High variability in SSU rDNA gene copy number among planktonic foraminifera revealed by single-cell qPCR

Quantitative assessment of reef foraminifera community from metabarcoding data

Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it is challenging to produce fast and accurate depiction of ecosystems due to methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative abundances of genes that may not correctly represent living communities from environmental DNA assessed with morphological methods. However, it has the potential to deliver fast descriptions of living communities provided that it is interpreted with validated species-specific calibrations and reference databases. Here, we developed a quantitative approach to retrieve from metabarcoding data the assemblages of living large benthic foraminifera (LBF), photosymbiotic calcifying protists, from Indonesian coral reefs that are under increasing anthropogenic pressure. To depict the diversity, we calculated taxon-specific correction factors to reduce biological biases by comparing surface area, biovolume and calcite volume, and the number of mitochondrial gene copies in seven common LBF species. To validate the approach, we compared calibrated datasets of morphological communities from mock samples with bulk reef sediment; both sample types were metabarcoded. The calibration of the data significantly improved the estimations of genus relative abundance, with a difference of ±5% on average, allowing for comparison of past morphological datasets with future molecular ones. Our results also highlight the application of our quantitative approach to support reef monitoring operations by capturing fine-scale processes, such as seasonal and pollution-driven dynamics, that require high-throughput sampling treatment.

Environmental DNA sheds new insight on molecular adaptation of foraminifera to temperature from laboratory-controlled culture experiment

Foraminifera is the most important temperature proxy of the ocean on long time scales. However, the absence of temperature-controlled experiments at different water depths hinders the advancement of paleotemperature reconstruction with foraminifera from the continental shelf. For the first time, this study investigated the response of benthic foraminifera to temperature change using microcosm culture and metabarcoding. Foraminiferal communities from three continental stations at varying water depths (6.0, 9.2, and 26.0 m) were cultured under five temperature gradients (6, 12, 18, 24, and 30°C), with each treatment performed in triplicate. The foraminifera were fed with microalgae every 4 days, and the filtered seawater (through 0.22 μm pores), acting as a medium, was changed accordingly. The experiment lasted for 80 days, and 47 DNA samples were obtained and analyzed, including three in situ samples. The results showed that foraminifera adjusted its growth rate within the low-temperature range and adopted an r-strategy to cope with high-temperature stress. In addition, the foraminifera from deeper water stations exhibited a pronounced vulnerability to diminishing read counts. The read counts, operational taxonomic units (OTU) counts and Margalef index of foraminifera and the read counts of Rotaliida exhibited a remarkably positive correlation with temperature. The recommended relationships were described as read counts = 1314.75*T + 44754.51; OTU counts = 1.13*T + 44.26; Margalef index =1.13*T + 44.26. This study established the first quantitative relationship between temperature and foraminifera molecular parameters that holds significant implications for long-time paleotemperature calibration in climate change.

Molecular monitoring of Dinophysis species assemblage in mussel farms in the Northwestern Adriatic Sea

Several Dinophysis species can produce potent lipophilic toxins that pose a risk to human health when contaminated seafood is consumed, especially filter-feeding bivalve mussels. In the mussel farms of the Northwestern Adriatic Sea, seawater and seafood are regularly monitored for the presence of Dinophysis species and their associated toxins, but the current methodological approaches, such as light microscopy determinations, require a long time to make results available to local authorities. A molecular qPCR-based assay can be used to quantify various toxic Dinophysis species in a shorter timeframe. However, this approach is not currently employed in official testing activities. In this study, field samples were collected monthly or bi-weekly over one year from various mussel farms along the Northwestern Adriatic coast. The abundance of Dinophysis species in the seawater was determined using both traditional microscopy and qPCR assays. In addition, the concentration of lipophilic toxins for DSP in mussel flesh was quantified using LC-MS/MS focusing on the okadaic acid group. Dinophysis spp. site-specific single cells were isolated and analysed by qPCR yielding a mean rDNA copy number per cell of 1.21 × 104 ± 1.81 × 103. The qPCR assay gave an efficiency of 98 % and detected up to 10 copies of the rDNA target gene. The qPCR and light microscopy determinations in environmental samples showed a significant positive correlation (Spearman rs = 0.57, p-value < 0.001) with a ratio of 2.24 between the two quantification methods, indicating that light microscopy estimates were generally 44.6 % lower than those obtained by the qPCR assay. The qPCR approach showed several advantages such as rapidity, sensitivity and efficiency over conventional microscopy analysis, showing its potential future role in phytoplankton monitoring under the Official Controls Regulations for shellfish.

The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton

The nature and extent of diversity in the plankton has fascinated scientists for over a century. Initially, the discovery of many new species in the remarkably uniform and unstructured pelagic environment appeared to challenge the concept of ecological niches. Later, it became obvious that only a fraction of plankton diversity had been formally described, because plankton assemblages are dominated by understudied eukaryotic lineages with small size that lack clearly distinguishable morphological features. The high diversity of the plankton has been confirmed by comprehensive metabarcoding surveys, but interpretation of the underlying molecular taxonomies is hindered by insufficient integration of genetic diversity with morphological taxonomy and ecological observations. Here we use planktonic foraminifera as a study model and reveal the full extent of their genetic diversity and investigate geographical and ecological patterns in their distribution. To this end, we assembled a global data set of ~7600 ribosomal DNA sequences obtained from morphologically characterised individual foraminifera, established a robust molecular taxonomic framework for the observed diversity, and used it to query a global metabarcoding data set covering ~1700 samples with ~2.48 billion reads. This allowed us to extract and assign 1 million reads, enabling characterisation of the structure of the genetic diversity of the group across ~1100 oceanic stations worldwide. Our sampling revealed the existence of, at most, 94 distinct molecular operational taxonomic units (MOTUs) at a level of divergence indicative of biological species. The genetic diversity only doubles the number of formally described species identified by morphological features. Furthermore, we observed that the allocation of genetic diversity to morphospecies is uneven. Only 16 morphospecies disguise evolutionarily significant genetic diversity, and the proportion of morphospecies that show genetic diversity increases poleward. Finally, we observe that MOTUs have a narrower geographic distribution than morphospecies and that in some cases the MOTUs belonging to the same morphospecies (cryptic species) have different environmental preferences. Overall, our analysis reveals that even in the light of global genetic sampling, planktonic foraminifera diversity is modest and finite. However, the extent and structure of the cryptic diversity reveals that genetic diversification is decoupled from morphological diversification, hinting at different mechanisms acting at different levels of divergence.

Directional selection, not the direction of selection, affects telomere length and copy number at ribosomal RNA loci

Many fisheries exert directional selection on traits such as body size and growth rate. Whether directional selection impacts regions of the genome associated with traits related to growth is unknown. To address this issue, we characterised copy number variation in three regions of the genome associated with cell division, (1) telomeric DNA, (2) loci transcribed as ribosomal RNA (rDNA), and (3) mitochondrial DNA (mtDNA), in three selection lines of zebrafish reared at three temperatures (22 °C, 28 °C, and 34 °C). Selection lines differed in (1) the direction of selection (two lines experienced directional selection for large or small body size) and (2) whether they experienced any directional selection itself. Lines that had experienced directional selection were smaller, had lower growth rate, shorter telomeres, and lower rDNA copy number than the line that experiencing no directional selection. Neither telomere length nor rDNA copy number were affected by temperature. In contrast, mtDNA content increased at elevated temperature but did not differ among selection lines. Though directional selection impacts rDNA and telomere length, direction of such selection did not matter, whereas mtDNA acts as a stress marker for temperature. Future work should examine the consequences of these genomic changes in natural fish stocks.

Hidden aliens: Application of digital PCR to track an exotic foraminifer across the Skagerrak (North Sea) correlates well with traditional morphospecies analysis

The problem of invasive species is a well-studied one, but knowledge of free-living unicellular eukaryotic invasive species is lacking. A potentially invasive foraminifer (Rhizaria), Nonionella sp. T1, was recently discovered in the Skagerrak and its fjords. Digital polymerase chain reaction (dPCR) was applied to track the spread of this non-indigenous species using a new dPCR assay (T1-1). The use of dPCR appears highly complementary to traditional hand picking of foraminiferal shells from the sediment, and is far less time-consuming. This study indicates that Nonionella sp. T1 has bypassed the outer Skagerrak strait, instead becoming established in Swedish west coast fjords, constituting up to half of the living foraminiferal community in fjord mouth areas. The ecology of Nonionella sp. T1 and its potential invasive impacts are still largely unknown, but it appears to be an opportunist using several energy sources such as nitrate respiration and kleptoplasty along with a possibly more efficient reproductive strategy to gain an advantage over the native foraminiferal species. Future ecological studies of Nonionella sp. T1 could be aided by dPCR and the novel Nonionella sp. T1-specific T1-1 assay.

Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms

The application of meta-barcoding, qPCR, and metagenomics to aquatic eukaryotic microbial communities requires knowledge of genomic copy number variability (CNV). CNV may be particularly relevant to functional genes, impacting dosage and expression, yet little is known of the scale and role of CNV in microbial eukaryotes. Here, we quantify CNV of rRNA and a gene involved in Paralytic Shellfish Toxin (PST) synthesis (sxtA4), in 51 strains of 4 Alexandrium (Dinophyceae) species. Genomes varied up to threefold within species and ~7-fold amongst species, with the largest (A. pacificum, 130 ± 1.3 pg cell-1 /~127 Gbp) in the largest size category of any eukaryote. Genomic copy numbers (GCN) of rRNA varied by 6 orders of magnitude amongst Alexandrium (102- 108 copies cell-1) and were significantly related to genome size. Within the population CNV of rRNA was 2 orders of magnitude (105 - 107 cell-1) in 15 isolates from one population, demonstrating that quantitative data based on rRNA genes needs considerable caution in interpretation, even if validated against locally isolated strains. Despite up to 30 years in laboratory culture, rRNA CNV and genome size variability were not correlated with time in culture. Cell volume was only weakly associated with rRNA GCN (20-22% variance explained across dinoflagellates, 4% in Gonyaulacales). GCN of sxtA4 varied from 0-102 copies cell-1, was significantly related to PSTs (ng cell-1), displaying a gene dosage effect modulating PST production. Our data indicate that in dinoflagellates, a major marine eukaryotic group, low-copy functional genes are more reliable and informative targets for quantification of ecological processes than unstable rRNA genes.

Distribution Patterns of Benthic Protist Communities Depending on Depth Revealed by Environmental Sequencing-From the Sublittoral to the Deep Sea

Protists are key components of the microbial food web in marine pelagic systems because they link algal and bacterial production to higher trophic levels. However, their functioning and bathymetric distribution in benthic deep-sea ecosystems are still only poorly understood. However, biogeographical patterns of communities can be coupled to the functioning of ecosystems and are therefore important to understand ecological and evolutionary processes. In this study, we investigated the diversity and distribution of benthic protist communities from the sublittoral down to the deep seafloor (50-2000 m) around three islands of the Azores in the North Atlantic Ocean. Using amplicon sequencing of the V9 region (18S rDNA) of 21 samples, we found that protist community compositions from different depths were significantly different. Three assemblages were separated along the following depths: 50 m, 150-500 m and 1000-2000 m, which indicate that deep-sea areas surrounding islands might act as isolating barriers for benthic protist species. A limited gene flow between the communities could favor speciation processes, leading to the unique protist communities found at the different investigated islands.

Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy

Protists (microbial eukaryotes) are a critically important but understudied group of microorganisms. They are ubiquitous, represent most of the genetic and functional diversity among eukaryotes, and play essential roles in nutrient and energy cycling. Yet, protists remain a black box in marine sedimentary ecosystems like the intertidal mudflats in the Bay of Fundy. The harsh conditions of the intertidal zone and high energy nature of tides in the Bay of Fundy provide an ideal system for gaining insights into the major food web players, diversity patterns and potential structuring influences of protist communities. Our 18S rDNA metabarcoding study quantified seasonal variations and vertical stratification of protist communities in Bay of Fundy mudflat sediments. Three 'SAR' lineages were consistently dominant (in terms of abundance, richness, and prevalence), drove overall community dynamics and formed the core microbiome in sediments. They are Cercozoa (specifically thecate, benthic gliding forms), Bacillariophyta (mainly cosmopolitan, typically planktonic diatoms), and Dinophyceae (dominated by a toxigenic, bloom-forming species). Consumers were the dominant trophic functional group and were comprised mostly of eukaryvorous and bacterivorous Cercozoa, and omnivorous Ciliophora, while phototrophs were dominated by Bacillariophyta. The codominance of Apicomplexa (invertebrate parasites) and Syndiniales (protist parasites) in parasite assemblages, coupled with broader diversity patterns, highlighted the combined marine and terrestrial influences on microbial communities inhabiting intertidal sediments. Our findings, the most comprehensive in a hypertidal benthic system, suggest that synergistic interactions of both local and regional processes (notably benthic-pelagic coupling) may drive heterogenous microbial distribution in high-energy coastal systems.

Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera

Ribosomal intragenomic variability in prokaryotes and eukaryotes is a genomic feature commonly studied for its inflationary impact on molecular diversity assessments. However, the evolutionary mechanisms and distribution of this phenomenon within a microbial group are rarely explored. Here, we investigate the intragenomic variability in 33 species of planktonic foraminifera, calcifying marine protists, by inspecting 2,403 partial SSU sequences obtained from single-cell clone libraries. Our analyses show that polymorphisms are common among planktonic foraminifera species, but the number of polymorphic sites significantly differs among clades. With our molecular simulations, we could assess that most of these mutations are located in paired regions that do not affect the secondary structure of the SSU fragment. Finally, by mapping the number of polymorphic sites on the phylogeny of the clades, we were able to discuss the evolution and potential sources of intragenomic variability in planktonic foraminifera, linking this trait to the distinctive nuclear and genomic dynamics of this microbial group.

COI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies

Monitoring community composition of Foraminifera (single-celled marine protists) provides valuable insights into environmental conditions in marine ecosystems. Despite the efficiency of environmental DNA (eDNA) and bulk-sample DNA (bulk-DNA) metabarcoding to assess the presence of multiple taxa, this has not been straightforward for Foraminifera partially due to the high genetic variability in widely used ribosomal markers. Here, we test the correctness in retrieving foraminiferal communities by metabarcoding of mock communities, bulk-DNA from coral reef sediment samples, and eDNA from their associated ethanol preservative using the recently sequenced cytochrome c oxidase subunit 1 (COI) marker. To assess the detection success, we compared our results with large benthic foraminiferal communities previously reported from the same sampling sites. Results from our mock communities demonstrate that all species were detected in two mock communities and all but one in the remaining four. Technical replicates were highly similar in number of reads for each assigned ASV in both the mock communities and bulk-DNA samples. Bulk-DNA showed a significantly higher species richness than their associated eDNA samples, and also detected additional species to what was already reported at the specific sites. Our study confirms that metabarcoding using the foraminiferal COI marker adequately retrieves the diversity and community composition of both the mock communities and the bulk-DNA samples. With its decreased variability compared with the commonly used nuclear 18 S rRNA, the COI marker renders bulk-DNA metabarcoding a powerful tool to assess foraminiferal community composition under the condition that the reference database is adequate to the target taxa.

Bacteria, Protists, and Fungi May Hold Clues of Seamount Impact on Diversity and Connectivity of Deep-Sea Pelagic Communities

The topography and hydrography around seamounts have a strong influence on plankton biogeography. The intrinsic properties of various biological taxa inherently also shape their distribution. Therefore, it is hypothesized that different pelagic groups respond differently to effects of seamounts regarding their distribution and connectivity patterns. Herein, bacterial, protist, and fungal diversity was investigated across the water column around the Kocebu Guyot in the western Pacific Ocean. A higher connectivity was detected for bacteria than for protists and an extremely low connectivity for fungi, which might be attributed to parasitic and commensal interactions of many fungal taxa. The seamount enhanced the vertical connectivity of bacterial and protist communities, but significantly reduced protist connectivity along horizontal dimension. Such effects provide ecological opportunities for eukaryotic adaption and diversification. All the bacterial, protist, and fungal communities were more strongly affected by deterministic than stochastic processes. Drift appeared to have a more significant role in influencing the fungal community than other groups. Our study indicates the impact of seamounts on the pelagic community distribution and connectivity and highlights the mechanism of horizontally restricted dispersal combined with vertical mixing, which promotes the diversification of eukaryotic life.