Monthly to interannual variability of microbial eukaryote assemblages at four depths in the eastern North Pacific

Recurring seasonality exposes dominant species and niche partitioning strategies of open ocean picoeukaryotic algae

Ocean spring phytoplankton blooms are dynamic periods important to global primary production. We document vertical patterns of a diverse suite of eukaryotic algae, the prasinophytes, in the North Atlantic Subtropical Gyre with monthly sampling over four years at the Bermuda Atlantic Time-series Study site. Water column structure was used to delineate seasonal stability periods more ecologically relevant than seasons defined by calendar dates. During winter mixing, tiny prasinophytes dominated by Class II comprise 46  ±  24% of eukaryotic algal (plastid-derived) 16S rRNA V1-V2 amplicons, specifically Ostreococcus Clade OII, Micromonas commoda, and Bathycoccus calidus. In contrast, Class VII are rare and Classes I and VI peak during warm stratified periods when surface eukaryotic phytoplankton abundances are low. Seasonality underpins a reservoir of genetic diversity from multiple prasinophyte classes during warm periods that harbor ephemeral taxa. Persistent Class II sub-species dominating the winter/spring bloom period retreat to the deep chlorophyll maximum in summer, poised to seed the mixed layer upon winter convection, exposing a mechanism for initiating high abundances at bloom onset. Comparisons to tropical oceans reveal broad distributions of the dominant sub-species herein. This unparalleled window into temporal and spatial niche partitioning of picoeukaryotic primary producers demonstrates how key prasinophytes prevail in warm oceans.

Biogeographical and biodiversity patterns of planktonic microeukaryotes along the tropical western to eastern Pacific Ocean transect revealed by metabarcoding

Microeukaryotic plankton (0.2-200 µm), which are morphologically and genetically highly diverse, play a crucial role in ocean productivity and carbon consumption. The Pacific Ocean (PO), one of the world's largest oligotrophic regions, remains largely unexplored in terms of the biogeography and biodiversity of microeukaryotes based on large-scale sampling. We investigated the horizontal distribution of microeukaryotes along a 16,000 km transect from the west to the east of the PO. The alpha diversity indices showed a distinct decreasing trend from west to east, which was highly correlated with water temperature. The microeukaryotic community, which was clustered into the western, central, and eastern PO groups, displayed a significant distance-decay relationship. Syndiniales, a lineage of parasitic dinoflagellates, was ubiquitously distributed along the transect and dominated the community in terms of both sequence and zero-radius operational taxonomic unit (ZOTU) proportions. The prevailing dominance of Syndiniales-affiliated ZOTUs and their close associations with dinoflagellates, diatoms, and radiolarians, as revealed by SparCC correlation analysis, suggested that parasitism may be an important trophic strategy in the surface waters of the PO. Geographical distance and temperature were the most important environmental factors that significantly correlated with community structure. Overall, our study sheds more light on the distribution pattern of both alpha and beta diversities of microeukaryotic communities and highlighted the importance of parasitisms by Syndiniales across the tropical PO.IMPORTANCEUnderstanding the biogeographical and biodiversity patterns of microeukaryotic communities is essential to comprehending their roles in biogeochemical cycling. In this study, planktonic microeukaryotes were collected along a west-to-east Pacific Ocean transect (ca. 16,000 km). Our study revealed that the alpha diversity indices were highly correlated with water temperature, and the microeukaryotic communities displayed a distinct geographical distance-driven pattern. The predominance of the parasitic dinoflagellate lineage Syndiniales and their close relationship with other microeukaryotic groups suggest that parasitism may be a crucial survival strategy for microeukaryotes in the surface waters of the Pacific Ocean. Our findings expand our understanding of the biodiversity and biogeographical pattern of microeukaryotes and highlight the significance of parasitic Syndiniales in the surface ocean.

Core taxa drive microeukaryotic community stability of a deep subtropical reservoir after complete mixing

Microeukaryotes are key for predicting the change of ecosystem processes in the face of a disturbance. However, their vertical responses to multiple interconnected factors caused by water mixing remain unknown. Here, we conducted a 12-month high-frequency study to compare the impacts of mixing disturbances on microeukaryotic community structure and stability over different depths in a stratified reservoir. We demonstrate that core and satellite microeukaryotic compositions and interactions in surface waters were not resistant to water mixing, but significantly recovered. This was because the water temperature rebounded to the pre-mixing level. Core microeukaryotes maintained community stability in surface waters with high recovery capacity after water mixing. In contrast, the changes in water temperature, chlorophyll-a, and nutrients resulted in steep and prolonged variations in the bottom core and satellite microeukaryotic compositions and interactions. Under low environmental fluctuation, the recovery of microbial communities did not affect nutrient cycling in surface waters. Under high environmental fluctuation, core and satellite microeukaryotic compositions in bottom waters were significantly correlated with the multi-nutrient cycling index. Our findings shed light on different mechanisms of plankton community resilience in reservoir ecosystems to a major disturbance over depths, highlighting the role of bottom microeukaryotes in nutrient cycling.

Integrated Biogeography and Assembly Mechanisms of Microeukaryotic Communities in Coastal Waters Near Shellfish Cultivation

The Lianjiang coast in the East China Sea is a typical subtropical marine ecosystem, and shellfish cultivation occupies almost all of the available tidal flats. Many studies have investigated the effects of shellfish cultivation on benthic organisms and sediments, while the impact of shellfish cultivation on plankton ecosystems is still poorly understood. This study investigated the biogeographical patterns of microeukaryotic communities from Lianjiang coastal waters in four seasons using 18S ribosomal RNA gene amplicon sequencing. Microeukaryotes were mainly comprised of Dinoflagellata, Diatomea, Arthropoda, Ciliophora, Chlorophyta, Protalveolata, Cryptophyceae, and Ochrophyta, and presented significant differences in three habitats (the aquaculture area, confluent area, and offshore area) and four seasons. Similarity percentage analysis revealed that Paracalanus parvus, Heterocapsa rotundata, Bestiolina similis, and five additional key taxa contributed to spatio-temporal differences. Seasonal environmental and spatial factors explained 27.47% of microeukaryotic community variation on average, with 11.11% of the variation shared. Environmental variables, particularly depth, pH, and nitrite concentration, were strongly associated with the microeukaryotic community compositions. The neutral community model further demonstrated that stochastic processes were sufficient in shaping substantial variation in microeukaryotic communities across four seasons, which may reveal the remaining unexplained microeukaryotic community variation. We further divided four seasons into the aquaculture stages and non-aquaculture stages, and speculated that aquaculture activities may increase the dispersal limitation of microeukaryotes in coastal waters, especially for the big bodied-microbes like Arthropoda. The results provide a better understanding of the biogeographical patterns, processes, and mechanisms of microeukaryotic communities near shellfish cultivation.

The photic-aphotic divide is a strong ecological and evolutionary force determining the distribution of ciliates (Alveolata, Ciliophora) in the ocean

The bulk of knowledge on marine ciliates is from shallow and/or sunlit waters. We studied ciliate diversity and distribution across epi- and mesopelagic oceanic waters, using DNA metabarcoding and phylogeny-based metrics. We analyzed sequences of the 18S rRNA gene (V4 region) from 369 samples collected at 12 depths (0-1000 m) at the Bermuda Atlantic Time-series Study site of the Sargasso Sea (North Atlantic) monthly for 3 years. The comprehensive depth and temporal resolutions analyzed led to three main findings. First, there was a gradual but significant decrease in alpha-diversity (based on Faith's phylogenetic diversity index) from surface to 1000-m waters. Second, multivariate analyses of beta-diversity (based on UniFrac distances) indicate that ciliate assemblages change significantly from photic to aphotic waters, with a switch from Oligotrichea to Oligohymenophorea prevalence. Third, phylogenetic placement of sequence variants and clade-level correlations (EPA-ng and GAPPA algorithms) show Oligotrichea, Litostomatea, Prostomatea, and Phyllopharyngea as anti-correlated with depth, while Oligohymenophorea (especially Apostomatia) have a direct relationship with depth. Two enigmatic environmental clades include either prevalent variants widely distributed in aphotic layers (the Oligohymenophorea OLIGO5) or subclades differentially distributed in photic versus aphotic waters (the Discotrichidae NASSO1). These results settle contradictory relationships between ciliate alpha-diversity and depth reported before, suggest functional changes in ciliate assemblages from photic to aphotic waters (with the prevalence of algivory and mixotrophy vs. omnivory and parasitism, respectively), and indicate that contemporary taxon distributions in the vertical profile have been strongly influenced by evolutionary processes. Integration of DNA sequences with organismal data (microscopy, functional experiments) and development of databases that link these sources of information remain as major tasks to better understand ciliate diversity, ecological roles, and evolution in the ocean.

Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series

Community dynamics are central in microbial ecology, yet we lack studies comparing diversity patterns among marine protists and prokaryotes over depth and multiple years. Here, we characterized microbes at the San-Pedro Ocean Time series (2005-2018), using SSU rRNA gene sequencing from two size fractions (0.2-1 and 1-80 μm), with a universal primer set that amplifies from both prokaryotes and eukaryotes, allowing direct comparisons of diversity patterns in a single set of analyses. The 16S + 18S rRNA gene composition in the small size fraction was mostly prokaryotic (>92%) as expected, but the large size fraction unexpectedly contained 46-93% prokaryotic 16S rRNA genes. Prokaryotes and protists showed opposite vertical diversity patterns; prokaryotic diversity peaked at mid-depth, protistan diversity at the surface. Temporal beta-diversity patterns indicated prokaryote communities were much more stable than protists. Although the prokaryotic communities changed monthly, the average community stayed remarkably steady over 14 years, showing high resilience. Additionally, particle-associated prokaryotes were more diverse than smaller free-living ones, especially at deeper depths, contributed unexpectedly by abundant and diverse SAR11 clade II. Eukaryotic diversity was strongly correlated with the diversity of particle-associated prokaryotes but not free-living ones, reflecting that physical associations result in the strongest interactions, including symbioses, parasitism, and decomposer relationships.

CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology

Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). CARD-FISH is commonly applied to study prokaryotes, but less so to microbial eukaryotes. Application of this technique revealed that Paraphysomonas or Spumella-like chrysophytes, considered to be among the most prominent members of protistan communities in pelagic environments, are omnipresent but actually less abundant than expected, in contrast to little known groups such as heterotrophic cryptophyte lineages (e.g., CRY1), cercozoans, katablepharids, or the MAST lineages. Combination of CARD-FISH with tracer techniques and application of double CARD-FISH allow visualization of food vacuole contents of specific flagellate groups, thus considerably challenging our current, simplistic view that they are predominantly bacterivores. Experimental manipulations with natural communities revealed that larger flagellates are actually omnivores ingesting both prokaryotes and other protists. These new findings justify our proposition of an updated model of microbial food webs in pelagic environments, reflecting more authentically the complex trophic interactions and specific roles of flagellated protists, with inclusion of at least two additional trophic levels in the nanoplankton size fraction. Moreover, we provide a detailed CARD-FISH protocol for protists, exemplified on mixo- and heterotrophic nanoplanktonic flagellates, together with tips on probe design, a troubleshooting guide addressing most frequent obstacles, and an exhaustive list of published probes targeting protists.

Structural Characteristics and Driving Factors of the Planktonic Eukaryotic Community in the Danjiangkou Reservoir, China

Planktonic eukaryotes are widespread in aquatic ecosystems, and the study of their community composition and driving factors is of great significance to protecting and maintaining the balance of these ecosystems. This study evaluates five typical ecological sites in the Danjiangkou Reservoir—the water source for the project. This was done to comprehensively understand the composition of Danjiangkou Reservoir planktonic eukaryotes, and ensure the ecological balance of the water source for the South-to-North Water Diversion Project. The diversity of the planktonic eukaryotes in surface water and the factors driving changes in their abundance are analyzed with an 18S ribosomal DNA sequencing approach. Monitoring shows that the Danjiangkou Reservoir has good water quality. The Danjiangkou Reservoir planktonic eukaryote community is mainly composed of 11 phyla, of which Cryptomonadales is dominant, accounting for an average percentage of 65.19% of the community (47.2–84.90%). LEFSe analysis shows significant differences among samples in the abundances of 13 phyla, 20 classes, 23 orders, 26 families, and 27 genera, and there are also significant differences in the diversity of planktonic eukaryotes at different temporal and spatial scales. Redundancy analysis (RDA) show that water temperature, DO, SD, TN, and Chla are significant factors that affect the composition of the planktonic eukaryote community. Spearman rank correlation analysis combined with taxonomic difference analysis shows that Kathablepharidae and Choanoflagellida are not sensitive to environmental or physicochemical factors and that the interannual variations in their abundance are not significant. Network analysis shows that Protalveolata, Basidiomycota, P1-31, Bicosoecida, and Ochrophyta represent important nodes in the single-factor network, while Chytridiomycota, P1-31, Cryptomycota, Ochrophyta, Ichthyosporea, Bicosoecida, Protalveolata, and physicochemical factors (ORP, TN, WT, DO, SD, NH3-N, and NO3-N) represent important nodes in the two-factor network.

Seven-year dynamics of testate amoeba communities driven more by stochastic than deterministic processes in two subtropical reservoirs

Testate amoebae are widely distributed in natural ecosystems and play an important role in the material cycle and energy flow. However, community assembly of testate amoebae is not well understood, especially with regard to the relative importance of the stochastic and deterministic processes over time. In this study, we used Illumina high-throughput sequencing to explore the community assembly of testate amoebae from surface waters in two reservoirs of subtropical China over a seven-year period. Majority of testate amoebae belonged to the rare taxa because their relative abundances were typically lower than 0.01% of the total eukaryotic plankton community. The testate amoeba community dynamics exhibited a stronger interannual than seasonal variation in both reservoirs. Further, species richness, rather than species turnover, accounted for the majority of community variation. Environmental variables explained less than 20% of the variation in community composition of testate amoebae, and the community assembly appeared to be strongly driven by stochastic processes. Based on the Sloan neutral community model, it was found that neutral processes explained more than 65% of community variation. More importantly, the Stegen null model analysis showed that the stochastic processes (e.g., ecological drift) explained a significantly higher percentage of community assembly than deterministic processes over seven years, although deterministic processes were more influential in certain years. Our results provide new perspectives for understanding the ecological patterns, processes and mechanisms of testate amoeba communities in freshwater ecosystems at temporal scale, and have important implications for monitoring plankton diversity and protecting drinking-water resources.

Time series are critical to understand microbial plankton diversity and ecology

How diverse are marine planktonic protist communities? How much seasonality do they exhibit? For a very long time, these two old and challenging questions in the field of plankton ecology could be addressed only for large-size protist species, based on cell counting under the microscope. The recent application of molecular techniques, notably massive marker-gene amplicon sequencing approaches (metabarcoding), has allowed investigating with unprecedented level of resolution the small-sized (<20 µm) planktonic eukaryotes too. An amazing diversity of these tiny organisms has been unveiled but details about their temporal dynamics remain much more elusive. In a From the Cover article in this issue of Molecular Ecology, Giner et al. (2019) introduce a new Recurrence Index (RI) to specifically look for seasonality in time-series metabarcoding data. They inspected the temporal dynamics of all operational taxonomic units (OTUs) in a rich sequence data set of pico- and nanoplanktonic eukaryotes in samples collected monthly during 10 years. Although most OTUs did not show seasonality, some abundant ones did, which explains why some averaging methods can find seasonality at the less detailed level of whole planktonic communities. Not surprisingly, the very complex small-sized eukaryotic plankton communities are composed of organisms with miscellaneous temporal dynamics.

Past President's Address: Protists of the Mesopelagic and a Bit on the Long Path to the Deep Sea

The deep sea has long been a mysterious and attractive habitat for protistologists. However, logistical difficulties severely limit sampling opportunities. Consequently, our knowledge of the protists in the deep sea, (arguably the largest habitat on earth), is relatively sparse. Here, we present a unique time-series concerning three different protist taxa that share only the characteristics of being relatively large, robust to sampling, and easily identifiable to species level using light microscopy: tintinnid ciliates, phaeogromid cercozoans (e.g. Challengerids) and amphisolenid dinoflagellates. We sampled a near-shore deep water site in the N.W. Mediterranean Sea at 250 m depth over a 2-yr period at approximately weekly intervals from January 2017 to December 2018. To our knowledge, no previous studies have employed sampling on a similar time scale. We found taxa that appear to be restricted to deep waters, distinct seasonal patterns of abundance in some taxa, and in others nonseasonal successional patterns. Based on data from sampling following a flash flood event, the Challengerid population appeared to respond positively to a pulse of terrigenous input. Some of the distinct mesopelagic tintinnid ciliates and amphisolinid dinoflagellates were also found in two samples from the North Atlantic mesopelagic gathered from near the Azores Islands in September 2018. We conclude that there are a variety of protist taxa endemic to the mesopelagic, that the populations are dynamic, and they may be widely distributed in the deep waters of the world ocean.

Integrated Space-Time Dataset Reveals High Diversity and Distinct Community Structure of Ciliates in Mesopelagic Waters of the Northern South China Sea

Little is known about diversity distribution and community structure of ciliates in mesopelagic waters, especially how they are related to spatial and temporal changes. Here, an integrative approach, combining high-throughput cDNA sequencing and quantitative protargol stain, was used to analyze ciliate communities collected temporally along a transect from coastal to oceanic regions at depths ranging from the surface to 1000 m. The mesopelagic zone exhibited comparable alpha diversity to surface water which was consistent over temporal variation, with high diversity occurring at the interface with the euphotic zone. Comparison with the northeastern and the western Pacific Ocean revealed consistency of this vertical distribution of ciliates across oceanic basins. Mesopelagic ciliates harbored distinct community structure without significant seasonal differences, with the vertical variations driven largely by members of the classes Spirotrichea and Oligohymenophorea. Operational taxonomic units (OTUs) affiliated with Scuticociliatia, Astomatida and Apostomatida, members of which are known to be bacterivorous and/or commensal/parasitic species, were more abundant in mesopelagic waters than above, implying they are an important component of food webs in the mesopelagic zone. A combination of depth, geographic distance and environment shaped the ciliate communities, with depth being the most influential factor. Phylogenetic null modeling analysis further indicated that 57.1 and 33.3% of mesopelagic community variation was governed by dispersal limitation and heterogeneous selection, respectively, probably due to the marked biochemical and physical gradients down the water column. This suggests that ciliate community structure in the mesopelagic zone is mainly controlled by stochastic processes. Collectively, this study reports mesopelagic ciliates exhibited high diversity and distinct community structure across spatiotemporal scales and informs the processes mediating ciliate assembly in the mesopelagic zone. These should be fully considered in future studies to build a more comprehensive understanding of mesopelagic microbial assemblages.

Long-term seasonal and interannual variability of marine aerobic anoxygenic photoheterotrophic bacteria

We studied the long-term temporal dynamics of the aerobic anoxygenic phototrophic (AAP) bacteria, a relevant functional group in the coastal marine microbial food web, using high-throughput sequencing of the pufM gene coupled with multivariate, time series and co-occurrence analyses at the Blanes Bay Microbial Observatory (NW Mediterranean). Additionally, using metagenomics, we tested whether the used primers captured accurately the seasonality of the most relevant AAP groups. Phylogroup K (Gammaproteobacteria) was the greatest contributor to community structure over all seasons, with phylogroups E and G (Alphaproteobacteria) being prevalent in spring. Diversity indices showed a clear seasonal trend, with maximum values in winter, which was inverse to that of AAP abundance. Multivariate analyses revealed sample clustering by season, with a relevant proportion of the variance explained by day length, temperature, salinity, phototrophic nanoflagellate abundance, chlorophyll a, and silicate concentration. Time series analysis showed robust rhythmic patterns of co-occurrence, but distinct seasonal behaviors within the same phylogroup, and even within different amplicon sequence variants (ASVs) conforming the same operational taxonomic unit (OTU). Altogether, our results picture the AAP assemblage as highly seasonal and recurrent but containing ecotypes showing distinctive temporal niche partitioning, rather than being a cohesive functional group.

Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations

Seasonality in marine microorganisms has been classically observed in phytoplankton blooms, and more recently studied at the community level in prokaryotes, but rarely investigated at the scale of individual microbial taxa. Here we test if specific marine eukaryotic phytoplankton, bacterial and archaeal taxa display yearly rhythms at a coastal site impacted by irregular environmental perturbations. Our seven-year study in the Bay of Banyuls (North Western Mediterranean Sea) shows that despite some fluctuating environmental conditions, many microbial taxa displayed significant yearly rhythms. The robust rhythmicity was found in both autotrophs (picoeukaryotes and cyanobacteria) and heterotrophic prokaryotes. Sporadic meteorological events and irregular nutrient supplies did, however, trigger the appearance of less common non-rhythmic taxa. Among the environmental parameters that were measured, the main drivers of rhythmicity were temperature and day length. Seasonal autotrophs may thus be setting the pace for rhythmic heterotrophs. Similar environmental niches may be driving seasonality as well. The observed strong association between Micromonas and SAR11, which both need thiamine precursors for growth, could be a first indication that shared nutritional niches may explain some rhythmic patterns of co-occurrence.

Microeukaryotic biogeography in the typical subtropical coastal waters with multiple environmental gradients

The determinants of microeukaryotic biogeography in coastal waters at a regional scale remain largely unclear. The coastal northern Zhejiang (in the East China Sea) is a typical subtropical marine ecosystem with multiple environmental gradients that has been extensively perturbed by anthropogenic activities. Thus, it is a valuable region to investigate the key drivers that shape microbial biogeography. We investigated microeukaryotic communities in surface waters from 115 stations in this region using 18S ribosomal RNA gene amplicon sequencing. The microeukaryotic communities were mainly comprised of Dinoflagellata, Ciliophora, Protalveolata, Rhizaria, Stramenopiles and Cryptophyceae. The top abundant operational taxonomic units (OTUs) were highly specific for distinct habitat types, exhibiting significant environment-conditioned features; however, the cosmopolitan OTUs were not strongly correlated with the measured environmental variables. Total phosphorus and suspended particles were major environmental determinants of microeukaryotic α-diversity. Environmental variables, particularly temperature, salinity, pH and silicate concentration, were strongly associated with the microeukaryotic community composition. Overall, environmental and spatial factors explained 55.92% of community variation in total with 34.03% of the variation shared, suggesting that spatially structured environmental variations mainly conditioned the microeukaryotic biogeography in this region. Additionally, dispersal limitation, as indicated by the great pure spatial effect and distance-decay pattern, was another important factor. In summary, our results reveal that spatially structured environmental variation and dispersal limitation mainly conditioned the microeukaryotic biogeography. The results may provide useful distribution patterns of microeukaryotes to determine sources of microbes from marine ecosystems that may facilitate the utilization of coastal resources.

Short-term dynamics and interactions of marine protist communities during the spring-summer transition

We examined the short-term variability, by daily to weekly sampling, of protist assemblages from March to July in surface water of the San Pedro Ocean Time-series station (eastern North Pacific), by V4 Illumina sequencing of the 18S rRNA gene. The sampling period encompassed a spring bloom followed by progression to summer conditions. Several protistan taxa displayed sharp increases and declines, with whole community Bray-Curtis dissimilarities of adjacent days being 66% in March and 40% in May. High initial abundance of parasitic Cercozoa Cryothecomonas longipes and Protaspis grandis coincided with a precipitous decline of blooming Pseudo-nitzschia diatoms, possibly suggesting their massive infection by these parasites; these cercozoans were hardly detectable afterwards. Canonical correspondence analysis indicated a limited predictability of community variability from environmental factors. This indicates that other factors are relevant in explaining changes in protist community composition at short temporal scales, such as interspecific relationships, stochastic processes, mixing with adjacent water, or advection of patches with different protist communities. Association network analysis revealed that interactions between the many parasitic OTUs and other taxa were overwhelmingly positive and suggest that although sometimes parasites may cause a crash of host populations, they may often follow their hosts and do not regularly cause enough mortality to potentially create negative correlations at the daily to weekly time scales we studied.

Distribution of Abundant and Active Planktonic Ciliates in Coastal and Slope Waters Off New England

Despite their important role of linking microbial and classic marine food webs, data on biogeographical patterns of microbial eukaryotic grazers are limited, and even fewer studies have used molecular tools to assess active (i.e., those expressing genes) community members. Marine ciliate diversity is believed to be greatest at the chlorophyll maximum, where there is an abundance of autotrophic prey, and is often assumed to decline with depth. Here, we assess the abundant (DNA) and active (RNA) marine ciliate communities throughout the water column at two stations off the New England coast (Northwest Atlantic)—a coastal station 43 km from shore (40 m depth) and a slope station 135 km off shore (1,000 m). We analyze ciliate communities using a DNA fingerprinting technique, Denaturing Gradient Gel Electrophoresis (DGGE), which captures patterns of abundant community members. We compare estimates of ciliate communities from SSU-rDNA (abundant) and SSU-rRNA (active) and find complex patterns throughout the water column, including many active lineages below the photic zone. Our analyses reveal (1) a number of widely-distributed taxa that are both abundant and active; (2) considerable heterogeneity in patterns of presence/absence of taxa in offshore samples taken 50 m apart throughout the water column; and (3) three distinct ciliate assemblages based on position from shore and depth. Analysis of active (RNA) taxa uncovers biodiversity hidden to traditional DNA-based approaches (e.g., clone library, rDNA amplicon studies).

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.

Marked seasonality and high spatial variability of protist communities in shallow freshwater systems

Small eukaryotes have key roles in aquatic ecosystems, influencing their local environment, global biogeochemical cycles and climate. Their impact depends on community structure, which varies along time. However, very few studies take into account temporal variation. This is especially true for small, shallow freshwater systems, which remain largely understudied despite their wide variety, global surface and intense microbial activity. We have monthly followed changes in the community structure of small microbial eukaryotes (0.2-5 μm cell diameter) for 2 years in four ponds and one brook located in North-Western France based on massive 18S rDNA amplicon 454 pyrosequencing. We detected a total of 3742 stringently defined operational taxonomic units (OTUs) encompassing all recognized eukaryotic supergroups and lineages of uncertain affiliation. Although geographically close, protist communities in the five ecosystems were contrasting, with very few shared OTUs, suggesting that environmental selection mainly drives community structure. The temporal dynamics of different high-rank taxa appeared complex and rapid at monthly scales. Despite this, a clear and reproducible seasonality was observed. As expected, low-abundance OTUs dominated the community. Although some of them appeared sporadically or remained at low frequencies during the survey, others occasionally reached relatively high abundances, sometimes recurrently. This shows that at least a fraction of low-abundance eukaryotes constitutes a seed bank. The annual proportion of primary producers, free-living heterotrophs and parasites appeared remarkably constant among the different ecosystems, suggesting underlying trends of ecosystem carrying capacity for these functional groups.

Patterns of rare and abundant marine microbial eukaryotes

BACKGROUND

Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions.

RESULTS

Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change.

CONCLUSIONS

We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time.