Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing

Revealing the intricate temporal dynamics and adaptive responses of prokaryotic and eukaryotic microbes in the coastal South China Sea

This comprehensive two-year investigation in the coastal South China Sea has advanced our understanding of marine microbes at both community and genomic levels. By combining metagenomics and metatranscriptomics, we have revealed the intricate temporal dynamics and remarkable adaptability of microbial communities and phytoplankton metagenome-assembled genomes (MAGs) in response to environmental fluctuations. We observed distinct seasonal shifts in microbial community composition and function: cyanobacteria were predominant during warmer months, whereas photosynthetic protists were more abundant during colder seasons. Notably, metabolic marker KOs of photosynthesis were consistently active throughout the year, underscoring the persistent role of these processes irrespective of seasonal changes. Our analysis reveals that environmental parameters such as temperature, salinity, and nitrate concentrations profoundly influence microbial community composition, while temperature and silicate have emerged as crucial factors shaping their functional traits. Through the recovery and analysis of 37 phytoplankton MAGs, encompassing nine prokaryotic cyanobacteria and 28 eukaryotic protists from diverse phyla, we have gained insights into their genetic diversity and metabolic capabilities. Distinct profiles of photosynthesis-related pathways including carbon fixation, carotenoid biosynthesis, photosynthesis-antenna proteins, and photosynthesis among the MAGs indicated their genetic adaptations to changing environmental conditions. This study not only enhances our understanding of microbial dynamics in coastal marine ecosystems but also sheds light on the ecological roles and adaptive responses of different microbial groups to environmental changes.

Strong seasonality and unsuspected diversity of haptophytes explored by metabarcoding analysis in the Chinese seas

The haptophytes, are essential components of the marine pico- and nano-plankton but little is known about their diversity and abundance due to the small size. In this study, the taxonomic composition, geographical distribution, and seasonal variation of the haptophytes in the Bohai Sea, the Yellow Sea, and the East China Sea were investigated using DNA metabarcoding in April and October of 2021. A total of 623 and 3756 haptophyte amplicon sequence variants (ASVs) were obtained in spring and autumn, respectively. All currently described or detected haptophyte orders were retrieved, including several deep-branching novel environmental lineages with relative high abundance. The predominant groups were Chrysochromulina, Clade HAP 2-3-4-5, Phaeocystis, and Prymnesium in spring, and Chrysochromulina, Phaeocystis, and Emiliania/Gephyrocapsa compelx in autumn. The richness and diversity showed seasonal variation, with higher alpha diversity occurred in autumn than that of spring. Different haptophyte taxa exhibited unique spatial distribution patterns and water temperature was significantly correlated with the observed community dissimilarities and was the most influential driving factor in both seasons. Our results highlight the high hidden diversity and seasonal variations of haptophytes in the Chinese seas.

Optimal growth conditions of the haptophyte Chrysochromulina leadbeateri causing massive fish mortality in Northern Norway

The haptophyte Chrysochromulina leadbeateri formed the most devastating fish-killing algal bloom ever recorded in Norway, in May and June 2019. The bloom resulted in the death of 14,500 tons of farmed salmon in Nordland and Troms Counties and large economic losses to the aquaculture industry in the region. Fish mortalities due to blooms of this species have occurred before in this region in 1991. Environmental conditions promoting bloom formation and growth of C. leadbeateri are, however, still poorly understood. Here we investigated growth as a function of temperature, salinity and irradiance in combinations using a high throughput experimental set-up. Three strains of C. leadbeateri isolated from the 2019 event and an earlier bloom in 1991 were examined. The highest maximal specific growth rate was found at salinities 28-30 and temperatures between 13 and 15 °C, with growth rate generally increasing with irradiance. The upper temperature tolerance for growth for all strains was at 17-19 °C. Further, analyses of the geographical distribution of C. leadbeateri in previous DNA-based studies compiled in the metaPR2 database revealed several ribotypes, and that a cold-water ribotype of C. leadbeateri caused both the 1991 and 2019 blooms.

Diversity and seasonal occurrence of haptophyta in northern South China Sea through size-fractionated metabarcoding

Haptophyta plays a key role in marine pico-nanoeukaryote communities but information on their diversity and ecology is extremely limited. A total of 103 water samples were collected in northern South China Sea to assess the diversity of haptophyta through metabarcoding targeting 18S V4 rDNA. Furthermore, we investigated the potential genetic differentiation among seasonal occurring Phaeocystis globosa using the high resolution molecular marker pgcp1. 18S V4 rDNA metabarcoding dataset revealed 41 species of haptophytes, with 16 of them as the first record in this region. Notably, six harmful species were detected, including Chrysochromulina leadbeateri, Phaeocystis globosa, and Prymnesium parvum. The pgcp1 marker revealed two clades of Phaeocystis globosa and both of them were present around the year. Clade I was found to predominate in warm season, while Clade III tended to bloom in cold waters. Our results highlight the risk potential of harmful haptophytes in the northern South China Sea.

Group 2i Isochrysidales thrive in marine and lacustrine systems with ice cover

Global warming is causing rapid changes to the cryosphere. Predicting the future trajectory of the cryosphere requires quantitative reconstruction of its past variations. A recently identified sea-ice-associated haptophyte, known as Group 2i Isochrysidales, has given rise to a new sea-ice proxy with its characteristic alkenone distributions. However, apart from the occurrence of Group 2i Isochrysidales in regions with sea ice, and the empirical relationship between C37:4 alkenone abundance and sea-ice concentration, little is known about the ecology of these haptophyte species. Here, we systematically mapped the spatial and temporal occurrence of known Group 2i Isochrysidales based on environmental DNA in both marine and lacustrine environments. Our results indicate Group 2i is widely distributed in icy marine and lacustrine environments in both Northern and Southern Hemisphere, but is absent in warm environments. Temporally, Group 2i is part of the sea-ice algae bloom during the cold seasons, in contrast to other Isochrysidales that bloom in open waters during warm seasons. Our results indicate that ice is a prerequisite for the occurrence of the psychrophilic Group 2i haptophytes in marine and lacustrine ecosystems and further affirms its value for past ice reconstructions.

A review: Marine aquaculture impacts marine microbial communities

Marine aquaculture is key for protein production but disrupts marine ecosystems by releasing excess feed and pharmaceuticals, thus affecting marine microbes. Though vital, its environmental impact often remains overlooked. This article delves into mariculture's effects on marine microbes, including bacteria, fungi, viruses, and antibiotic-resistance genes in seawater and sediments. It highlights how different mariculture practices-open, pond, and cage culture-affect these microbial communities. Mariculture's release of nutrients, antibiotics, and heavy metals alters the microbial composition, diversity, and functions. Integrated multi-trophic aquaculture, a promising sustainable approach, is still developing and needs refinement. A deep understanding of mariculture's impact on microbial ecosystems is crucial to minimize pollution and foster sustainable practices, paving the way for the industry's sustainable advancement.

Functional and structural responses of plankton communities toward consecutive experimental heatwaves in Mediterranean coastal waters

The frequency of marine heatwaves (HWs) is projected to increase in the Mediterranean Sea over the next decades. An in situ mesocosm experiment was performed in a Mediterranean lagoon for 33 days. Three mesocosms were used as controls following the natural temperature of the lagoon. In three others, two HWs of + 5 °C compared to the controls were applied from experimental day (d) 1 to d5 (HW1) and from d11 to d15 (HW2). High-frequency data of oxygen, chlorophyll-a (chl-a), temperature, salinity and light from sensors immersed in all mesocosms were used to calculate gross primary production (GPP), respiration (R) and phytoplankton growth (µ) and loss (L) rates. Nutrients and phytoplankton community structure from pigments were also analyzed. HW1 significantly increased GPP, R, chl-a, µ and L by 7 to 38%. HW2 shifted the system toward heterotrophy by only enhancing R. Thus, the effects of the first HW resulted in the attenuation of those of a second HW on phytoplankton processes, but not on community respiration, which was strongly regulated by temperature. In addition, natural phytoplankton succession from diatoms to haptophytes was altered by both HWs as cyanobacteria and chlorophytes were favored at the expense of haptophytes. These results indicate that HWs have pronounced effects on Mediterranean plankton communities.

Biodiversity and Interannual Variation of Harmful Algal Bloom Species in the Coastal Sea of Qinhuangdao, China

For the frequent occurrence of harmful algal blooms (HABs) in the Qinhuangdao coastal sea (QCS) of the Bohai Sea in summer, we tested the hypothesis that high-biodiversity HAB species exist in the area, and a series of censuses of HAB species were conducted in the QCS in the summers of 2014-2019. Through morphological identification, we found 100 algae species representing 42 genera in 3 phytoplankton phyla in this study, among which Bacillariophyta was the most dominant phylum. We also found that the population density of Dinoflagellata increased from 2016 to 2019. In total, 59 HAB species were annotated in this study, including 39 of Bacillariophyta, 18 of Dinoflagellata and 2 of Ochrophyta, of which 13 HAB species were reported in the Bohai Sea for the first time, and most HAB species were widely distributed in the QCS in summer. Notably, four dominant HAB species displayed unique temporal and spatial distribution characteristics, while their distribution ranges and population densities increased from 2014 to 2019. The distributions of five environmental factors were different in the QCS, while the temperature, salinity, and dissolved inorganic nitrogen might be the key environmental factors influencing the distribution of dominant HAB species in the summer. In conclusion, this study provides a detailed evaluation of phytoplankton diversity and interannual variation in the QCS. The existence of a high level of biodiversity of algal bloom species suggests the need for long-term monitoring in order to further study and prevent potential HABs.

Haptophyte communities along the Kuroshio current reveal their geographical sources and ecological traits

Haptophytes are one of the most ecologically successful phytoplankton groups in the modern ocean and tend to maintain balanced and stable communities across various environments. However, little is known about the mechanisms that enable community stability and ecological success. To reveal the community characteristics and interactions among haptophytes, we conducted comprehensive observations from the upstream to downstream regions of the Kuroshio Current. Haptophyte abundance and taxonomy were assessed using quantitative polymerase chain reaction and metabarcoding of 18S rRNA sequences, respectively. The haptophyte community structure changed abruptly at sites on the shelf-slope of the East China Sea, indicating the strong influence of shelf waters with high phytoplankton biomass on downstream communities. Correlation network analysis combined with the phylogeny suggested that haptophytes can coexist with their close relatives, possibly owing to their nutritional flexibility, thereby escaping from resource competition. Consistently, some noncalcifying haptophyte genera with high mixotrophic capacities such as Chrysochromulina constituted a major component of the co-occurrence network, whereas coccolithophores such as Emiliania/Gephyrocapsa were rarely observed. Our study findings suggest that noncalcifying haptophytes play crucial roles in community diversity and stability, and in sustaining the food web structure in the Kuroshio ecosystems.

Changes in phytoplankton community structure over a century in relation to environmental factors

Changes in phytoplankton abundance and biomass during the period 1933-2020 were examined by statistical modeling using data from the Inner Oslofjorden phytoplankton database. The phytoplankton abundances increased with eutrophication from 1930s to 1970s, but with the implementation of sewage cleaning measures and a resulting reduction in nutrient releases, the phytoplankton abundance has since then decreased significantly. The onset of the seasonal blooms has started progressively later during the last 15 years, especially the spring bloom. The delayed spring bloom co-occurred with increasing temperature in winter and spring. The diatom biomass decreased more than that of dinoflagellates and other microeukaryotes. The diatom genus Skeletonema dominated the spring bloom and was found to be the key taxa in explaining these changes in abundance and phenology. Extensive summer blooms of the coccolithophore Emiliania huxleyi, which has been characteristic for the inner Oslofjorden, has also gradually decreased during the last decades, along with reducing eutrophication. Dinoflagellates have not had the same reduction in abundance as the other groups. Despite an increasing proportion of dinoflagellates compared with other taxa, there are no clear indications of increased occurrence of toxic algal blooms in inner Oslofjorden. However, the introduction of new "toxin-producing" species may cause concern.

Spatial and biological oceanographic insights into the massive fish-killing bloom of the haptophyte Chrysochromulina leadbeateri in northern Norway

A bloom of the fish-killing haptophyte Chrysochromulina leadbeateri in northern Norway during May and June 2019 was the most harmful algal event ever recorded in the region, causing massive mortalities of farmed salmon. Accordingly, oceanographic and biodiversity aspects of the bloom were studied in unprecedented detail, based on metabarcoding and physico-chemical and biotic factors related with the dynamics and distribution of the bloom. Light- and electron-microscopical observations of nanoplankton samples from diverse locations confirmed that C. leadbeateri was dominant in the bloom and the primary cause of associated fish mortalities. Cell counts by light microscopy and flow cytometry were obtained throughout the regional bloom within and adjacent to five fjord systems. Metabarcoding sequences of the V4 region of the 18S rRNA gene from field material collected during the bloom and a cultured isolate from offshore of Tromsøy island confirmed the species identification. Sequences from three genetic markers (18S, 28S rRNA gene and ITS region) verified the close if not identical genetic similarity to C. leadbeateri from a previous massive fish-killing bloom in 1991 in northern Norway. The distribution and cell abundance of C. leadbeateri and related Chrysochromulina species in the recent incident were tracked by integrating observations from metabarcoding sequences of the V4 region of the 18S rRNA gene. Metabarcoding revealed at least 14 distinct Chrysochromulina variants, including putative cryptic species. C. leadbeateri was by far the most abundant of these species, but with high intraspecific genetic variability. Highest cell abundance of up to 2.7 × 10⁷ cells L ^- 1 of C. leadbeateri was found in Balsfjorden; the high cell densities were associated with stratification near the pycnocline (at ca. 12 m depth) within the fjord. The cell abundance of C. leadbeateri showed positive correlations with temperature, negative correlation with salinity, and a slightly positive correlation with ambient phosphate and nitrate concentrations. The spatio-temporal succession of the C. leadbeateri bloom suggests independent initiation from existing pre-bloom populations in local zones, perhaps sustained and supplemented over time by northeastward advection of the bloom from the fjords.

Cultivation of different seaweed species and seasonal changes cause divergence of the microbial community in coastal seawaters

Although the effects of certain species of seaweed on the microbial community structure have long been a research focus in marine ecology, the response of the microbial community to seasons and different seaweed species is poorly understood. In the present study, a total of 39 seawater samples were collected during 3 months from three zones: Neoporphyra haitanensis cultivation zones (P), Gracilaria lemaneiformis-Saccharina japonica mixed cultivation zones (G), and control zones (C). These samples were then analyzed using 18S and 16S rRNA gene sequencing to ascertain the fungal and bacterial communities, respectively, along with the determination of environmental factors. Our results showed that increased dissolved oxygen (DO), decreased inorganic nutrients, and released dissolved organic matter (DOM) in seaweed cultivation zone predominantly altered the variability of eukaryotic and prokaryotic microbial communities. Certain microbial groups such as Aurantivirga, Pseudomonas, and Woeseia were stimulated and enriched in response to seaweed cultivation, and the enriched microorganisms varied across seaweed cultivation zones due to differences in the composition of released DOM. In addition, seasonal changes in salinity and temperature were strongly correlated with microbial community composition and structure. Our study provides new insights into the interactions between seaweed and microbial communities.

Metabarcoding of harmful algal bloom species in sediments from four coastal areas of the southeast China

In the past three decades, harmful algal blooms (HAB) have become more frequent and widespread in southeast Chinese sea areas. Resting stages are regarded as the "seed bank" of algal blooms, and play an important role in initiating HABs. The distribution of resting stages in sediments especially those of HAB species can make good predictions about the potential risk of future blooms, however with limited reports. In this study, surface sediment samples were collected in the four sea areas along the southeast Chinese coasts, including Dafeng Port (DF) in the southern Yellow Sea, Xiangshan Bay (XS), Funing Bay (FN), and Dongshan Bay (DS) in the East China Sea. Diversity and community structure of eukaryotic microalgae in surface sediments were assessed by metabarcoding V4 region of the 18S rDNA, focusing on the distribution of HAB species. Biogenic elements including total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP), biogenic silicon (BSi), and moisture content (MC) were analyzed. A total of 454 eukaryotic algal OTUs were detected, which belonged to 31 classes of 9 phyla. Altogether 149 algal species were detected in this study, and 59 taxa have been reported to form resting stages. Eukaryotic algal community was similar in XS, FN and DS of the East China Sea, which were predominated by dinoflagellates. However, algal community was different in DF of the Yellow Sea, and characterized by the dominance of chrysophytes and low OTU richness. The distribution of most abundant HAB species showed positive correlations with TN, BSi, and TOC, suggesting that eutrophication and consequent increase in diatom productivity may have a significant influence on the distribution of HAB species and facilitate the occurrence of HABs. Furthermore, HAB species occurred more abundantly and widely in FN. Our results suggest high potential risks of HABs in the southeast Chinese coast especially in Funing Bay.

Fine-scale differences in eukaryotic communities inside and outside salmon aquaculture cages revealed by eDNA metabarcoding

Aquaculture impacts on marine benthic ecosystems are widely recognized and monitored. However, little is known about the community changes occurring in the water masses surrounding aquaculture sites. In the present study, we studied the eukaryotic communities inside and outside salmonid aquaculture cages through time to assess the community changes in the neighbouring waters of the farm. Water samples were taken biweekly over five months during the production phase from inside the cages and from nearby points located North and South of the salmon farm. Eukaryotic communities were analyzed by eDNA metabarcoding of the partial COI Leray-XT fragment. The results showed that eukaryotic communities inside the cages were significantly different from those in the outside environment, with communities inside the cages having higher diversity values and more indicator species associated with them. This is likely explained by the appearance of fouling species that colonize the artificial structures, but also by other species that are attracted to the cages by other means. Moreover, these effects were highly localized inside the cages, as the communities identified outside the cages, both North and South, had very similar eukaryotic composition at each point in time. Overall, the eukaryotic communities, both inside and outside the cages, showed similar temporal fluctuations through the summer months, with diversity peaks occurring at the end of July, beginning of September, and in the beginning of November, with the latter showing the highest Shannon diversity and richness values. Hence, our study suggests that seasonality, together with salmonid aquaculture, are the main drivers of eukaryotic community structure in surface waters surrounding the farm.

Seasonal dynamics of marine protist communities in tidally mixed coastal waters

Major seasonal community reorganizations and associated biomass variations are landmarks of plankton ecology. However, the processes of plankton community turnover rates have not been fully elucidated so far. Here, we analyse patterns of planktonic protist community succession in temperate latitudes, based on quantitative taxonomic data from both microscopy counts (cells >10 μm) and ribosomal DNA metabarcoding (size fraction >3 μm, 18S rRNA gene) from plankton samples collected bimonthly over 8 years (2009–2016) at the SOMLIT‐Astan station (Roscoff, Western English Channel). Based on morphology, diatoms were clearly the dominating group all year round and over the study period. Metabarcoding uncovered a wider diversity spectrum and revealed the prevalence of Dinophyceae and diatoms but also of Cryptophyta, Chlorophyta, Cercozoa, Syndiniales and Ciliophora in terms of read counts and or richness. The use of morphological and molecular analyses in combination allowed improving the taxonomic resolution and to identify the sequence of the dominant species and OTUs (18S V4 rDNA‐derived taxa) that drive annual plankton successions. We detected that some of these dominant OTUs were benthic as a result of the intense tidal mixing typical of the French coasts in the English Channel. Our analysis of the temporal structure of community changes point to a strong seasonality and resilience. The temporal structure of environmental variables (especially Photosynthetic Active Radiation, temperature and macronutrients) and temporal structures generated by species life cycles and or species interactions, are key drivers of the observed cyclic annual plankton turnover.

Comparing PCR-generated artifacts of different polymerases for improved accuracy of DNA metabarcoding

Accuracy of PCR amplification is vital for obtaining reliable amplicon-sequencing results by metabarcoding. Here, we performed a comparative analysis of error profiles in the PCR products by 14 different PCR kits using a mock eukaryotic community DNA sample mimicking metabarcoding analysis. To prepare a mock eukaryotic community from the marine environment, equal amounts of plasmid DNA from 40 microalgal species were mixed and used for amplicon-sequencing by a high-throughput sequencing approach. To compare the differences in PCR kits used for this experiment, we focused on the following seven parameters: 1) Quality, 2) Chimera, 3) Blast top hit accuracy, 4) Deletion, 5) Insertion, 6) Base substitution and 7) Amplification bias amongst species. The results showed statistically significant differences (p < 0.05) for all of the seven parameters depending on the PCR kits used. These differences may result from the different DNA polymerases included in each kit, although the result can also be influenced by PCR reaction conditions. Simultaneous analysis of several parameters suggested that kits containing KOD plus Neo (TOYOBO) and HotStart Taq DNA polymerase (BiONEER, CA, US) at the annealing temperature of 65 °C displayed better results in terms of parameters associated with chimeras, top hit similarity and deletions.

Adaptive evolution of viruses infecting marine microalgae (haptophytes), from acute infections to stable coexistence

Collectively known as phytoplankton, photosynthetic microbes form the base of the marine food web, and account for up to half of the primary production on Earth. Haptophytes are key components of this phytoplankton community, playing important roles both as primary producers and as mixotrophs that graze on bacteria and protists. Viruses influence the ecology and diversity of phytoplankton in the ocean, with the majority of microalgae-virus interactions described as 'boom and bust' dynamics, which are characteristic of acute virus-host systems. Most haptophytes are, however, part of highly diverse communities and occur at low densities, decreasing their chance of being infected by viruses with high host specificity. Viruses infecting these microalgae have been isolated in the laboratory, and there are several characteristics that distinguish them from acute viruses infecting bloom-forming haptophytes. Herein we synthesise what is known of viruses infecting haptophyte hosts in the ocean, discuss the adaptive evolution of haptophyte-infecting viruses -from those that cause acute infections to those that stably coexist with their host - and identify traits of importance for successful survival in the ocean.

The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae

Haptophytes are biogeochemically and industrially important protists with underexplored genomic diversity. We present a nuclear genome assembly for the class Pavlovales, which was assembled with PacBio long-read data into highly contiguous sequences. We sequenced strain Diacronema lutheri NIVA-4/92, formerly known as Pavlova lutheri, because it has established roles in aquaculture and has been a key organism for studying microalgal lipid biosynthesis. Our data show that D. lutheri has the smallest and most streamlined haptophycean genome assembled to date, with an assembly size of 43.503 Mb and 14,446 protein-coding genes. Together with its high nuclear GC content, Diacronema is an important genus for investigating selective pressures on haptophyte genome evolution, contrasting with the much larger and more repetitive genome of the coccolithophore Emiliania huxleyi. The D. lutheri genome will be a valuable resource for resolving the genetic basis of algal lipid biosynthesis and metabolic remodeling that takes place during adaptation and stress response in natural and engineered environments.

Diverse harmful microalgal community assemblages in the Johor Strait and the environmental effects on its community dynamics

Coastal ecosystems are often subjected to anthropogenic disturbances that lead to water quality deterioration and an increase in harmful algal bloom (HAB) events. Using the next-generation molecular tool of 18S rDNA metabarcoding, we examined the community assemblages of HAB species in the Johor Strait, Malaysia between May 2018 and September 2019, covering 19 stations across the strait. The molecular operational taxonomic units (OTUs) of HAB taxa retrieved from the dataset (n = 194) revealed a much higher number of HAB taxa (26 OTUs) than before, with 12 taxa belong to new records in the strait. As revealed in the findings of this study, the diversity and community structure of HAB taxa varied significantly over time and space. The most common and abundant HAB taxa in the strait (frequency of occurrence >70%) comprised Heterosigma akashiwo, Fibrocapsa japonica, Pseudo-nitzschia pungens, Dinophysis spp., Gymnodinium catenatum, Alexandrium leei, and A. tamiyavanichii. Also, our results demonstrated that the HAB community assemblages in the strait were dependent on the interplay of environmental variables that influence by the monsoonal effects. Different HAB taxa, constitute various functional types, occupied and prevailed in different environmental niches across space and time, leading to diverse community assemblages and population density. This study adds to the current understandings of HAB dynamics and provides a robust overview of temporal-spatial changes in HAB community assemblages along the environmental gradients in a tropical eutrophic coastal ecosystem.

High genetic diversity of the harmful algal bloom species Phaeocystis globosa revealed using the molecular marker COX1

Accumulating evidence indicates that the haptophyte species Phaeocystis globosa, which plays an important role in climate control and may cause harmful algal blooms (HABs), displays a rich genetic diversity that may be responsible for differences in colonial sizes, different toxicity during blooms, and differential optimum growth temperature. In this project, we demonstrated that COX1 can be used as an effective molecular marker for its low intra-genome variations and high resolution in differentiating different P. globosa strains. Analyzing 57 P. globosa strains and seven field samples revealed high P. globosa genetic diversity with at least seven distinct clades. This study not only demonstrated for the first time that the common molecular marker COX1 can be used for differentiating P. globosa strains with high-resolution, and for tracking dynamics of different P. globosa strains during bloom development, but also revealed that P. globosa had high genetic diversity in the field.

Molecular characterization of harmful algal blooms in the Bohai Sea using metabarcoding analysis

Although the occurrences of harmful algal blooms (HABs) have been intensifying, many HABs in coastal waters may have been neglected despite their damaging impact directly on ecology and indirectly on human and animal health. The current detection of HABs depends primarily on the water coloration, chlorophyll intensity, cell density, and mortality due to HAB toxicity. Such methods may not be adequately sensitive to detecting HABs that are relatively transient or small scale. The Bohai Sea is the largest inlet of the Yellow Sea located on the northeast coast of China and famous for shipping and marine aquacultures. HABs frequently occur in the Bohai Sea. In this study, we explored the composition, diversity, and distribution of HAB species using the metabarcoding approach. Through sequencing and the analyzing the 18S rDNA V4 region of 15 samples collected from spatially isolated sites in the Bohai Sea during an expedition in the summer of 2019, we identified 74 potential HAB species including 34 that had not been reported in the Bohai Sea in previous studies. This project provided a detailed analysis of phytoplankton composition, and molecular detection of HAB species in the Bohai Sea. In particular, these analyses revealed extremely high relative abundances of the ichthyotoxic phytoplankton species Vicicitus globosus (Dictyochophyceae) at multiple adjacent sampling sites in the Bohai Bay, which were close to the Yellow River Estuary during the expedition. The results revealed the occurrence of a potential HAB event that would be otherwise undetected using conventional methods, highlighting the sensitivity and power of metabarcoding analysis in detecting HABs and HAB species. This research suggested the value for routine and long-term monitoring of HAB species as an approach for monitoring HABs.

A persistent giant algal virus, with a unique morphology, encodes an unprecedented number of genes involved in energy metabolism

Viruses have long been viewed as entities possessing extremely limited metabolic capacities. Over the last decade, however, this view has been challenged, as metabolic genes have been identified in viruses possessing large genomes and virions-the synthesis of which is energetically demanding. Here, we unveil peculiar phenotypic and genomic features of Prymnesium kappa virus RF01 (PkV RF01), a giant virus of the Mimiviridae family. We found that this virus encodes an unprecedented number of proteins involved in energy metabolism, such as all four succinate dehydrogenase (SDH) subunits (A-D) as well as key enzymes in the β-oxidation pathway. The SDHA gene was transcribed upon infection, indicating that the viral SDH is actively used by the virus- potentially to modulate its host's energy metabolism. We detected orthologous SDHA and SDHB genes in numerous genome fragments from uncultivated marine Mimiviridae viruses, which suggests that the viral SDH is widespread in oceans. PkV RF01 was less virulent compared with other cultured prymnesioviruses, a phenomenon possibly linked to the metabolic capacity of this virus and suggestive of relatively long co-evolution with its hosts. It also has a unique morphology, compared to other characterized viruses in the Mimiviridae family. Finally, we found that PkV RF01 is the only alga-infecting Mimiviridae virus encoding two aminoacyl-tRNA synthetases and enzymes corresponding to an entire base-excision repair pathway, as seen in heterotroph-infecting Mimiviridae These Mimiviridae encoded-enzymes were found to be monophyletic and branching at the root of the eukaryotic tree of life. This placement suggests that the last common ancestor of Mimiviridae was endowed with a large, complex genome prior to the divergence of known extant eukaryotes.IMPORTANCE Viruses on Earth are tremendously diverse in terms of morphology, functionality, and genomic composition. Over the last decade, the conceptual gap separating viruses and cellular life has tightened because of the detection of metabolic genes in viral genomes that express complex virus phenotypes upon infection. Here, we describe Prymnesium kappa virus RF01, a large alga-infecting virus with a unique morphology, an atypical infection profile, and an unprecedented number of genes involved in energy metabolism (such as the tricarboxylic (TCA) cycle and the β-oxidation pathway). Moreover, we show that the gene corresponding to one of these enzymes (the succinate dehydrogenase subunit A) is transcribed during infection and is widespread among marine viruses. This discovery provides evidence that a virus has the potential to actively regulate energy metabolism with its own gene.

Photosynthetic Picoeukaryotes Diversity in the Underlying Ice Waters of the White Sea, Russia

The White Sea is a unique basin combining features of temperate and arctic seas. The current state of its biocenoses can serve as a reference point in assessing the expected desalination of the ocean as a result of climate change. A metagenomic study of under-ice ice photosynthetic picoeukaryotes (PPEs) was undertaken by Illumina high-throughput sequencing of the 18S rDNA V4 region from probes collected in March 2013 and 2014. The PPE biomass in samples was 0.03–0.17 µg C·L−1 and their abundance varied from 10 cells·mL−1 to 140 cells·mL−1. There were representatives of 16 algae genera from seven classes and three supergroups, but Chlorophyta, especially Mamiellophyceae, dominated. The most represented genera were Micromonas and Mantoniella. For the first time, the predominance of Mantoniella (in four samples) and Bolidophyceae (in one sample) was observed in under-ice water. It can be assumed that a change in environmental conditions will lead to a considerable change in the structure of arctic PPE communities.

Toxic HAB species from the Sea of Okhotsk detected by a metagenetic approach, seasonality and environmental drivers

During recent decades, the distribution of harmful algal bloom (HAB) species has expanded worldwide together with the increase of blooms and toxicity events. In this study, the presence of toxic HAB species in the Sea of Okhotsk was investigated based on metagenetic data collected during 6 years of weekly monitoring. Operational taxonomic units (OTUs) associated with the toxic HAB species were detected based on amplifying 18S V7-V9 and 28S D1 rRNA gene regions. In total, 43 unique OTUs associated with toxic HAB species were revealed, with 26 of those previously not reported from the Sea of Okhotsk. More OTUs belonging to dinoflagellates were detected by 18S, whereas a similar number of OTUs associated with dinoflagellates and diatoms were detected by targeting the 28S region. Species belonging to genera Alexandrium, Karenia and Karlodinium were mainly associated with OTUs under Dinophyceae, whereas Bacillariophyceae was represented by the species belonging to genus Pseudo-nitzschia. From the detected OTUs, 22 showed a clear seasonal pattern with the majority of those appearing during summer-autumn. For Alexandrium pacificum, Aureococcus anophagefferens, and Pseudo-nitzschia pungens, the seasonal pattern was detected based on both rRNA regions. Additionally, 14 OTUs were detected during all seasons and two OTUs appeared sporadically. OTUs associated with the toxic species had low relative read abundances, which together with other factors such as similar and variable morphology as well as usage of fixatives, may explain why those species have previously not been detected by light microscopy. Environmental parameters, especially water temperature, significantly (<0.05) influenced the variability in OTU relative abundances and displayed significant (<0.05) correlations with the unique OTUs. The results of this study demonstrate the usefulness of the metagenetic approach for phytoplankton monitoring, which is especially relevant for detecting toxic HAB species.

Protist Diversity and Seasonal Dynamics in Skagerrak Plankton Communities as Revealed by Metabarcoding and Microscopy

Protist community composition and seasonal dynamics are of major importance for the production of higher trophic levels, such as zooplankton and fish. Our aim was to reveal how the protist community in the Skagerrak changes through the seasons by combining high-throughput sequencing and microscopy of plankton collected monthly over two years. The V4 region of the 18S rRNA gene was amplified by eukaryote universal primers from the total RNA/cDNA. We found a strong seasonal variation in protist composition and proportional abundances, and a difference between two depths within the euphotic zone. Highest protist richness was found in late summer-early autumn, and lowest in winter. Temperature was the abiotic factor explaining most of the variation in diversity. Dinoflagellates was the most abundant and diverse group followed by ciliates and diatoms. We found about 70 new taxa recorded for the first time in the Skagerrak. The seasonal pattern in relative read abundance of major phytoplankton groups was well in accordance with microscopical biovolumes. This is the first metabarcoding study of the protist plankton community of all taxonomic groups and through seasons in the Skagerrak, which may serve as a baseline for future surveys to reveal effects of climate and environmental changes.

Resolving phytoplankton taxa based on high-throughput sequencing during brown tides in the Bohai Sea, China

Large-scale blooms formed by pico-sized phytoplankton, which strongly inhibited feeding activity and growth of cultured scallops, have been recorded along the coast of Qinhuangdao in the Bohai Sea since 2009. Based on pigment profiles and clone library analysis of phytoplankton samples during the blooms, the major bloom-forming species was primarily identified as pelagophyte Aureococcus anophagefferens Hargraves et Sieburth, the causative species of intensive brown tides in the United States and South Africa. Due to the indistinct morphological features of the bloom-forming microalgae and limited knowledge on the composition of phytoplankton communities, there were still disputes concerning the causative species of the blooms. In this study, the method of high-throughput sequencing targeted 18S rDNA V4 region was used to study the composition of pico- and nano-sized phytoplankton communities in 2013 and 2014. A total of 18 groups of eukaryotic microalgae at the class level and more than 2000 operational taxonomic units (OTUs) were identified in phytoplankton samples collected from the brown-tide zone in the Qinhuangdao coastal waters. For both years, A. anophagefferens was the most dominant species during the bloom period and its maximum relative abundance exceeded 60 percent. Along with other evidence, the results further confirm that A. anophagefferens is the major causative species of the pico-sized phytoplankton blooms in the Bohai Sea. The outbreak of brown tide exhibited a strong inter-annual variation between 2013 and 2014, and an increasing dominance of dinoflagellates could be observed in the Qinhuangdao coastal waters.

High contribution of Rhizaria (Radiolaria) to vertical export in the California Current Ecosystem revealed by DNA metabarcoding

Passive sinking of particulate organic matter (POM) is the main mechanism through which the biological pump transports surface primary production to the ocean interior. However, the contribution and variability of different biological sources to vertical export is not fully understood. Here, we use DNA metabarcoding of the 18S rRNA gene and particle interceptor traps (PITs) to characterize the taxonomic composition of particles sinking out of the photic layer in the California Current Ecosystem (CCE), a productive system with high export potential. The PITs included formalin-fixed and 'live' traps to investigate eukaryotic communities involved in the export and remineralization of sinking particles. Sequences affiliated with Radiolaria dominated the eukaryotic assemblage in fixed traps (90%), with Dinophyta and Metazoa making minor contributions. The prominence of Radiolaria decreased drastically in live traps, possibly due to selective consumption by copepods, heterotrophic nanoflagellates, and phaeodarians that were heavily enriched in these traps. These patterns were consistent across the water masses surveyed extending from the coast to offshore, despite major differences in productivity and trophic structure of the epipelagic plankton community. Our findings identify Radiolaria as major actors in export fluxes in the CCE.

Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

Picoeukaryotes play an important role in the biogenic element cycle and energy flow in oligotrophic ecosystems. However, their biodiversity and activity are poorly studied in open ocean systems, such as the northwestern Pacific Ocean, which is characterized by a complex hydrological setting. Here, we investigated the diversity and activity of picoeukaryotes in the northwestern Pacific Ocean using high-throughput sequencing targeting the V9 region of 18S rDNA and rRNA. Our results showed that the DNA picoeukaryotic communities were mainly represented by Mamiellophyceae, MAST, MALV-II, Spirotrichea, Prymnesiophyceae, and MALV-I (69.33% of the total DNA reads), and the RNA communities were dominated by Spirotrichea, Mamiellophyceae, MAST, Pelagophyceae, and MALV-II (67.46% of the total RNA reads). The number of operational taxonomic units (OTUs) was significantly affected by temperature and salinity, and was decreased with the increasing nutrient concentration both in the DNA and RNA surveys. Significant differences were observed in the community composition between DNA-based and RNA-based molecular approaches, and these differences were mainly attributed to Mamiellophyceae, Spirotrichea, and Pelagophyceae. The RNA: DNA ratio was used as a proxy for relative metabolic activity of the individual OTUs. We found that the relative metabolic activities of Mamiellophyceae, Spirotrichea, and Pelagophyceae species in the northwestern Pacific Ocean were highly affected by the nutrient concentration, i.e., the NO₃ + NO₂ and SiO₃ concentration. Overall, our study shed light on picoeukaryotic diversity and distribution in the northwestern Pacific Ocean and revealed the correlation between the diversity, relative metabolic activities of marine picoeukaryotes, and the environmental factors.

Diatom diversity through HTS-metabarcoding in coastal European seas

Diatoms constitute a diverse lineage of unicellular organisms abundant and ecologically important in aquatic ecosystems. Compared to other protists, their biology and taxonomy are well-studied, offering the opportunity to combine traditional approaches and new technologies. We examined a dataset of diatom 18S rRNA- and rDNA- (V4 region) reads from different plankton size-fractions and sediments from six European coastal marine sites, with the aim of identifying peculiarities and commonalities with respect to the whole protistan community. Almost all metabarcodes (99.6%) were assigned to known genera (121) and species (236), the most abundant of which were those already known from classic studies and coincided with those seen in light microscopy. rDNA and rRNA showed comparable patterns for the dominant taxa, but rRNA revealed a much higher diversity particularly in the sediment communities. Peculiar to diatoms is a tight bentho-pelagic coupling, with many benthic or planktonic species colonizing both water column and sediments and the dominance of planktonic species in both habitats. Overall metabarcoding results reflected the marked specificity of diatoms compared to other protistan groups in terms of morphological and ecological characteristics, at the same time confirming their great potential in the description of protist communities.

Protist Biodiversity and Biogeography in Lakes From Four Brazilian River-Floodplain Systems

The biodiversity and biogeography of protists inhabiting many ecosystems have been intensely studied using different sequencing approaches, but tropical ecosystems are relatively under-studied. Here, we sampled planktonic waters from 32 lakes associated with four different river-floodplains systems in Brazil, and sequenced the DNA using a metabarcoding approach with general eukaryotic primers. The lakes were dominated by the largely free-living Discoba (mostly the Euglenida), Ciliophora, and Ochrophyta. There was low community similarity between lakes even within the same river-floodplain. The protists inhabiting these floodplain systems comprise part of the large and relatively undiscovered diversity in the tropics.

Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria

Symbioses between eukaryotic algae and nitrogen-fixing cyanobacteria have been recognized in recent years as a key source of new nitrogen in the oceans. We investigated the composition of the small photosynthetic eukaryote communities associated with nitrogen-fixing cyanobacteria in the Brazilian South Atlantic Bight using a combination of flow cytometry sorting and high throughput sequencing of two genes: the V4 region of 18S rRNA and nifH. Two distinct eukaryotic communities were often encountered, one dominated by the Mamiellophyceae Bathycoccus and Ostreococcus, and one dominated by a prymnesiophyte known to live in symbiosis with the UCYN-A1 nitrogen-fixing cyanobacterium. Among nifH sequences, those from UCYN-A1 were most abundant but three other UCYN-A clades (A2, A3, A4) were also found. Network analysis confirmed the relation between A1 and A2 clades and their hypothesized hosts and pointed out to the potential association between novel clade A4 with Braarudosphaera bigelowii, previously hypothesized to host A2.

Dynamic microbial populations along the Cuyahoga River

The study of the microbial communities has gained traction in recent years with the advent of next-generation sequencing with, or without, PCR-based amplification of the 16S ribosomal RNA region. Such studies have been applied to topics as diverse as human health and environmental ecology. Fewer studies have investigated taxa outside of bacteria, however. We present here data demonstrating the utility of studying taxa outside of bacteria including algae, diatoms, archaea and fungi. Here, we show how location along the Cuyahoga River as well as a transient rainfall event heavily influence the microbial composition. Our data reveal how individual OTUs vary between samples and how the patterns of OTU abundance can accurately predict sampling location. The clustering of samples reveals that these taxa are all sensitive to water conditions in unique ways and demonstrate that, for our dataset, algae was most distinctive between sample groups, surpassing bacteria. Diversity between sampling sites could allow studies investigating pollution or water quality to identify marker OTUs or patterns of OTU abundance as indicators to assess environmental conditions or the impact of human activity. We also directly compare data derived from primers amplifying distinct taxa and show that taxa besides bacteria are excellent indicators of water condition.

Applicability of massively parallel sequencing on monitoring harmful algae at Varna Bay in the Black Sea

In this study the plankton diversity in 13 environmental samples from Varna Bay (in the western Black Sea) was analyzed using massively parallel sequencing (MPS). This preliminary study was undertaken to assess the potential of this technology for future implementation in monitoring programs in the Black Sea. Amplicon sequences of the 18S rRNA gene (V4-5 regions) were obtained using the Illumina MiSeq 250PE platform. A total of 1137 operational taxonomic units (OTUs) were obtained among which 242 OTUs with >0.990 BLAST top hit similarity (21.3% of all detected OTUs) closely related to sequences belonging to -protists. A large portion (175 OTUs=72.3%) was identified at the species levels, including species typical for the Bulgarian Black Sea plankton community, as well as many that haven't been reported earlier in the Bulgarian Black Sea coast (124 OTUs=51.2%). Dinoflagellates were represented by the highest species number (77 OTUs comprising 31.8% of protist species), with dominant genera Gyrodinium and Heterocapsa. The present survey revealed the presence of 12 species listed as harmful, some of which have been previously overlooked, such as Cochlodinium polykrikoides, Karenia bicuneiformis, and Karlodinium veneficum. Species identification was possible for 10.3-36.0% of the detected OTUs in the six major supergroups. The frequency in Rhizaria was significantly lower than that in other major groups (p<0.05-0.01), implying difficulties in the classification from morphology-based observations. The metagenetic data had an insufficient resolution of the 18S rRNA gene for species identification in many genera. These issues may hamper the implementation of MPS-based surveys for plankton monitoring, especially for detecting harmful algal blooms (HAB). The sequencing technology is steadily improving and it is expected that sequence length and quality issues will be resolved in the near future. The ongoing efforts to register taxonomic information and quality controls in the international nucleotide sequence databases (INSDs) will be essential for improving taxonomic identification power.

Strengths and Biases of High-Throughput Sequencing Data in the Characterization of Freshwater Ciliate Microbiomes

Molecular surveys of eukaryotic microbial communities employing high-throughput sequencing (HTS) techniques are rapidly supplanting traditional morphological approaches due to their larger data output and reduced bench work time. Here, we directly compare morphological and Illumina data obtained from the same samples, in an effort to characterize ciliate faunas from sediments in freshwater environments. We show how in silico processing affects the final outcome of our HTS analysis, providing evidence that quality filtering protocols strongly impact the number of predicted taxa, but not downstream conclusions such as biogeography patterns. We determine the abundance distribution of ciliates, showing that a small fraction of abundant taxa dominates read counts. At the same time, we advance reasons to believe that biases affecting HTS abundances may be significant enough to blur part of the underlying biological picture. We confirmed that the HTS approach detects many more taxa than morphological inspections, and highlight how the difference varies among taxonomic groups. Finally, we hypothesize that the two datasets actually correspond to different conceptions of "diversity," and consequently that neither is entirely superior to the other when investigating environmental protists.

Seasonal Dynamics of Haptophytes and dsDNA Algal Viruses Suggest Complex Virus-Host Relationship

Viruses influence the ecology and diversity of phytoplankton in the ocean. Most studies of phytoplankton host-virus interactions have focused on bloom-forming species like Emiliania huxleyi or Phaeocystis spp. The role of viruses infecting phytoplankton that do not form conspicuous blooms have received less attention. Here we explore the dynamics of phytoplankton and algal viruses over several sequential seasons, with a focus on the ubiquitous and diverse phytoplankton division Haptophyta, and their double-stranded DNA viruses, potentially with the capacity to infect the haptophytes. Viral and phytoplankton abundance and diversity showed recurrent seasonal changes, mainly explained by hydrographic conditions. By 454 tag-sequencing we revealed 93 unique haptophyte operational taxonomic units (OTUs), with seasonal changes in abundance. Sixty-one unique viral OTUs, representing Megaviridae and Phycodnaviridae, showed only distant relationship with currently isolated algal viruses. Haptophyte and virus community composition and diversity varied substantially throughout the year, but in an uncoordinated manner. A minority of the viral OTUs were highly abundant at specific time-points, indicating a boom-bust relationship with their host. Most of the viral OTUs were very persistent, which may represent viruses that coexist with their hosts, or able to exploit several host species.

Biogeography and diversity of Collodaria (Radiolaria) in the global ocean

Collodaria are heterotrophic marine protists that exist either as large colonies composed of hundreds of cells or as large solitary cells. All described species so far harbour intracellular microalgae as photosymbionts. Although recent environmental diversity surveys based on molecular methods demonstrated their consistently high contribution to planktonic communities and their worldwide occurrence, our understanding of their diversity and biogeography is still very limited. Here we estimated the 18S ribosomal DNA (rDNA) gene copies per collodarian cell for solitary (5770±1960 small subunit (SSU) rDNA copies) and colonial specimens (37 474±17 799 SSU rDNA copies, for each individual cell within a colony) using single-specimen quantitative PCR. We then investigated the environmental diversity of Collodaria within the photic zone through the metabarcoding survey from the Tara Oceans expedition and found that the two collodarian families Collosphaeridae and Sphaerozoidae contributed the most to the collodarian diversity and encompassed mostly cosmopolitan taxa. Although the biogeographical patterns were homogeneous within each biogeochemical biome considered, we observed that coastal biomes were consistently less diverse than oceanic biomes and were dominated by the Sphaerozoidae while the Collosphaeridae were dominant in the open oceans. The significant relationships with six environmental variables suggest that collodarian diversity is influenced by the trophic status of oceanic provinces and increased towards more oligotrophic regions.

Haptophyte Diversity and Vertical Distribution Explored by 18S and 28S Ribosomal RNA Gene Metabarcoding and Scanning Electron Microscopy

Haptophyta encompasses more than 300 species of mostly marine pico‐ and nanoplanktonic flagellates. Our aims were to investigate the Oslofjorden haptophyte diversity and vertical distribution by metabarcoding, and to improve the approach to study haptophyte community composition, richness and proportional abundance by comparing two rRNA markers and scanning electron microscopy (SEM). Samples were collected in August 2013 at the Outer Oslofjorden, Norway. Total RNA/cDNA was amplified by haptophyte‐specific primers targeting the V4 region of the 18S, and the D1‐D2 region of the 28S rRNA. Taxonomy was assigned using curated haptophyte reference databases and phylogenetic analyses. Both marker genes showed Chrysochromulinaceae and Prymnesiaceae to be the families with highest number of Operational Taxonomic Units (OTUs), as well as proportional abundance. The 18S rRNA data set also contained OTUs assigned to eight supported and defined clades consisting of environmental sequences only, possibly representing novel lineages from family to class. We also recorded new species for the area. Comparing coccolithophores by SEM with metabarcoding shows a good correspondence with the 18S rRNA gene proportional abundances. Our results contribute to link morphological and molecular data and 28S to 18S rRNA gene sequences of haptophytes without cultured representatives, and to improve metabarcoding methodology.

Benthic protists: the under-charted majority

Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed.

Comparison of three clustering approaches for detecting novel environmental microbial diversity

Discovery of novel diversity in high-throughput sequencing studies is an important aspect in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on the discovery of novel diversity, we clustered an environmental marine high-throughput sequencing dataset of protist amplicons together with reference sequences from the taxonomically curated Protist Ribosomal Reference (PR²) database using three de novo approaches: sequence similarity networks, USEARCH, and Swarm. The potentially novel diversity uncovered by each clustering approach differed drastically in the number of operational taxonomic units (OTUs) and in the number of environmental amplicons in these novel diversity OTUs. Global pairwise alignment comparisons revealed that numerous amplicons classified as potentially novel by USEARCH and Swarm were more than 97% similar to references of PR². Using shortest path analyses on sequence similarity network OTUs and Swarm OTUs we found additional novel diversity within OTUs that would have gone unnoticed without further exploiting their underlying network topologies. These results demonstrate that graph theory provides powerful tools for microbial ecology and the analysis of environmental high-throughput sequencing datasets. Furthermore, sequence similarity networks were most accurate in delineating novel diversity from previously discovered diversity.

18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species

The potential of the 18S rRNA V9 metabarcoding approach for diet assessment was explored using MiSeq paired‐end (PE; 2 × 150 bp) technology. To critically evaluate the method′s performance with degraded/digested DNA, the diets of two zooplanktivorous fish species from the Bay of Biscay, European sardine (Sardina pilchardus) and European sprat (Sprattus sprattus), were analysed. The taxonomic resolution and quantitative potential of the 18S V9 metabarcoding was first assessed both in silico and with mock and field plankton samples. Our method was capable of discriminating species within the reference database in a reliable way providing there was at least one variable position in the 18S V9 region. Furthermore, it successfully discriminated diet between both fish species, including habitat and diel differences among sardines, overcoming some of the limitations of traditional visual‐based diet analysis methods. The high sensitivity and semi‐quantitative nature of the 18S V9 metabarcoding approach was supported by both visual microscopy and qPCR‐based results. This molecular approach provides an alternative cost and time effective tool for food‐web analysis.

Getting specific: making taxonomic and ecological sense of large sequencing data sets

Eukaryotic microbes comprise a diverse collection of phototrophic and heterotrophic creatures known to play fundamental roles in ecological processes. Some can be identified by light microscopy, generally the largest and with conspicuous shapes, while the smallest can be counted by epifluorescence microscopy or flow cytometry but remain largely unidentified. Microbial diversity studies greatly advanced with the analysis of phylogenetic markers sequenced from natural assemblages. Molecular surveys began in 1990 targeting marine bacterioplankton (Giovannoni et al. ) and first approached microbial eukaryotes in three studies published in 2001 (Díez et al. ; López-García et al. ; Moon-van der Staay et al. ). These seminal studies, based on cloning and Sanger sequencing the complete 18S rDNA, were critical for obtaining broad pictures of microbial diversity in contrasted habitats and for describing novel lineages by robust phylogenies, but were limited by the number of sequences obtained. So, inventories of species richness in a given sample and community comparisons through environmental gradients were very incomplete. These limitations have been overcome with the advent of high-throughput sequencing (HTS) methods, initially 454-pyrosequencing, today Illumina and soon others to come. In this issue of Molecular Ecology, Egge et al. () show a nice example of the use of HTS to study the biodiversity and seasonal succession of a particularly important group of marine microbial eukaryotes, the haptophytes. Temporal changes were analysed first at the community level, then at the clade level, and finally at the lowest rank comparable to species. Interesting and useful ecological insights were obtained at each taxonomic scale. Haptophyte diversity differed along seasons in a systematic manner, with some species showing seasonal preferences and others being always present. Many of these species had no correspondence with known species, pointing out the high level of novelty in microbial assemblages, only accessible by molecular tools. Moreover, the number of species detected was limited, agreeing with a putative scenario of constrained evolutionary diversification in free-living small eukaryotes. This study illustrates the potential of HTS to address ecological relevant questions in an accessible way by processing large data sets that, nonetheless, need to be treated with a fair understanding of their limitations.

Microbial eukaryotic diversity and distribution in a river plume and cyclonic eddy-influenced ecosystem in the South China Sea

To evaluate microbial eukaryotic diversity and distribution in mesoscale processes, we investigated 18S rDNA diversity in a river plume and cyclonic eddy-influenced ecosystem in the southwestern South China Sea (SCS). Restriction fragment length polymorphism analysis was carried out using multiple primer sets. Relative to a wide range of previous similar studies, we observed a significantly higher proportion of sequences of pigmented taxa. Among the photosynthetic groups, Haptophyta accounted for 27.7% of the sequenced clones, which belonged primarily to Prymnesiophyceae. Unexpectedly, five operational taxonomic units of Cryptophyta were closely related to freshwater species. The Chlorophyta mostly fell within the Prasinophyceae, which was comprised of six clades, including Clade III, which is detected in the SCS for the first time in this study. Among the photosynthetic stramenopiles, Chrysophyceae was the most diverse taxon, which included seven clades. The majority of 18S rDNA sequences affiliated with the Dictyochophyceae, Eustigmatophyceae, and Pelagophyceae were closely related to those of pure cultures. The results of redundancy analysis and the permutation Mantel test based on unweighted UniFrac distances, conducted for spatial analyses of the Haptophyta subclades suggested that the Mekong River plume and cyclonic eddy play important roles in regulating microbial eukaryotic diversity and distribution in the southwestern SCS.

Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.