revealed that pico-eukaryote distribution is closely related to water mass distribution in the euphotic zone of the Arctic Ocean. Phaeocystaceae, Micromonas sp., Dinophyceae and Syndiniales constitute a high proportion of sequence reads, while sequence abundance of autotrophic Phaeocystaceae and mixotrophic Micromonas sp. was inversely correlated. Highest sequence abundances of Phaeocystaceae were observed in the warm Atlantic Waters in Fram Strait, while Micromonas sp. dominated the abundant biosphere in the arctic halocline. Our results are of particular interest considering existing hypotheses that environmental conditions in Nansen Basin might become more similar to the current conditions in Fram Strait. We propose that in response, biodiversity and biomass of pico-eukaryotes in Nansen Basin could resemble those currently observed in Fram Strait in the future. This would significantly alter biogeochemical cycles in a large part of the Central Arctic Ocean.

Information on recent biomass distribution and biogeography of photosynthetic marine protists with adequate temporal and spatial resolution is urgently needed to better understand the consequences of environmental change for marine ecosystems. Here we introduce and review a molecular-based observation strategy for high-resolution assessment of these protists in space and time. It is the result of extensive technology developments, adaptations and evaluations which are documented in a number of different publications, and the results of the recently completed field testing which are introduced in this paper. The observation strategy is organized at four different levels. At level 1, samples are collected at high spatiotemporal resolution using the remotely controlled automated filtration system AUTOFIM. Resulting samples can either be preserved for later laboratory analyses, or directly subjected to molecular surveillance of key species aboard the ship via an automated biosensor system or quantitative polymerase chain reaction (level 2). Preserved samples are analyzed at the next observational levels in the laboratory (levels 3 and 4). At level 3 this involves molecular fingerprinting methods for a quick and reliable overview of differences in protist community composition. Finally, selected samples can be used to generate a detailed analysis of taxonomic protist composition via the latest next generation sequencing technology (NGS) at level 4. An overall integrated dataset of the results based on the different analyses provides comprehensive information on the diversity and biogeography of protists, including all related size classes. At the same time the cost of the observation is optimized with respect to analysis effort and time.

Between Greenland and Spitsbergen, Fram Strait is a region where cold ice-covered Polar Water exits the Arctic Ocean with the East Greenland Current (EGC) and warm Atlantic Water enters the Arctic Ocean with the West Spitsbergen Current (WSC). In this compilation, we present two different data sets from plankton ecological observations in Fram Strait: (1) long-term measurements of satellite-derived (1998–2012) and in situ chlorophyll a (chl a) measurements (mainly summer cruises, 1991–2012) plus protist compositions (a station in WSC, eight summer cruises, 1998–2011); and (2) short-term measurements of a multidisciplinary approach that includes traditional plankton investigations, remote sensing, zooplankton, microbiological and molecular studies, and biogeochemical analyses carried out during two expeditions in June/July in the years 2010 and 2011. Both summer satellite-derived and in situ chl a concentrations showed slight trends towards higher values in the WSC since 1998 and 1991, respectively. In contrast, no trends were visible in the EGC. The protist composition in the WSC showed differences for the summer months: a dominance of diatoms was replaced by a dominance of Phaeocystis pouchetii and other small pico- and nanoplankton species. The observed differences in eastern Fram Strait were partially due to a warm anomaly in the WSC. Although changes associated with warmer water temperatures were observed, further long-term investigations are needed to distinguish between natural variability and climate change in Fram Strait. Results of two summer studies in 2010 and 2011 revealed the variability in plankton ecology in Fram Strait.Keywords: Plankton; ecology; biogeochemistry; Fram Strait; Arctic Ocean; climate change.(Published: 1 December 2015)Citation: Polar Research 2015, 34, 23349, http://dx.doi.org/10.3402/polar.v34.23349To access the supplementary material for this article, please see supplementary files in the column to the right (under Article Tools).

Protists in the central Arctic Ocean are adapted to the harsh environmental conditions of its various habitats. During the Polarstern cruise ARK-XXVI/3 in 2011, at one sea-ice station, large aggregates accumulated at the bottom of the melt ponds. In this study, the protist assemblages of the bottom layer of the sea-ice and melt-pond aggregate were investigated using flow cytometry and 454-pyrosequencing. The objective is to provide a first molecular overview of protist biodiversity in these habitats and to consider the overlaps and/or differences in the community compositions. Results of flow cytometry pointed to a cell size distribution that was dominated by 3–10 µm nanoflagellates. The phylogenetic classification of all sequences was conducted at a high taxonomic level, while a selection of abundant (≥1% of total reads) sequences was further classified at a lower level. At a high taxonomic level, both habitats showed very similar community structures, dominated by chrysophytes and chlorophytes. At a lower taxonomic level, dissimilarities in the diversity of both groups were encountered in the abundant biosphere. While sea-ice chlorophytes and chrysophytes were dominated by Chlamydomonas/Chloromonas spp. and Ochromonas spp., the melt-pond aggregate was dominated by Carteria sp., Ochromonas spp. and Dinobryon faciluiferum. We suppose that the similarities in richness and community structure are a consequence of melt-pond freshwater seeping through porous sea ice in late summer. Differences in the abundant biosphere nevertheless indicate that environmental conditions in both habitats vary enough to select for different dominant species. Keywords: 18S rDNA; Arctic Ocean; biodiversity; next-generation sequencing; flow cytometry To access the supplementary material for this article, please see supplementary files in the column to the right (under Article Tools) (Published: 5 November 2014) Citation: Polar Research 2014, 33 , 23466, http://dx.doi.org/10.3402/polar.v33.23466

Knowledge about the protist diversity of the Pacific sector of the Southern Ocean is scarce. We tested the hypothesis that distinct protist community assemblages characterize large-scale water masses. Therefore, we determined the composition and biogeography of late summer protist assemblages along a transect from the coast of New Zealand to the eastern Ross Sea. We used state of the art molecular approaches, such as automated ribosomal intergenic spacer analysis and 454-pyrosequencing, combined with high-performance liquid chromatography pigment analysis to study the protist assemblage. We found distinct biogeographic patterns defined by the environmental conditions in the particular region. Different water masses harbored different microbial communities. In contrast to the Arctic Ocean, picoeukaryotes had minor importance throughout the investigated transect and showed very low contribution south of the Polar Front. Dinoflagellates, Syndiniales, and small stramenopiles were dominating the sequence assemblage in the Subantarctic Zone, whereas the relative abundance of diatoms increased southwards, in the Polar Frontal Zone and Antarctic Zone. South of the Polar Front, most sequences belonged to haptophytes. This study delivers a comprehensive and taxon detailed overview of the protist composition in the investigated area during the austral summer 2010.

It is important to characterize and understand the diversity of marine protists because of their relevance for ecosystem functioning. In the era of molecular science, diversity studies have received renewed attention. High-throughput, cost-intensive next generation sequencing provides deep insight in protist diversity but limits the volume of studied samples. Protist observations with high spatiotemporal resolution, therefore, require a quick and cost-effective tool to channelize the large sample volume and help select representatives for diversity studies. In this study, we evaluated the validity of “Automated Ribosomal Intergenic Spacer Analysis” (ARISA) as a means of estimating variability in marine protist communities. The evaluation was based on statistical correlation of ARISA data and 454-pyrosequencing data from samples collected in the Southern Ocean and Arctic Ocean. Here, we provide evidence that differences in ARISA profiles reflect taxon-specific differences observed in 454-pyrosequencing data sets. Calculated similarity indices for the ARISA profiles and 454- pyrosequencing data of 27 marine protist samples revealed strong agreements between the results of both methods regarding the extent of variability among protist communities. We suggest that ARISA might become an important tool for surveillance of differences in marine protist communities with high spatiotemporal resolution. Furthermore, it might serve as a preselection tool to identify representative samples in large data sets.