A molecular survey of protist diversity through the central Arctic Ocean

RNA outperforms DNA-based metabarcoding in assessing the diversity and response of microeukaryotes to environmental variables in the Arctic Ocean

The Arctic Ocean (AO) has a harsh environment characterized by low temperatures, extensive ice coverage, and periodic freezing and melting of sea ice, which has provided diverse habitats for microorganisms. Prior studies primarily focused on microeukaryote communities in the upper water or sea ice based on environmental DNA, leaving the composition of active microeukaryotes in the diverse AO environments largely unknown. This study provided a vertical assessment of microeukaryote communities in the AO from snow and ice to sea water at a depth of 1670 m using high-throughput sequencing of co-extracted DNA and RNA. RNA extracts depicted microeukaryote community structure and intergroup correlations more accurately and responded more sensitively to environmental conditions than those derived from DNA. Using RNA:DNA ratios as a proxy for relative activity of major taxonomic groups, the metabolic activities of major microeukaryote groups were determined along depth. Analysis of co-occurrence networks showed that parasitism between Syndiniales and dinoflagellates/ciliates in the deep ocean may be significant. This study increased our knowledge of the diversity of active microeukaryote communities and highlighted the importance of using RNA-based sequencing over DNA-based sequencing to examine the relationship between microeukaryote assemblages and the responses of microeukaryotes to environmental variables in the AO.

Covariance of Marine Nucleocytoplasmic Large DNA Viruses with Eukaryotic Plankton Communities in the Sub-Arctic Kongsfjorden Ecosystem: A Metagenomic Analysis of Marine Microbial Ecosystems

Nucleocytoplasmic large DNA viruses (NCLDVs) infect various marine eukaryotes. However, little is known about NCLDV diversity and their relationships with eukaryotic hosts in marine environments, the elucidation of which will advance the current understanding of marine ecosystems. This study characterizes the interplay between NCLDVs and the eukaryotic plankton community (EPC) in the sub-Arctic area using metagenomics and metabarcoding to investigate NCLDVs and EPC, respectively, in the Kongsfjorden ecosystem of Svalbard (Norway) in April and June 2018. Gyrodinium helveticum (Dinophyceae) is the most prevalent eukaryotic taxon in the EPC in April, during which time Mimiviridae (31.8%), Poxviridae (25.1%), Phycodnaviridae (14.7%) and Pandoraviridae (13.1%) predominate. However, in June, the predominant taxon is Aureococcus anophagefferens (Pelagophyceae), and the NCLDVs, Poxviridae (32.9%), Mimiviridae (29.1%), and Phycodnaviridae (18.5%) appear in higher proportions with an increase in Pelagophyceae, Bacillariophyceae, and Chlorophyta groups. Thus, differences in NCLDVs may be caused by changes in EPC composition in response to environmental changes, such as increases in water temperature and light intensity. Taken together, these findings are particularly relevant considering the anticipated impact of NCLDV-induced EPC control mechanisms on polar regions and, therefore, improve the understanding of the Sub-Arctic Kongsfjorden ecosystem.

Phytoplankton Surveys in the Arctic Fram Strait Demonstrate the Tiny Eukaryotic Alga Micromonas and Other Picoprasinophytes Contribute to Deep Sea Export

Critical questions exist regarding the abundance and, especially, the export of picophytoplankton (≤2 µm diameter) in the Arctic. These organisms can dominate chlorophyll concentrations in Arctic regions, which are subject to rapid change. The picoeukaryotic prasinophyte Micromonas grows in polar environments and appears to constitute a large, but variable, proportion of the phytoplankton in these waters. Here, we analyze 81 samples from the upper 100 m of the water column from the Fram Strait collected over multiple years (2009−2015). We also analyze sediment trap samples to examine picophytoplankton contributions to export, using both 18S rRNA gene qPCR and V1-V2 16S rRNA Illumina amplicon sequencing to assess the Micromonas abundance within the broader diversity of photosynthetic eukaryotes based on the phylogenetic placement of plastid-derived 16S amplicons. The material sequenced from the sediment traps in July and September 2010 showed that 11.2 ± 12.4% of plastid-derived amplicons are from picoplanktonic prasinophyte algae and other green lineage (Viridiplantae) members. In the traps, Micromonas dominated (83.6 ± 21.3%) in terms of the overall relative abundance of Viridiplantae amplicons, specifically the species Micromonas polaris. Temporal variations in Micromonas abundances quantified by qPCR were also observed, with higher abundances in the late-July traps and deeper traps. In the photic zone samples, four prasinophyte classes were detected in the amplicon data, with Micromonas again being the dominant prasinophyte, based on the relative abundance (89.4 ± 8.0%), but with two species (M. polaris and M. commoda-like) present. The quantitative PCR assessments showed that the photic zone samples with higher Micromonas abundances (>1000 gene copies per mL) had significantly lower standing stocks of phosphate and nitrate, and a shallower average depth (20 m) than those with fewer Micromonas. This study shows that despite their size, prasinophyte picophytoplankton are exported to the deep sea, and that Micromonas is particularly important within this size fraction in Arctic marine ecosystems.

Contrasting Community Composition and Co-Occurrence Relationships of the Active Pico-Sized Haptophytes in the Surface and Subsurface Chlorophyll Maximum Layers of the Arctic Ocean in Summer

Haptophytes (Hacrobia: Haptophyta), which can perform phototrophic, phagotrophic, or mixotrophic nutritional modes, are critical for element cycling in a variety of aquatic ecosystems. However, their diversity, particularly in the changing Arctic Ocean (AO), remains largely unknown. In the present study, the biodiversity, community composition, and co-occurrence networks of pico-sized haptophytes in the surface water and subsurface chlorophyll maximum (SCM) layer of the AO were explored. Our results found higher alpha diversity estimates in the surface water compared with in the SCM based on high-throughput sequencing of haptophyte specific 18S rRNA. The community composition of the surface water was significantly different from that of the SCM, and water temperature was identified as the primary factor shaping the community compositions. Prymnesiales (mostly Chrysochromulina), uncultured Prymnesiophyceae, and Phaeocystis dominated the surface water communities, whereas Phaeocystis dominated the SCM communities, followed by Chrysochromulina, uncultured Prymnesiophyceae, and the remaining taxa. The communities of the surface water and SCM layer developed relatively independent modules in the metacommunity network. Nodes in the surface water were more closely connected to one another than those in the SCM. Network stability analysis revealed that surface water networks were more stable than SCM networks. These findings suggest that SCM communities are more susceptible to environmental fluctuations than those in surface water and that future global changes (e.g., global warming) may profoundly influence the development, persistence, and service of SCM in the AO.

No evidence of Phago-mixotropy in Micromonas polaris (Mamiellophyceae), the Dominant Picophytoplankton Species in the Arctic

In the Arctic Ocean, the small green alga Micromonas polaris dominates picophytoplankton during the summer months but is also present in winter. It has been previously hypothesized to be phago-mixotrophic (capable of bacteria ingestion) based on laboratory and field experiments. Prey uptake was analyzed in several M. polaris strains isolated from different regions and depths of the Arctic Ocean and in Ochromonas triangulata, a known phago-mixotroph used as a control. Measuring ingestion of either fluorescent beads or fluorescently labeled bacteria by flow cytometry, we found no evidence of phago-mixotrophy in any M. polaris strain while O. triangulata was ingesting both beads and bacteria. In addition, in silico predictions revealed that members of the genus Micromonas lack a genetic signature of phagocytotic capacity.

Implications of increasing Atlantic influence for Arctic microbial community structure

Increasing influence of Atlantic water in the Arctic Ocean has the potential to significantly impact regional water temperature and salinity. Here we use a rDNA barcoding approach to reveal how microbial communities are partitioned into distinct assemblages across a gradient of Atlantic-Polar Water influence in the Norwegian Sea. Data suggest that temperate adapted bacteria may replace cold water taxa under a future scenario of increasing Atlantic influence, but the eukaryote response is more complex. Some abundant eukaryotic cold water taxa could persist, while less abundant eukaryotic taxa may be replaced by warmer adapted temperate species. Furthermore, within lineages, different taxa display evidence of increased relative abundance in reaction to favourable conditions and we observed that rare microbial taxa are sample site rather than region specific. Our findings have significant implications for the vulnerability of polar associated community assemblages, which may change, impacting the ecosystem services they provide, under predicted increases of Atlantic mixing and warming within the Arctic region.

Uncovering the intricacies of microbial community dynamics at Helgoland Roads at the end of a spring bloom using automated sampling and 18S meta-barcoding

In May 2016, the remote-controlled Automated Filtration System for Marine Microbes (AUTOFIM) was implemented in parallel to the Long Term Ecological Research (LTER) observatory Helgoland Roads in the German Bight. We collected samples for characterization of dynamics within the eukaryotic microbial communities at the end of a phytoplankton bloom via 18S meta-barcoding. Understanding consequences of environmental change for key marine ecosystem processes, such as phytoplankton bloom dynamics requires information on biodiversity and species occurrences with adequate temporal and taxonomic resolution via time series observations. Sampling automation and molecular high throughput methods can serve these needs by improving the resolution of current conventional marine time series observations. A technical evaluation based on an investigation of eukaryotic microbes using the partial 18S rRNA gene suggests that automated filtration with the AUTOFIM device and preservation of the plankton samples leads to highly similar 18S community profiles, compared to manual filtration and snap freezing. The molecular data were correlated with conventional microscopic counts. Overall, we observed substantial change in the eukaryotic microbial community structure during the observation period. A simultaneous decline of diatom and ciliate sequences succeeded a peak of Miracula helgolandica, suggesting a potential impact of these oomycete parasites on diatom bloom dynamics and phenology in the North Sea. As oomycetes are not routinely counted at Helgoland Roads LTER, our findings illustrate the benefits of combining automated filtration with metabarcodingto augment classical time series observations, particularly for taxa currently neglected due to methodological constraints.

Contrasting Community Composition of Active Microbial Eukaryotes in Melt Ponds and Sea Water of the Arctic Ocean Revealed by High Throughput Sequencing

Melt ponds (MPs), form as the result of thawing of snow and sea ice in the summer, have lower albedo than the sea ice and are thus partly responsible for the polar amplification of global warming. Knowing the community composition of MP organisms is key to understanding their roles in the biogeochemical cycles of nutrients and elements. However, the community composition of MP microbial eukaryotes has rarely been studied. In the present study, we assessed the microbial eukaryote biodiversity, community composition, and assembly processes in MPs and surface sea water (SW) using high throughput sequencing of 18S rRNA of size-fractionated samples. Alpha diversity estimates were lower in the MPs than SW across all size fractions. The community composition of MPs was significantly different from that of SW. The MP communities were dominated by members from Chrysophyceae, the ciliate classes Litostomatea and Spirotrichea, and the cercozoan groups Filosa-Thecofilosea. One open MP community was similar to SW communities, which was probably due to the advanced stage of development of the MP enabling the exchange of species between it and adjacent SW. High portions of shared species between MPs and SW may indicate the vigorous exchange of species between these two major types of environments in the Arctic Ocean. SW microbial eukaryote communities are mainly controlled by dispersal limitation whereas those of MP are mainly controlled by ecological drift.

Chytrid fungi distribution and co-occurrence with diatoms correlate with sea ice melt in the Arctic Ocean

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.

Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime

One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5 m), subsurface (20 or 50 m), and mesopelagic (250 m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.

High colored dissolved organic matter (CDOM) absorption in surface waters of the central-eastern Arctic Ocean: Implications for biogeochemistry and ocean color algorithms

As consequences of global warming sea-ice shrinking, permafrost thawing and changes in fresh water and terrestrial material export have already been reported in the Arctic environment. These processes impact light penetration and primary production. To reach a better understanding of the current status and to provide accurate forecasts Arctic biogeochemical and physical parameters need to be extensively monitored. In this sense, bio-optical properties are useful to be measured due to the applicability of optical instrumentation to autonomous platforms, including satellites. This study characterizes the non-water absorbers and their coupling to hydrographic conditions in the poorly sampled surface waters of the central and eastern Arctic Ocean. Over the entire sampled area colored dissolved organic matter (CDOM) dominates the light absorption in surface waters. The distribution of CDOM, phytoplankton and non-algal particles absorption reproduces the hydrographic variability in this region of the Arctic Ocean which suggests a subdivision into five major bio-optical provinces: Laptev Sea Shelf, Laptev Sea, Central Arctic/Transpolar Drift, Beaufort Gyre and Eurasian/Nansen Basin. Evaluating ocean color algorithms commonly applied in the Arctic Ocean shows that global and regionally tuned empirical algorithms provide poor chlorophyll-a (Chl-a) estimates. The semi-analytical algorithms Generalized Inherent Optical Property model (GIOP) and Garver-Siegel-Maritorena (GSM), on the other hand, provide robust estimates of Chl-a and absorption of colored matter. Applying GSM with modifications proposed for the western Arctic Ocean produced reliable information on the absorption by colored matter, and specifically by CDOM. These findings highlight that only semi-analytical ocean color algorithms are able to identify with low uncertainty the distribution of the different optical water constituents in these high CDOM absorbing waters. In addition, a clustering of the Arctic Ocean into bio-optical provinces will help to develop and then select province-specific ocean color algorithms.

Abundant and rare picoeukaryotic sub-communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern Pacific Ocean

In this work, they compared patterns of abundant and rare picoeukaryotic sub-communities in the epipelagic waters (surface and 40-75 m depth subsurface layers) of the East and South China Seas across seasons via 454 pyrosequencing of the V4 region of 18S rDNA. They also examined the relative effects of environmental filtering, dispersal limitations and seasonality on community assembly. Their results indicated that (i) in the surface layer, abundant taxa are primarily influenced by dispersal limitations and rare taxa are primarily influenced by environmental filtering, whereas (ii) in the subsurface layer, both abundant and rare sub-communities are only weakly influenced by environmental filtering but are strongly influenced by dispersal limitations. Moreover, (iii) abundant taxa exhibit stronger temporal variability than rare taxa. They also found that abundant and rare sub-communities display similar spatial richness patterns that are negatively correlated with latitude and chlorophyll a and positively correlated with temperature. In summary, environmental filtering and dispersal limitations have different effects on abundant and rare picoeukaryotic sub-communities in different layers. Thus, depth appears as an essential variable that governs the structuring patterns of picoeukaryotic communities in the oceans and should be thoroughly considered to develop a more comprehensive understanding of oceanic microbial assemblages.

Limited sinking of Phaeocystis during a 12 days sediment trap study

There is a controversy discussion about the contribution of the genus Phaeocystis to the vertical carbon export with evidence for and against sedimentation of Phaeocystis. So far, the presence of Phaeocystis in sinking matter was investigated with methods depending on morphological features (microscopy) and fast degradable substances (biochemical analyses). In this study, we determine the occurrence and abundance of Phaeocystis antarctica in short-term sediment traps and the overlying water column during a 12-day time period in the Atlantic sector of the Southern Ocean with 454-pyrosequencing and microscopy counting. In the sediment trap samples, we only found few sequences belonging to Phaeocystis, which was not reflecting the situation in the water column above. The cell counts showed the same results. We conclude that Phaeocystis cells are not generally transported downwards by active sinking or other sinking processes.

Biogeography and Photosynthetic Biomass of Arctic Marine Pico-Eukaroytes during Summer of the Record Sea Ice Minimum 2012

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.

Strong Seasonality of Marine Microbial Eukaryotes in a High-Arctic Fjord (Isfjorden, in West Spitsbergen, Norway)

The Adventfjorden time series station (IsA) in Isfjorden, West Spitsbergen, Norway, was sampled frequently from December 2011 to December 2012. The community composition of microbial eukaryotes (size, 0.45 to 10 μm) from a depth of 25 m was determined using 454 sequencing of the 18S V4 region amplified from both DNA and RNA. The compositional changes throughout the year were assessed in relation to in situ fjord environmental conditions. Size fractionation analyses of chlorophyll a showed that the photosynthetic biomass was dominated by small cells (<10 μm) most of the year but that larger cells dominated during the spring and summer. The winter and early-spring communities were more diverse than the spring and summer/autumn communities. Dinophyceae were predominant throughout the year. The Arctic Micromonas ecotype was abundant mostly in the early-bloom and fall periods, whereas heterotrophs, such as marine stramenopiles (MASTs), Picozoa, and the parasitoid marine alveolates (MALVs), displayed higher relative abundance in the winter than in other seasons. Our results emphasize the extreme seasonality of Arctic microbial eukaryotic communities driven by the light regime and nutrient availability but point to the necessity of a thorough knowledge of hydrography for full understanding of their succession and variability.