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Satellite remote sensing is a powerful tool to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here, we present an approach to identify community types from a global plankton network that includes phytoplankton and heterotrophic protists and to predict their biogeography using global satellite observations. Six plankton community types were identified from a co-occurrence network inferred using a novel rDNA 18 S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to construct a model that predicted these community types from satellite data. The model showed an overall 67% accuracy in the prediction of the community types. The prediction using 17 satellite-derived parameters showed better performance than that using only temperature and/or the concentration of chlorophyll a. The constructed model predicted the global spatiotemporal distribution of community types over 19 years. The predicted distributions exhibited strong seasonal changes in community types in the subarctic-subtropical boundary regions, which were consistent with previous field observations. The model also identified the long-term trends in the distribution of community types, which suggested responses to ocean warming.
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Viral lysis of phytoplankton is one of the most common forms of death on Earth. Building on an assay used extensively to assess rates of phytoplankton loss to predation by grazers, lysis rates are increasingly quantified through dilution-based techniques. In this approach, dilution of viruses and hosts are expected to reduce infection rates and thus increase host net growth rates (i.e., accumulation rates). The difference between diluted and undiluted host growth rates is interpreted as a measurable proxy for the rate of viral lytic death. These assays are usually conducted in volumes ≥ 1 L. To increase throughput, we implemented a miniaturized, high-throughput, high-replication, flow cytometric microplate dilution assay to measure viral lysis in environmental samples sourced from a suburban pond and the North Atlantic Ocean. The most notable outcome we observed was a decline in phytoplankton densities that was exacerbated by dilution, instead of the increased growth rates expected from lowered virus-phytoplankton encounters. We sought to explain this counterintuitive outcome using theoretical, environmental, and experimental analyses. Our study shows that, while die-offs could be partly explained by a 'plate effect' due to small incubation volumes and cells adhering to walls, the declines in phytoplankton densities are not volume-dependent. Rather, they are driven by many density- and physiology-dependent effects of dilution on predation pressure, nutrient limitation, and growth, all of which violate the original assumptions of dilution assays. As these effects are volume-independent, these processes likely occur in all dilution assays that our analyses show to be remarkably sensitive to dilution-altered phytoplankton growth and insensitive to actual predation pressure. Incorporating altered growth as well as predation, we present a logical framework that categorizes locations by the relative dominance of these mechanisms, with general applicability to dilution-based assays.
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Conducta Predatoria , Virus , Animales , Fitoplancton , Océano Atlántico , EstanquesRESUMEN
Periodic blooms of salps (pelagic tunicates) can result in high export of organic matter, leading to an "outsized" role in the ocean's biological carbon pump (BCP). However, due to their episodic and patchy nature, salp blooms often go undetected and are rarely included in measurements or models of the BCP. We quantified salp-mediated export processes in the northeast subarctic Pacific Ocean in summer of 2018 during a bloom of Salpa aspera. Salps migrated from 300 to 750 m during the day into the upper 100 m at night. Salp fecal pellet production comprised up to 82% of the particulate organic carbon (POC) produced as fecal pellets by the entire epipelagic zooplankton community. Rapid sinking velocities of salp pellets (400-1,200 m d-1) and low microbial respiration rates on pellets (<1% of pellet C respired day-1) led to high salp pellet POC export from the euphotic zone-up to 48% of total sinking POC across the 100 m depth horizon. Salp active transport of carbon by diel vertical migration and carbon export from sinking salp carcasses was usually <10% of the total sinking POC flux. Salp-mediated export markedly increased BCP efficiency, increasing by 1.5-fold the proportion of net primary production exported as POC across the base of the euphotic zone and by 2.6-fold the proportion of this POC flux persisting 100 m below the euphotic zone. Salps have unique and important effects on ocean biogeochemistry and, especially in low flux settings, can dramatically increase BCP efficiency and thus carbon sequestration.
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Under most natural marine conditions, phytoplankton cells suspended in the water column are too distantly spaced for direct competition for resources (i.e., overlapping cell boundary layers) to be a routine occurrence. Accordingly, resource-based competitive exclusion should be rare. In contrast, contemporary ecosystem models typically predict an exclusion of larger phytoplankton size classes under low-nutrient conditions, an outcome interpreted as reflecting the competitive advantage of small cells having much higher nutrient 'affinities' than larger cells. Here, we develop mechanistically-focused expressions for steady-state, nutrient-limited phytoplankton growth that are consistent with the discrete, distantly-spaced cells of natural populations. These expressions, when encompassed in a phytoplankton-zooplankton model, yield sustained diversity across all size classes over the full range in nutrient concentrations observed in the ocean. In other words, our model does not exhibit resource-based competitive exclusion between size classes previously associated with size-dependent differences in nutrient 'affinities'.
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Ecosistema , Fitoplancton , Animales , Nutrientes , Agua , ZooplanctonRESUMEN
Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the 'seascape') by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.
Oceans are brimming with life invisible to our eyes, a myriad of species of bacteria, viruses and other microscopic organisms essential for the health of the planet. These 'marine plankton' are unable to swim against currents and should therefore be constantly on the move, yet previous studies have suggested that distinct species of plankton may in fact inhabit different oceanic regions. However, proving this theory has been challenging; collecting plankton is logistically difficult, and it is often impossible to distinguish between species simply by examining them under a microscope. However, within the last decade, a research schooner called Tara has travelled the globe to gather thousands of plankton samples. At the same time, advances in genomics have made it possible to identify species based only on fragments of their DNA sequence. To understand the hidden geography of plankton communities in Earth's oceans, Richter et al. pored over DNA from the Tara Oceans expedition. This revealed that, despite being unable to resist the flow of water, various planktonic species which live close to the surface manage to occupy distinct, stable provinces shaped by currents. Different sizes of plankton are distributed in different sized provinces, with the smallest organisms tending to inhabit the smallest areas. Comparing DNA similarities and speeds of currents at the ocean surface revealed how these might stretch and mix plankton communities. Plankton play a critical role in the health of the ocean and the chemical cycles of planet Earth. These results could allow deeper investigation by marine modellers, ecologists, and evolutionary biologists. Meanwhile, work is already underway to investigate how climate change might impact this hidden geography.
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Ecosistema , Plancton , Genómica , Geografía , Océanos y Mares , Plancton/genéticaRESUMEN
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.
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Genoma Viral , Virus ARN , Virus , Evolución Biológica , Ecosistema , Océanos y Mares , Filogenia , ARN , Virus ARN/genética , Viroma/genética , Virus/genéticaRESUMEN
Quantitative imaging instruments produce a large number of images of plankton and marine snow, acquired in a controlled manner, from which the visual characteristics of individual objects and their in situ concentrations can be computed. To exploit this wealth of information, machine learning is necessary to automate tasks such as taxonomic classification. Through a review of the literature, we highlight the progress of those machine classifiers and what they can and still cannot be trusted for. Several examples showcase how the combination of quantitative imaging with machine learning has brought insights on pelagic ecology. They also highlight what is still missing and how images could be exploited further through trait-based approaches. In the future, we suggest deeper interactions with the computer sciences community, the adoption of data standards, and the more systematic sharing of databases to build a global community of pelagic image providers and users.
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Aprendizaje Automático , Plancton , Sedimentos GeológicosRESUMEN
The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during the Tara Oceans Polar Circle expedition, to evaluate the ecology, metabolic potential and activity of resident bacteria and archaea. We assembled 530 metagenome-assembled genomes (MAGs) to form the Arctic MAGs catalogue comprising 526 species. A total of 441 MAGs belonged to species that have not previously been reported and 299 genomes showed an exclusively polar distribution. Most Arctic MAGs have large genomes and the potential for fast generation times, both of which may enable adaptation to a copiotrophic lifestyle in nutrient-rich waters. We identified 38 habitat generalists and 111 specialists in the Arctic Ocean. We also found a general prevalence of 14 mixotrophs, while chemolithoautotrophs were mostly present in the mesopelagic layer during spring and autumn. We revealed 62 MAGs classified as key Arctic species, found only in the Arctic Ocean, showing the highest gene expression values and predicted to have habitat-specific traits. The Artic MAGs catalogue will inform our understanding of polar microorganisms that drive global biogeochemical cycles.
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Archaea/genética , Bacterias/genética , Agua de Mar/microbiología , Archaea/clasificación , Archaea/aislamiento & purificación , Regiones Árticas , Bacterias/clasificación , Bacterias/aislamiento & purificación , Ecosistema , Genoma Arqueal , Genoma Bacteriano , Metagenoma , FilogeniaRESUMEN
Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump.
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Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network-the community interactome-and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change.
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Earth's aquatic food webs are overwhelmingly supported by planktonic microalgae that live in the sunlit water column where only a minimum number of physical niches are readily identifiable. Despite this paucity of environmental differentiation, these "phytoplankton" populations exhibit a rich biodiversity, an observation not easily reconciled with broadly accepted rules of resource-based competitive exclusion. This conundrum is referred to as the "Paradox of the Plankton". Consideration of physical distancing between nutrient depletion zones around individual phytoplankton, however, suggests a competition-neutral resource landscape. Application of neutral theory to the sheer number of phytoplankton in physically-mixed water masses yields a prediction of astronomical biodiversity, suggesting the inverted paradox: Why are there so few phytoplankton species? Here, we introduce a trophic constraint on phytoplankton that, when combined with stochastic principals of ecological drift, predicts only modest levels of diversity in an otherwise competition-neutral landscape. Our "trophic exclusion" principle predicts diversity to be independent of population size and yields a species richness across cell-size classes that is consistent with broad oceanographic survey observations.
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Phytoplankton accessory pigments are commonly used to estimate phytoplankton size classes, particularly during development and validation of biogeochemical models and satellite ocean color-based algorithms. The diagnostic pigment analysis (DPA) is based on bulk measurements of pigment concentrations and relies on assumptions regarding the presence of specific pigments in different phytoplankton taxonomic groups. Three size classes are defined by the DPA: picoplankton, nanoplankton, and microplankton. Until now, the DPA has not been evaluated against an independent approach that provides phytoplankton size calculated on a per-cell basis. Automated quantitative cell imagery of microplankton and some nanoplankton, used in combination with conventional flow cytometry for enumeration of picoplankton and nanoplankton, provide a novel opportunity to perform an independent evaluation of the DPA. Here, we use a data set from the North Atlantic Ocean that encompasses all seasons and a wide range of chlorophyll concentrations (0.18-5.14 mg m-3). Results show that the DPA overestimates microplankton and picoplankton when compared to cytometry data, and subsequently underestimates the contribution of nanoplankton to total biomass. In contrast to the assumption made by the DPA that the microplankton size class is largely made up of diatoms and dinoflagellates, imaging-in-flow cytometry shows significant presence of diatoms and dinoflagellates in the nanoplankton size class. Additionally, chlorophyll b is commonly attributed solely to picoplankton by the DPA, but Chl b-containing phytoplankton are observed with imaging in both nanoplankton and microplankton size classes. We suggest revisions to the DPA equations and application of uncertainties when calculating size classes from diagnostic pigments.
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Nucleocytoplasmic large DNA viruses (NCLDVs) are ubiquitous in marine environments and infect diverse eukaryotes. However, little is known about their biogeography and ecology in the ocean. By leveraging the Tara Oceans pole-to-pole metagenomic data set, we investigated the distribution of NCLDVs across size fractions, depths and biomes, as well as their associations with eukaryotic communities. Our analyses reveal a heterogeneous distribution of NCLDVs across oceans, and a higher proportion of unique NCLDVs in the polar biomes. The community structures of NCLDV families correlate with specific eukaryotic lineages, including many photosynthetic groups. NCLDV communities are generally distinct between surface and mesopelagic zones, but at some locations they exhibit a high similarity between the two depths. This vertical similarity correlates to surface phytoplankton biomass but not to physical mixing processes, which suggests a potential role of vertical transport in structuring mesopelagic NCLDV communities. These results underscore the importance of the interactions between NCLDVs and eukaryotes in biogeochemical processes in the ocean.
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Virus Gigantes , Virus ADN , Eucariontes , Virus Gigantes/genética , Humanos , Océanos y Mares , FilogeniaRESUMEN
During the North Atlantic Aerosols and Marine Ecosystems Study in the western North Atlantic, float-based profiles of fluorescent dissolved organic matter and backscattering exhibited distinct spike layers at â¼ 300 m. The locations of the spikes were at depths similar or shallower to where a ship-based scientific echo sounder identified layers of acoustic backscatter, an Underwater Vision Profiler detected elevated concentration of zooplankton, and mesopelagic fish were sampled by a mesopelagic net tow. The collocation of spike layers in bio-optical properties with mesopelagic organisms suggests that some can be detected with float-based bio-optical sensors. This opens the door to the investigation of such aggregations/layers in observations collected by the global biogeochemical-Argo array allowing the detection of mesopelagic organisms in remote locations of the open ocean under-sampled by traditional methods.
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The North Atlantic phytoplankton spring bloom is the pinnacle in an annual cycle that is driven by physical, chemical, and biological seasonality. Despite its important contributions to the global carbon cycle, transitions in plankton community composition between the winter and spring have been scarcely examined in the North Atlantic. Phytoplankton composition in early winter was compared with latitudinal transects that captured the subsequent spring bloom climax. Amplicon sequence variants (ASVs), imaging flow cytometry, and flow-cytometry provided a synoptic view of phytoplankton diversity. Phytoplankton communities were not uniform across the sites studied, but rather mapped with apparent fidelity onto subpolar- and subtropical-influenced water masses of the North Atlantic. At most stations, cells < 20-µm diameter were the main contributors to phytoplankton biomass. Winter phytoplankton communities were dominated by cyanobacteria and pico-phytoeukaryotes. These transitioned to more diverse and dynamic spring communities in which pico- and nano-phytoeukaryotes, including many prasinophyte algae, dominated. Diatoms, which are often assumed to be the dominant phytoplankton in blooms, were contributors but not the major component of biomass. We show that diverse, small phytoplankton taxa are unexpectedly common in the western North Atlantic and that regional influences play a large role in modulating community transitions during the seasonal progression of blooms.
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Cianobacterias , Diatomeas , Biomasa , Cianobacterias/genética , Diatomeas/genética , Fitoplancton , Estaciones del AñoRESUMEN
Climate driven increases in ocean temperature and pCO2 have the potential to alter the growth and prevalence of future Harmful Algal Blooms (HABs), but systematic studies on how climate drivers influence toxic algal species relative to non-toxic phytoplankton are lacking. In particular, little is known about how future climate scenarios will affect the growth of the toxic dinoflagellate Alexandrium catenella, which is responsible for the paralytic shellfish poisoning (PSP) events that threaten the health and economy of coastal communities in the Gulf of Maine and elsewhere. The growth responses of A. catenella and two other naturally co-occurring dinoflagellates in the Gulf of Maine-Scrippsiella sp., and Amphidinium carterae-were studied in mono and mixed species cultures. Experimental treatments tested the effects of elevated temperature (20 °C), lower pH (7.8), and the combination of elevated temperature and lower pH on growth rates relative to those in near-current conditions (15 °C; pH 8.1). Growth rates of A. catenella decreased under elevated temperature and lower pH conditions, a response that was largely attributable to the effect of temperature. In contrast, growth rates of Scrippsiella sp. and A. carterae increased under elevated temperature and lower pH conditions, with temperature also being the primary driver of the response. These trends did not change substantially when these species were grown in mixed cultures (A. catenella + Scrippsiella sp., and A. catenella + A. carterae), indicating that allelopathic or competitive interactions did not affect the experimental outcome under the conditions tested. These findings suggest that A. catenella blooms may become less prevalent in the southern regions of the Gulf of Maine, but potentially more prevalent in the northeastern regions of the Gulf of Maine with continued climate change.
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Dinoflagelados , Intoxicación por Mariscos , Humanos , Concentración de Iones de Hidrógeno , Maine , TemperaturaRESUMEN
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 21st 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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Biodiversidad , Plancton/fisiología , Agua de Mar/microbiología , Geografía , Modelos Teóricos , Océanos y Mares , FilogeniaRESUMEN
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.
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Regulación de la Expresión Génica , Metagenoma , Océanos y Mares , Transcriptoma/genética , Geografía , Microbiota/genética , Anotación de Secuencia Molecular , ARN Mensajero/genética , ARN Mensajero/metabolismo , Agua de Mar/microbiología , TemperaturaRESUMEN
Four North Atlantic Aerosol and Marine Ecosystems Study (NAAMES) field campaigns from winter 2015 through spring 2018 sampled an extensive set of oceanographic and atmospheric parameters during the annual phytoplankton bloom cycle. This unique dataset provides four seasons of open-ocean observations of wind speed, sea surface temperature (SST), seawater particle attenuation at 660 nm (cp,660, a measure of ocean particulate organic carbon), bacterial production rates, and sea-spray aerosol size distributions and number concentrations (NSSA). The NAAMES measurements show moderate to strong correlations (0.56 < R < 0.70) between NSSA and local wind speeds in the marine boundary layer on hourly timescales, but this relationship weakens in the campaign averages that represent each season, in part because of the reduction in range of wind speed by multiday averaging. NSSA correlates weakly with seawater cp,660 (R = 0.36, P << 0.01), but the correlation with cp,660, is improved (R = 0.51, P < 0.05) for periods of low wind speeds. In addition, NAAMES measurements provide observational dependence of SSA mode diameter (dm) on SST, with dm increasing to larger sizes at higher SST (R = 0.60, P << 0.01) on hourly timescales. These results imply that climate models using bimodal SSA parameterizations to wind speed rather than a single SSA mode that varies with SST may overestimate SSA number concentrations (hence cloud condensation nuclei) by a factor of 4 to 7 and may underestimate SSA scattering (hence direct radiative effects) by a factor of 2 to 5, in addition to overpredicting variability in SSA scattering from wind speed by a factor of 5.