Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes

Simple, inexpensive, and rapid approach to detect changes in the structure of soil free-living nematodes

A general limitation of ecological investigations based on nematodes is related to the difficult and time-consuming taxonomic identification of species. Therefore, nematologists are investing many efforts to develop alternative approaches as proxies applicable in biomonitoring assessment. Recently, an alternative method that combines morpho-functional traits was proposed for detecting assemblage changes of marine nematodes. In view of the promising results, it was tested the same approach to document taxonomic structure changes of soil free-living and plant parasitic nematodes. Specifically, this attempt was carried out using three data sets that include studies from various European regions and different types of ecosystems: forests, grasslands and maize crops. Multivariate statistical analysis revealed that the simple combination of the four traits (i.e., buccal cavity cuticularization occurrence, amphideal fovea size and shape, morphology of the cuticle and pharynx) in a single code number perfectly mirrors the taxonomic structure trends of the nematode assemblage at genus level. Therefore, we predict that similar results can be also obtained by directly encoding nematode specimens with the selected traits and we point to new important advances if this procedure can be coupled with advanced machine learning.

Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton

Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested on protists. Here, we applied a microarray single-cell sequencing (MASC-seq) technology, that generates microscope images of cells in parallel with capturing their transcriptomes, on three species representing important plankton groups with different cell structures; the ciliate Tetrahymena thermophila, the diatom Phaeodactylum tricornutum, and the dinoflagellate Heterocapsa sp. Both the cell fixation and permeabilization steps were adjusted. For the ciliate and dinoflagellate, the number of transcripts of microarray spots with single cells were significantly higher than for background spots, and the overall expression patterns were correlated with that of bulk RNA, while for the much smaller diatom cells, it was not possible to separate single-cell transcripts from background. The MASC-seq method holds promise for investigating "microbial dark matter", although further optimizations are necessary to increase the signal-to-noise ratio.

Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.

Diverse eukaryotic phytoplankton from around the Marquesas Islands documented by combined microscopy and molecular techniques

Oceanic phytoplankton serve as a base for the food webs within the largest planetary ecosystem. Despite this, surprisingly little is known about species composition, function and ecology of phytoplankton communities, especially for vast areas of the open ocean. In this study we focus on the marine phytoplankton microflora from the vicinity of the Marquesas Islands in the Southern Pacific Ocean collected during the Tara Oceans expedition. Multiple samples from four sites and two depths were studied in detail using light microscopy, scanning electron microscopy, and automated confocal laser scanning microscopy. In total 289 taxa were identified, with Dinophyceae and Bacillariophyceae contributing 60% and 32% of taxa, respectively, to phytoplankton community composition. Notwithstanding, a large number of cells could not be assigned to any known species. Coccolithophores and other flagellates together contributed less than 8% to the species list. Observed cell densities were generally low, but at sites of high autotrophic biomass, diatoms reached the highest cell densities (1.26 × 10⁴ cells L^-1). Overall, 18S rRNA metabarcode-based community compositions matched microscopy-based estimates, particularly for the main diatom taxa, indicating consistency and complementarity between different methods, while the wide range of microscopy-based methods permitted several unknown and poorly studied taxa to be revealed and identified.

Grazing on Marine Viruses and Its Biogeochemical Implications

Viruses are the most abundant biological entities in the ocean and show great diversity in terms of size, host specificity, and infection cycle. Lytic viruses induce host cell lysis to release their progeny and thereby redirect nutrients from higher to lower trophic levels. Studies continue to show that marine viruses can be ingested by nonhost organisms. However, not much is known about the role of viral particles as a nutrient source and whether they possess a nutritional value to the grazing organisms. This review seeks to assess the elemental composition and biogeochemical relevance of marine viruses, including roseophages, which are a highly abundant group of bacteriophages in the marine environment. We place a particular emphasis on the phylum Nucleocytoviricota (NCV) (formerly known as nucleocytoplasmic large DNA viruses [NCLDVs]), which comprises some of the largest viral particles in the marine plankton that are well in the size range of prey for marine grazers. Many NCVs contain lipid membranes in their capsid that are rich carbon and energy sources, which further increases their nutritional value. Marine viruses may thus be an important nutritional component of the marine plankton, which can be reintegrated into the classical food web by nonhost organism grazing, a process that we coin the "viral sweep." Possibilities for future research to resolve this process are highlighted and discussed in light of current technological advancements.

Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf

The planktonic diversity throughout the oceans is vital to ecosystem functioning and linked to environmental change. Plankton monitoring tools have advanced considerably with high-throughput in-situ digital cameras and genomic sequencing, opening new challenges for high-frequency observations of community composition, structure, and species discovery. Here, we combine multi-marker metabarcoding based on nuclear 18S (V4) and plastidial 16S (V4–V5) rRNA gene amplicons with a digital in-line holographic microscope to provide a synoptic diversity survey of eukaryotic plankton along the Newfoundland Shelf (Canada) during the winter transition phase of the North Atlantic bloom phenomenon. Metabarcoding revealed a rich eukaryotic diversity unidentifiable in the imaging samples, confirming the presence of ecologically important saprophytic protists which were unclassifiable in matching images, and detecting important groups unobserved or taxonomically unresolved during similar sequencing campaigns in the Northwest Atlantic Ocean. In turn, imaging analysis provided quantitative observations of widely prevalent plankton from every trophic level. Despite contrasting plankton compositions portrayed by each sampling method, both capture broad spatial differences between the northern and southern sectors of the Newfoundland Shelf and suggest complementary estimations of important features in eukaryotic assemblages. Future tasks will involve standardizing digital imaging and metabarcoding for wider use and consistent, comparable ocean observations.

A robust approach to estimate relative phytoplankton cell abundances from metagenomes

Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.

Plankton reconstruction through robust statistical optical tomography

Plankton interact with the environment according to their size and three-dimensional (3D) structure. To study them outdoors, these translucent specimens are imaged in situ. Light projects through a specimen in each image. The specimen has a random scale, drawn from the population's size distribution and random unknown pose. The specimen appears only once before drifting away. We achieve 3D tomography using such a random ensemble to statistically estimate an average volumetric distribution of the plankton type and specimen size. To counter errors due to non-rigid deformations, we weight the data, drawing from advanced models developed for cryo-electron microscopy. The weights convey the confidence in the quality of each datum. This confidence relies on a statistical error model. We demonstrate the approach on live plankton using an underwater field microscope.

Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (<0.2–2000 μm). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton (<0.2 μm) to mesoplankton (180–2000 μm) communities, while images predict numerous symbiotic and colony-forming diazotrophs (>20 µm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 μm) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow.

Nitrogen fixation by diazotrophs is critical for marine primary production. Using Tara Oceans datasets, this study combines a quantitative image analysis pipeline with metagenomic mining to provide an improved global overview of diazotroph abundance, diversity and distribution.

Plankton classification with high-throughput submersible holographic microscopy and transfer learning

BACKGROUND

Plankton are foundational to marine food webs and an important feature for characterizing ocean health. Recent developments in quantitative imaging devices provide in-flow high-throughput sampling from bulk volumes-opening new ecological challenges exploring microbial eukaryotic variation and diversity, alongside technical hurdles to automate classification from large datasets. However, a limited number of deployable imaging instruments have been coupled with the most prominent classification algorithms-effectively limiting the extraction of curated observations from field deployments. Holography offers relatively simple coherent microscopy designs with non-intrusive 3-D image information, and rapid frame rates that support data-driven plankton imaging tasks. Classification benchmarks across different domains have been set with transfer learning approaches, focused on repurposing pre-trained, state-of-the-art deep learning models as classifiers to learn new image features without protracted model training times. Combining the data production of holography, digital image processing, and computer vision could improve in-situ monitoring of plankton communities and contribute to sampling the diversity of microbial eukaryotes.

RESULTS

Here we use a light and portable digital in-line holographic microscope (The HoloSea) with maximum optical resolution of 1.5 μm, intensity-based object detection through a volume, and four different pre-trained convolutional neural networks to classify > 3800 micro-mesoplankton (> 20 μm) images across 19 classes. The maximum classifier performance was quickly achieved for each convolutional neural network during training and reached F1-scores > 89%. Taking classification further, we show that off-the-shelf classifiers perform strongly across every decision threshold for ranking a majority of the plankton classes.

CONCLUSION

These results show compelling baselines for classifying holographic plankton images, both rare and plentiful, including several dinoflagellate and diatom groups. These results also support a broader potential for deployable holographic microscopes to sample diverse microbial eukaryotic communities, and its use for high-throughput plankton monitoring.

A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes

The procedures and methodologies employed to study microbial eukaryotic plankton have been thoroughly discussed. Two main schools exist—one insisting on classic microscopy methodologies and the other supporting modern high-throughput sequencing (DNA metabarcoding). However, few studies have attempted to combine both these approaches; most studies implement one method while ignoring the other. This work aims to contribute to this discussion and examine the advantages and disadvantages of each methodology by comparing marine plankton community results from microscopy and DNA metabarcoding. The results obtained by the two methodologies do not vary significantly for Bacillariophyta, although they do for Dinoflagellata and Ciliophora. The lower the taxonomic level, the higher the inconsistency between the two methodologies for all the studied groups. Considering the different characteristics of microscopy-based identification and DNA metabarcoding, this work underlines that each method should be chosen depending on the aims of the study. DNA metabarcoding provides a better estimate of the taxonomic richness of an ecosystem while microscopy provides more accurate quantitative results regarding abundance and biomass. In any case, the combined use of the two methods, if properly standardized, can provide much more reliable and accurate results for the study of marine microbial eukaryotes.

A community perspective on the concept of marine holobionts: current status, challenges, and future directions

Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.

Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging

Eukaryotic phytoplankton have a small global biomass but play major roles in primary production and climate. Despite improved understanding of phytoplankton diversity and evolution, we largely ignore the cellular bases of their environmental plasticity. By comparative 3D morphometric analysis across seven distant phytoplankton taxa, we observe constant volume occupancy by the main organelles and preserved volumetric ratios between plastids and mitochondria. We hypothesise that phytoplankton subcellular topology is modulated by energy-management constraints. Consistent with this, shifting the diatom Phaeodactylum from low to high light enhances photosynthesis and respiration, increases cell-volume occupancy by mitochondria and the plastid CO₂-fixing pyrenoid, and boosts plastid-mitochondria contacts. Changes in organelle architectures and interactions also accompany Nannochloropsis acclimation to different trophic lifestyles, along with respiratory and photosynthetic responses. By revealing evolutionarily-conserved topologies of energy-managing organelles, and their role in phytoplankton acclimation, this work deciphers phytoplankton responses at subcellular scales.

Global Trends in Marine Plankton Diversity across Kingdoms of Life

The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21^st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation.

Video Abstract

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Most epipelagic planktonic groups exhibit a poleward decline of diversity

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No latitudinal diversity gradient was observed below the photic zone

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Temperature emerges as the best predictor of epipelagic plankton diversity

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Global warming may increase plankton diversity, particularly at high latitudes

Foresight Workshop on Advances in Ocean Biological Observations: a sustained system for deep-ocean meroplankton

Recent advances in technology have enabled an unprecedented development of underwater research, extending from near shore to the deepest regions of the globe. However, monitoring of biodiversity is not fully implemented in political agendas and biological observations in the deep ocean have been even more limited in space and time.

The Foresight Workshop on Advances in Ocean Biological Observations: a sustained system for deep-ocean meroplankton was convened to to foster advances in the knowledge on deep-ocean invertebrate larval distributions and improve our understanding of fundamental deep-ocean ecological processes such as connectivity and resilience of benthic communities to natural and human-induced disturbance. This Meroplankton Observations Workshop had two specific goals: 1) review the state-of-the-art instrumentation available for meroplankton observations; 2) develop a strategy to implement technological innovations for in-situ meroplankton observation. Presentations and discussions are summarised in this report covering: i) key challenges and priorities for advancing the knowledge of deep-sea larval diversity and distribution: ii) recent developments in technology and future needs for plankton observation, iii) data integration and oceanographic modelling; iv) synergies and added value of a sustained observation system for meroplankton; v) steps for developing a sustained observation system for deep-ocean meroplankton and plans to maximise collaborative opportunities.

Tara Oceans: towards global ocean ecosystems biology

A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 globally distributed sites at depths down to 1,000 m. We describe publicly available resources of molecular, morphological and environmental data, and discuss how an ecosystems biology approach has expanded our understanding of plankton diversity and ecology in the ocean as a planetary, interconnected ecosystem. These efforts illustrate how global-scale concepts and data can help to integrate biological complexity into models and serve as a baseline for assessing ecosystem changes and the future habitability of our planet in the Anthropocene epoch.

Phytoplankton in the Tara Ocean

Photosynthesis evolved in the ocean more than 2 billion years ago and is now performed by a wide range of evolutionarily distinct organisms, including both prokaryotes and eukaryotes. Our appreciation of their abundance, distributions, and contributions to primary production in the ocean has been increasing since they were first discovered in the seventeenth century and has now been enhanced by data emerging from the Tara Oceans project, which performed a comprehensive worldwide sampling of plankton in the upper layers of the ocean between 2009 and 2013. Largely using recent data from Tara Oceans, here we review the geographic distributions of phytoplankton in the global ocean and their diversity, abundance, and standing stock biomass. We also discuss how omics-based information can be incorporated into studies of photosynthesis in the ocean and show the likely importance of mixotrophs and photosymbionts.

The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean

Diatoms are a diverse and ecologically important group of phytoplankton. Although most species are considered free living, several are known to interact with other organisms within the plankton. Detailed imaging and molecular characterization of any such partnership is, however, limited, and an appraisal of the large-scale distribution and ecology of such consortia was never attempted. Here, observation of Tara Oceans samples from the Benguela Current led to the detection of an epibiotic association between a pennate diatom and a tintinnid ciliate. We identified the diatom as Fragilariopsis doliolus that possesses a unique feature to form barrel-shaped chains, associated with seven different genera of tintinnids including five previously undescribed associations. The organisms were commonly found together in the Atlantic and Pacific Ocean basins, and live observations of the interaction have been recorded for the first time. By combining confocal and scanning electron microscopy of individual consortia with the sequencing of high-resolution molecular markers, we analyzed their distribution in the global ocean, revealing morpho-genetically distinct tintinnid haplotypes and biogeographically structured diatom haplotypes. The diatom was among the most abundant in the global ocean. We show that the consortia were particularly prevalent in nutrient-replete conditions, rich in potential predators. These observations support the hypothesis of a mutualistic symbiosis, wherein diatoms acquire increased motility and tintinnids benefit from silicification through increased protection, and highlight that such associations may be more prevalent than currently appreciated.