Global latitudinal variations in marine copepod diversity and environmental factors

Biodiversity patterns of epipelagic copepods in the South Pacific Ocean: Strengths and limitations of current data bases

Basin-scale patterns of biodiversity for zooplankton in the ocean may provide valuable insights for understanding the impact of climate change and global warming on the marine ecosystem. However, studies on this topic remain scarce or unavailable in vast regions of the world ocean, particularly in large regions where the amount and quality of available data are limited. In this study, we used a 27-year (1993-2019) database on species occurrence of planktonic copepods in the South Pacific, along with associated oceanographic variables, to examine their spatial patterns of biodiversity in the upper 200 m of the ocean. The aim of this study was to identify ecological regions and the environmental predictors explaining such patterns. It was found that hot and cold spots of diversity, and distinctive species assemblages were linked to major ocean currents and large regions over the basin, with increasing species richness over the subtropical areas on the East and West sides of the South Pacific. While applying the spatial models, we showed that the best environmental predictors for diversity and species composition were temperature, salinity, chlorophyll-a concentration, oxygen concentration, and the residual autocorrelation. Nonetheless, the observed spatial patterns and derived environmental effects were found to be strongly influenced by sampling coverage over space and time, revealing a highly under-sampled basin. Our findings provide an assessment of copepods diversity patterns and their potential drivers for the South Pacific Ocean, but they also stress the need for strengthening the data bases of planktonic organisms, as they can act as suitable indicators of ecosystem response to climate change at basin scale.

Divergent patterns of zooplankton connectivity in the epipelagic and mesopelagic zones of the eastern North Pacific

Due to historical under-sampling of the deep ocean, the distributional ranges of mesopelagic zooplankton are not well documented, leading to uncertainty about the mechanisms that shape midwater zooplankton community composition. Using a combination of DNA metabarcoding (18S-V4 and mtCOI) and trait-based analysis, we characterized zooplankton diversity and community composition in the upper 1000 m of the northeast Pacific Ocean. We tested whether the North Pacific Transition Zone is a biogeographic boundary region for mesopelagic zooplankton. We also tested whether zooplankton taxa occupying different vertical habitats and exhibiting different ecological traits differed in the ranges of temperature, Chl-a, and dissolved oxygen conditions inhabited. The depth of the maximum taxonomic richness deepened with increasing latitude in the North Pacific. Community similarity in the mesopelagic zone also increased in comparison with the epipelagic zone, and no evidence was found for a biogeographic boundary between previously delineated mesopelagic biogeochemical provinces. Epipelagic zooplankton exhibited broader temperature and Chl-a ranges than mesopelagic taxa. Within the epipelagic, taxa with broader temperature and Chl-a ranges also had broader distributional ranges. However, mesopelagic taxa were distributed across wider dissolved oxygen ranges, and within the mesopelagic, only oxygen ranges covaried with distributional ranges. Environmental and distributional ranges also varied among traits, both for epipelagic taxa and mesopelagic taxa. The strongest differences in both environmental and distributional ranges were observed for taxa with or without diel vertical migration behavior. Our results suggest that species traits can influence the differential effects of physical dispersal and environmental selection in shaping biogeographic distributions.

Modeling present and future distribution of plankton populations in a coastal upwelling zone: the copepod Calanus chilensis as a study case

Predicting species distribution in the ocean has become a crucial task to assess marine ecosystem responses to ongoing climate change. In the Humboldt Current System (HCS), the endemic copepod Calanus chilensis is one of the key species bioindicator of productivity and water masses. Here we modeled the geographic distribution of Calanus chilensis for two bathymetric ranges, 0-200 and 200-400 m. For the 0-200 m layer, we used the Bayesian Additive Regression Trees (BART) method, whereas, for the 200-400 m layer, we used the Ensembles of Small Models (ESMs) method and then projected the models into two future scenarios to assess changes in geographic distribution patterns. The models were evaluated using the multi-metric approach. We identified that chlorophyll-a (0.34), Mixed Layer Depth (0.302) and salinity (0.36) explained the distribution of C. chilensis. The geographic prediction of the BART model revealed a continuous distribution from Ecuador to the southernmost area of South America for the 0-200 m depth range, whereas the ESM model indicated a discontinuous distribution with greater suitability for the coast of Chile for the 200-400 m depth range. A reduction of the distribution range of C. chilensis is projected in the future. Our study suggests that the distribution of C. chilensis is conditioned by productivity and mesoscale processes, with both processes closely related to upwelling intensity. These models serve as a tool for proposing indicators of changes in the ocean. We further propose that the species C. chilensis is a high productivity and low salinity indicator at the HCS. We recommend further examining multiple spatial and temporal scales for stronger inference.

Effects of warming on the structure of aquatic communities in tropical bromeliad microecosystems

Freshwaters are among the most vulnerable ecosystems to climate warming, with projected temperature increases over the coming decades leading to significant losses of aquatic biodiversity. Experimental studies that directly warm entire natural ecosystems in the tropics are needed, for understanding the disturbances on aquatic communities. Therefore, we conducted an experiment to test the impacts of predicted future warming on density, alpha diversity, and beta diversity of freshwater aquatic communities, inhabiting natural microecosystems-Neotropical tank bromeliads. Aquatic communities within the tanks bromeliads were experimentally exposed to warming, with temperatures ranging from 23.58 to 31.72°C. Linear regression analysis was used to test the impacts of warming. Next, distance-based redundancy analysis was performed to assess how warming might alter total beta diversity and its components. This experiment was conducted across a gradient of habitat size (bromeliad water volume) and availability of detrital basal resources. A combination of the highest detritus biomass and higher experimental temperatures resulted in the greatest density of flagellates. However, the density of flagellates declined in bromeliads with higher water volume and lower detritus biomass. Moreover, the combination of the highest water volume and high temperature reduced density of copepods. Finally, warming changed microfauna species composition, mostly through species substitution (β _repl component of total beta-diversity). These findings indicate that warming strongly structures freshwater communities by reducing or increasing densities of different aquatic communities groups. It also enhances beta-diversity, and many of these effects are modulated by habitat size or detrital resources.

Towards an Understanding of Large-Scale Biodiversity Patterns on Land and in the Sea

This review presents a recent theory named ‘macroecological theory on the arrangement of life’ (METAL). This theory is based on the concept of the ecological niche and shows that the niche-environment (including climate) interaction is fundamental to explain many phenomena observed in nature from the individual to the community level (e.g., phenology, biogeographical shifts, and community arrangement and reorganisation, gradual or abrupt). The application of the theory in climate change biology as well as individual and species ecology has been presented elsewhere. In this review, I show how METAL explains why there are more species at low than high latitudes, why the peak of biodiversity is located at mid-latitudes in the oceanic domain and at the equator in the terrestrial domain, and finally why there are more terrestrial than marine species, despite the fact that biodiversity has emerged in the oceans. I postulate that the arrangement of planetary biodiversity is mathematically constrained, a constraint we previously called ‘the great chessboard of life’, which determines the maximum number of species that may colonise a given region or domain. This theory also makes it possible to reconstruct past biodiversity and understand how biodiversity could be reorganised in the context of anthropogenic climate change.

Seasonal Patterns of Phytoplankton Taxon Richness in Lakes: Effects of Temperature, Turnover and Abundance

Species richness is a key ecological characteristic that influences numerous ecosystem functions. Here we analyse the patterns and possible causes of phytoplankton taxon richness in seasonal datasets from twenty contrasting lakes in the English Lake District over six years and near-weekly datasets over 33 years from Windermere. Taxon richness was lowest in winter and highest in summer or autumn in all of the lakes. Observed richness was very similar to richness estimated from coverage and sampling effort, implying that it closely reflected true seasonal patterns. Summer populations were dominated by Chlorophyta and functional groups X1, F, N and P (sensu Reynolds). In Windermere, weekly taxon richness was strongly positively correlated with surface water temperature, as was the number of functional groups and the number of taxa per functional group. Turnover in richness of taxa and functional groups were positively correlated and both were related to surface temperature. This suggests that high taxon richness in summer is linked to higher water temperature, promoting a turnover in richness of taxa and functional groups in these lakes. However, since the number of taxa per unit concentration of chlorophyll a decreased with increasing concentration of chlorophyll a, competition might occur when abundance is high.

Identification and characterization of homeobox gene clusters in harpacticoid and calanoid copepods

In this study, we have identified the entire complement of typical homeobox (Hox) genes (Lab, Pb, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) in harpacticoid and calanoid copepods and compared them with the cyclopoid copepod Paracyclopina nana. The harpacticoid copepods Tigriopus japonicus and Tigriopus kingsejongensis have seven Hox genes (Lab, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) and the Pb and Ftz genes are also present in the cyclopoid copepod P. nana. In the Hox gene cluster of the calanoid copepod Eurytemora affinis, all the Hox genes were present linearly in the genome but the Antp gene was duplicated. Of the three representative copepods, the P. nana Hox gene cluster was the most compact due to its small genome size. The Hox gene expression profile patterns in the three representative copepods were stage-specific. The Lab, Dfd, Scr, Pb, Ftz, and Hox3 genes showed a high expression in early developmental stages but Antp, Ubx, Abd-A, and Abd-B genes were mostly expressed in later developmental stages, implying that these Hox genes may be closely associated with the development of segment identity during early development.

Plankton biogeography in the North Atlantic Ocean and its adjacent seas: Species assemblages and environmental signatures

Plankton biodiversity is a key component of marine pelagic ecosystems. They are at the base of the food web, control the productivity of marine ecosystems, and provide many provisioning and regulating ecological services. It is therefore important to understand how plankton are organized in both space and time. Here, we use data of varying taxonomic resolution, collected by the Continuous Plankton Recorder (CPR) survey, to map phytoplankton and zooplankton biodiversity in the North Atlantic and its adjacent seas. We then decompose biodiversity into 24 species assemblages and investigate their spatial distribution using ecological units and ecoregions recently proposed. Finally, we propose a descriptive method, which we call the environmental chromatogram, to characterize the environmental signature of each plankton assemblage. The method is based on a graphic that identifies where species of an assemblage aggregate along an environmental gradient composed of multiple ecological dimensions. The decomposition of the biodiversity into species assemblages allows us to show (a) that most marine regions of the North Atlantic are composed of coenoclines (i.e., gradients of biocoenoses or communities) and (b) that the overlapping spatial distribution of assemblages is the result of their environmental signatures. It follows that neither the ecoregions nor the ecological units identified in the North Atlantic are characterized by a unique assemblage but instead by a mosaic of assemblages that overlap in many places.

Global warming is causing a more pronounced dip in marine species richness around the equator

The latitudinal gradient in species richness, with more species in the tropics and richness declining with latitude, is widely known and has been assumed to be stable over recent centuries. We analyzed data on 48,661 marine animal species since 1955, accounting for sampling variation, to assess whether the global latitudinal gradient in species richness is being impacted by climate change. We confirm recent studies that show a slight dip in species richness at the equator. Moreover, richness across latitudinal bands was sensitive to temperature, reaching a plateau or declining above a mean annual sea surface temperature of 20 °C for most taxa. In response, since the 1970s, species richness has declined at the equator relative to an increase at midlatitudes and has shifted north in the northern hemisphere, particularly among pelagic species. This pattern is consistent with the hypothesis that climate change is impacting the latitudinal gradient in marine biodiversity at a global scale. The intensification of the dip in species richness at the equator, especially for pelagic species, suggests that it is already too warm there for some species to survive.

Truncated bimodal latitudinal diversity gradient in early Paleozoic phytoplankton

The latitudinal diversity gradient (LDG)-the decline in species richness from the equator to the poles-is classically considered as the most pervasive macroecological pattern on Earth, but the timing of its establishment, its ubiquity in the geological past, and explanatory mechanisms remain uncertain. By combining empirical and modeling approaches, we show that the first representatives of marine phytoplankton exhibited an LDG from the beginning of the Cambrian, when most major phyla appeared. However, this LDG showed a single peak of diversity centered on the Southern Hemisphere, in contrast to the equatorial peak classically observed for most modern taxa. We find that this LDG most likely corresponds to a truncated bimodal gradient, which probably results from an uneven sediment preservation, smaller sampling effort, and/or lower initial diversity in the Northern Hemisphere. Variation of the documented LDG through time resulted primarily from fluctuations in annual sea-surface temperature and long-term climate changes.

eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters

Zooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; however, the visual identification of early-stage larvae (the "missing biomass") is difficult and laborious. Here, eDNA metabarcoding was employed to detect zooplankton species of interest for fisheries from open and coastal waters. High-Throughput sequencing (HTS) from environmental samples using small water volumes has been proposed to detect species of interest whose DNA is the most abundant. We analyzed 6-L water samples taken from subtropical and tropical waters using Cytochrome oxidase I (COI) gene as metabarcode. In the open ocean, several commercial fish larvae and invertebrate species important in fish diet were found from metabarcodes and confirmed from individual barcoding. Comparing Atlantic, Mediterranean, Red Sea, and Pacific samples we found a lower taxonomic depth of OTU assignments in samples from tropical waters than in those from temperate ones, suggesting large gaps in reference databases for those areas; thus a higher effort of zooplankton barcoding in tropical oceans is highly recommended. This and similar simplified sampling protocols could be applied in early detection of species important for fisheries.

Environmental Gradients and Spatial Patterns of Calanoid Copepods in the Southeast Pacific

Understanding the mechanisms maintaining the biodiversity of plankton communities in marine ecosystems subject to a strongly variable ocean has become a critical issue for modern oceanography. Here, we used data on distribution of calanoid copepods in the upper layer of the ocean (0–500 m), a widely distributed taxonomic group in the pelagic realm, to assess the effects of changing oceanographic conditions on their diversity patterns and family and species richness. Copepods abundance and occurrence were evaluated from 2002 to 2015 covering the region extended between the coastal upwelling zone (CUP-Z) and the offshore region of Chile at subtropical and temperate areas. We used spatial analyses of community structure descriptors, such as abundance and diversity (family and species richness), multivariate analysis and General Additive Models (GAMS) in order to study the effect of surface temperature and its gradients, mixed layer depth, salinity and Chlorophyll-a on copepod diversity. Seventeen families were identified comprising 151 species distributed in 3 predefined zones in the onshore-offshore gradient covering the coastal upwelling, the coastal transition and the oligotrophic zones, whereas over the alongshore gradient, same families were majorly linked to the northern and southern portions of the sampled area (20–40°S). Families and species were significantly structured over the zonal gradient, revealing the dominant habitat for each of the families. Spatial patterns revealed the presence of transitional zones comprised by mixed taxa. Over the alongshore gradient this transition zone was linked to the subtropical convergence (30°S). The spatial variation of sea surface temperature (SST) revealed strong environmental zonation of temperature gradients across onshore-offshore and alongshore dimensions. Mean SST combined with mean mixed layer depth explained about 40% and about 29% of variation in family and species richness, respectively over the onshore-offshore axis. We thus conclude that the environmental zonation imposed by SST and its spatial gradients, considered as ecological barriers, is the key driver for maintaining diversity of copepods in the southeast Pacific.

Pan-regional marine benthic cryptobiome biodiversity patterns revealed by metabarcoding Autonomous Reef Monitoring Structures

Autonomous Reef Monitoring Structures (ARMS) have been applied worldwide to characterize the critical yet frequently overlooked biodiversity patterns of marine benthic organisms. In order to disentangle the relevance of environmental factors in benthic patterns, here, through standardized metabarcoding protocols, we analyse sessile and mobile (<2 mm) organisms collected using ARMS deployed across six regions with different environmental conditions (3 sites × 3 replicates per region): Baltic, Western Mediterranean, Adriatic, Black and Red Seas, and the Bay of Biscay. A total of 27,473 Amplicon Sequence Variants (ASVs) were observed ranging from 1,404 in the Black Sea to 9,958 in the Red Sea. No ASVs were shared among all regions. The highest number of shared ASVs was between the Western Mediterranean and the Adriatic Sea (116) and Bay of Biscay (115). Relatively high numbers of ASVs (103), mostly associated with the genus Amphibalanus, were also shared between the lower salinity seas (Baltic and Black Seas). We found that compositional differences in spatial patterns of rocky-shore benthos are determined slightly more by dispersal limitation than environmental filtering. Dispersal limitation was similar between sessile and mobile groups, while the sessile group had a larger environmental niche breadth than the mobile group. Further, our study can provide a foundation for future evaluations of biodiversity patterns in the cryptobiome, which can contribute up to 70% of the local biodiversity.

The mathematical influence on global patterns of biodiversity

Although we understand how species evolve, we do not appreciate how this process has filled an empty world to create current patterns of biodiversity. Here, we conduct a numerical experiment to determine why biodiversity varies spatially on our planet. We show that spatial patterns of biodiversity are mathematically constrained and arise from the interaction between the species' ecological niches and environmental variability that propagates to the community level. Our results allow us to explain key biological observations such as (a) latitudinal biodiversity gradients (LBGs) and especially why oceanic LBGs primarily peak at midlatitudes while terrestrial LBGs generally exhibit a maximum at the equator, (b) the greater biodiversity on land even though life first evolved in the sea, (c) the greater species richness at the seabed than at the sea surface, and (d) the higher neritic (i.e., species occurring in areas with a bathymetry lower than 200 m) than oceanic (i.e., species occurring in areas with a bathymetry higher than 200 m) biodiversity. Our results suggest that a mathematical constraint originating from a fundamental ecological interaction, that is, the niche-environment interaction, fixes the number of species that can establish regionally by speciation or migration.

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

Large-scale metabarcoding analysis of epipelagic and mesopelagic copepods in the Pacific

A clear insight into the large-scale community structure of planktonic copepods is critical to understanding the mechanisms controlling diversity and biogeography of marine taxa in terms of their high abundance, ubiquity, and sensitivity to environmental changes. Here, we applied a 28S metabarcoding approach to large-scale communities of epipelagic and mesopelagic copepods at 70 stations across the Pacific Ocean and three stations in the Arctic Ocean. Major patterns of community structure and diversity, influenced by water mass structures, agreed with results from previous morphology-based studies. However, a large-scale metabarcoding approach could detect community changes even under stable environmental conditions, including changes in the north/south subtropical gyres and east/west areas within each subtropical gyre. There were strong effects of the epipelagic environment on mesopelagic communities, and community subdivisions were observed in the environmentally stable mesopelagic layer. In each sampling station, higher operational taxonomic unit (OTU) numbers and lower phylogenetic diversity were observed in the mesopelagic layer than in the epipelagic layer, indicating a recent rapid increase in species numbers in the mesopelagic layer. The phylogenetic analysis utilizing representative sequences of OTUs revealed trends of recent emergence of cold-water OTUs, which are mainly distributed at high latitudes with low water temperatures. Conversely, the high diversity of copepods at low latitudes was suggested to have been formed through long evolution under high water temperature conditions. The metabarcoding results suggest that evolutionary processes have strong impacts on current patterns of copepod diversity, and support the “out of the tropics” theory explaining latitudinal diversity gradients of copepods. Diversity patterns in both epipelagic and mesopelagic copepods was highly correlated to sea surface temperature; thus, predicted global warming may have a significant impact on copepod diversity in both layers.

Marine biodiversity and the chessboard of life

Species richness is greater in places where the number of potential niches is high. Consequently, the niche may be fundamental for understanding the arrangement of life and especially, the establishment and maintenance of the well-known Latitudinal Biodiversity Gradient (LBG). However, not all potential niches may be occupied fully in a habitat, as measured by niche vacancy/saturation. Here, we theoretically reconstruct oceanic biodiversity and analyse modeled and observed data together to examine patterns in niche saturation (i.e. the ratio between observed and theoretical biodiversity of a given taxon) for several taxonomic groups. Our results led us to hypothesize that the arrangement of marine life is constrained by the distribution of the maximal number of species’ niches available, which represents a fundamental mathematical limit to the number of species that can co-exist locally. We liken this arrangement to a type of chessboard where each square on the board is a geographic area, itself comprising a distinct number of sub-squares (species’ niches). Each sub-square on the chessboard can accept a unique species of a given ecological guild, whose occurrence is determined by speciation/extinction. Because of the interaction between the thermal niche and changes in temperature, our study shows that the chessboard has more sub-squares at mid-latitudes and we suggest that many clades should exhibit a LBG because their probability of emergence should be higher in the tropics where more niches are available. Our work reveals that each taxonomic group has its own unique chessboard and that global niche saturation increases when organismal complexity decreases. As a result, the mathematical influence of the chessboard is likely to be more prominent for taxonomic groups with low (e.g. plankton) than great (e.g. mammals) biocomplexity. Our study therefore reveals the complex interplay between a fundamental mathematical constraint on biodiversity resulting from the interaction between the species’ ecological niche and fluctuations in the environmental regime (here, temperature), which has a predictable component and a stochastic-like biological influence (diversification rates, origination and clade age) that may alter or blur the former.

Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454

Metagenetics is a rapid and taxonomically comprehensive method for revealing community structures within environmental samples, based on large amounts of sequence data produced by high-throughput sequencers. Because community structures of planktonic copepods are important in the ocean owing to their high diversity and abundance, a metagenetic analysis of the 28S D2 region using Roche 454 was previously developed. However, the Illumina MiSeq platform with a high sequence output is being used more frequently in metagenetics, and non-calanoid copepods have not previously been fully evaluated. Here, we evaluated an Illumina MiSeq-based metagenetic analysis using a mock community and field-collected samples that were examined in a previous study using Roche 454, and the community structure, including non-calanoid copepods, was compared among morphological and metagenetic analyses. We removed a singleton read and applied an appropriate abundance threshold to remove erroneous Molecular Operational Taxonomic Units (MOTUs) with low-abundance sequences in the MiSeq-based analysis. Results showed that the copepod community was successfully characterized using Illumina MiSeq. Higher-quality sequences were obtained using MiSeq than by Roche 454, which reduced the overestimation of diversity, especially at a strict 99% similarity threshold for MOTU clustering. Taxonomic compositions in terms of both biomass and presence/absence of species, including non-calanoids, were more appropriately represented in the MiSeq- than in Roche 454-based analysis. Our data showed that metagenetic analysis using Illumina MiSeq is more useful for revealing copepod communities than Roche 454, owing to the lower cost and higher quality.

Pontellid copepods, Labidocera spp., affected by ocean acidification: A field study at natural CO2 seeps

CO₂ seeps in coral reefs were used as natural laboratories to study the impacts of ocean acidification on the pontellid copepod, Labidocera spp. Pontellid abundances were reduced by ∼70% under high-CO₂ conditions. Biological parameters and substratum preferences of the copepods were explored to determine the underlying causes of such reduced abundances. Stage- and sex-specific copepod lengths, feeding ability, and egg development were unaffected by ocean acidification, thus changes in these physiological parameters were not the driving factor for reduced abundances under high-CO₂ exposure. Labidocera spp. are demersal copepods, hence they live amongst reef substrata during the day and emerge into the water column at night. Deployments of emergence traps showed that their preferred reef substrata at control sites were coral rubble, macro algae, and turf algae. However, under high-CO₂ conditions they no longer had an association with any specific substrata. Results from this study indicate that even though the biology of a copepod might be unaffected by high-CO₂, Labidocera spp. are highly vulnerable to ocean acidification.

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.

Planktonic equatorial diversity troughs: fact or artifact? Latitudinal diversity gradients in Radiolaria

In contrast to the classical notion of an increasing biodiversity from the poles to the equator, a number of studies concluded that the diversity of marine species is highest at the middle latitudes, and decreases at the equator. Using a worldwide database critically compiled from 72 surveys (307 species, 4,807 water column and surface sediment samples), we analyzed the latitudinal gradients in species richness (LGSR) of a highly diversified group of marine holoplanktonic protists, the polycystine Radiolaria. Species richness values were corrected for uneven sample coverage and sample size, and contrasted with gradients in 11 environmental variables. Radiolarian species richness decreases from the equator to the poles both in the water column and in the surface sediments and is tightly coupled with temperature throughout the entire thermal range of marine waters. In the tropical Pacific Ocean, a conspicuous east-west gradient in diversity is also associated with temperature. Globally, diversity is negatively correlated with mean annual concentrations of nutrients (N, P, Si) and chlorophyll a. Disagreements with results reported for many other oceanic plankton may stem from the reduction of 3D distributional patterns onto 2D or 1D spaces, to the intermittent mixing of Subtropical and Subpolar species at the middle latitudes, and to a Mid-Domain Effect. The fact that radiolarian LGSR do not show this drop at the equator is partly due to methodological and database-related differences, and probably also in part a reflection of taxon-specific traits.

Environmental Predictors of Diversity in Recent Planktonic Foraminifera as Recorded in Marine Sediments

Global diversity patterns are thought to result from a combination of environmental and historical factors. This study tests the set of ecological and evolutionary hypotheses proposed to explain the global variation in present-day coretop diversity in the macroperforate planktonic foraminifera, a clade with an exceptional fossil record. Within this group, marine surface sediment assemblages are thought to represent an accurate, although centennial to millennial time-averaged, representation of recent diversity patterns. Environmental variables chosen to capture ocean temperature, structure, productivity and seasonality were used to model a range of diversity measures across the world's oceans. Spatial autoregressive models showed that the same broad suite of environmental variables were important in shaping each of the four largely independent diversity measures (rarefied species richness, Simpson's evenness, functional richness and mean evolutionary age). Sea-surface temperature explains the largest portion of diversity in all four diversity measures, but not in the way predicted by the metabolic theory of ecology. Vertical structure could be linked to increased diversity through the strength of stratification, but not through the depth of the mixed layer. There is limited evidence that seasonal turnover explains diversity patterns. There is evidence for functional redundancy in the low-latitude sites. The evolutionary mechanism of deep-time stability finds mixed support whilst there is relatively little evidence for an out-of-the-tropics model. These results suggest the diversity patterns of planktonic foraminifera cannot be explained by any one environmental variable or proposed mechanism, but instead reflect multiple processes acting in concert.

In situ imaging reveals the biomass of giant protists in the global ocean

Planktonic organisms play crucial roles in oceanic food webs and global biogeochemical cycles. Most of our knowledge about the ecological impact of large zooplankton stems from research on abundant and robust crustaceans, and in particular copepods. A number of the other organisms that comprise planktonic communities are fragile, and therefore hard to sample and quantify, meaning that their abundances and effects on oceanic ecosystems are poorly understood. Here, using data from a worldwide in situ imaging survey of plankton larger than 600 μm, we show that a substantial part of the biomass of this size fraction consists of giant protists belonging to the Rhizaria, a super-group of mostly fragile unicellular marine organisms that includes the taxa Phaeodaria and Radiolaria (for example, orders Collodaria and Acantharia). Globally, we estimate that rhizarians in the top 200 m of world oceans represent a standing stock of 0.089 Pg carbon, equivalent to 5.2% of the total oceanic biota carbon reservoir. In the vast oligotrophic intertropical open oceans, rhizarian biomass is estimated to be equivalent to that of all other mesozooplankton (plankton in the size range 0.2-20 mm). The photosymbiotic association of many rhizarians with microalgae may be an important factor in explaining their distribution. The previously overlooked importance of these giant protists across the widest ecosystem on the planet changes our understanding of marine planktonic ecosystems.

Open science resources for the discovery and analysis of Tara Oceans data

The Tara Oceans expedition (2009–2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events.

Next generation sequencing reveals the hidden diversity of zooplankton assemblages

Background

Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel.

Methodology/Principle Findings

Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups.

Conclusions

Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.

Biodiversity tracks temperature over time

The geographic distribution of life on Earth supports a general pattern of increase in biodiversity with increasing temperature. However, some previous analyses of the 540-million-year Phanerozoic fossil record found a contrary relationship, with paleodiversity declining when the planet warms. These contradictory findings are hard to reconcile theoretically. We analyze marine invertebrate biodiversity patterns for the Phanerozoic Eon while controlling for sampling effort. This control appears to reverse the temporal association between temperature and biodiversity, such that taxonomic richness increases, not decreases, with temperature. Increasing temperatures also predict extinction and origination rates, alongside other abiotic and biotic predictor variables. These results undermine previous reports of a negative biodiversity-temperature relationship through time, which we attribute to paleontological sampling biases. Our findings suggest a convergence of global scale macroevolutionary and macroecological patterns for the biodiversity-temperature relationship.

Biologging, remotely-sensed oceanography and the continuous plankton recorder reveal the environmental determinants of a seabird wintering hotspot

Marine environments are greatly affected by climate change, and understanding how this perturbation affects marine vertebrates is a major issue. In this context, it is essential to identify the environmental drivers of animal distribution. Here, we focused on the little auk (Alle alle), one of the world’s most numerous seabirds and a major component in Arctic food webs. Using a multidisciplinary approach, we show how little auks adopt specific migratory strategies and balance environmental constraints to optimize their energy budgets. Miniature electronic loggers indicate that after breeding, birds from East Greenland migrate >2000 km to overwinter in a restricted area off Newfoundland. Synoptic data available from the Continuous Plankton Recorder (CPR) indicate that this region harbours some of the highest densities of the copepod Calanus finmarchicus found in the North Atlantic during winter. Examination of large-scale climatic and oceanographic data suggests that little auks favour patches of high copepod abundance in areas where air temperature ranges from 0°C to 5°C. These results greatly advance our understanding of animal responses to extreme environmental constraints, and highlight that information on habitat preference is key to identifying critical areas for marine conservation.

Large-scale biodiversity patterns in freshwater phytoplankton

Our planet shows striking gradients in the species richness of plants and animals, from high biodiversity in the tropics to low biodiversity in polar and high-mountain regions. Recently, similar patterns have been described for some groups of microorganisms, but the large-scale biogeographical distribution of freshwater phytoplankton diversity is still largely unknown. We examined the species diversity of freshwater phytoplankton sampled from 540 lakes and reservoirs distributed across the continental United States and found strong latitudinal, longitudinal, and altitudinal gradients in phytoplankton biodiversity, demonstrating that microorganisms can show substantial geographic variation in biodiversity. Detailed analysis using structural equation models indicated that these large-scale biodiversity gradients in freshwater phytoplankton diversity were mainly driven by local environmental factors, although there were residual direct effects of latitude, longitude, and altitude as well. Specifically, we found that phytoplankton species richness was an increasing saturating function of lake chlorophyll a concentration, increased with lake surface area and possibly increased with water temperature, resembling effects of productivity, habitat area, and temperature on diversity patterns commonly observed for macroorganisms. In turn, these local environmental factors varied along latitudinal, longitudinal, and altitudinal gradients. These results imply that changes in land use or climate that affect these local environmental factors are likely to have major impacts on large-scale biodiversity patterns of freshwater phytoplankton.

Biodiversity and ecosystem function in the Gulf of Maine: pattern and role of zooplankton and pelagic nekton

This paper forms part of a broader overview of biodiversity of marine life in the Gulf of Maine area (GoMA), facilitated by the GoMA Census of Marine Life program. It synthesizes current data on species diversity of zooplankton and pelagic nekton, including compilation of observed species and descriptions of seasonal, regional and cross-shelf diversity patterns. Zooplankton diversity in the GoMA is characterized by spatial differences in community composition among the neritic environment, the coastal shelf, and deep offshore waters. Copepod diversity increased with depth on the Scotian Shelf. On the coastal shelf of the western Gulf of Maine, the number of higher-level taxonomic groups declined with distance from shore, reflecting more nearshore meroplankton. Copepod diversity increased in late summer, and interdecadal diversity shifts were observed, including a period of higher diversity in the 1990s. Changes in species diversity were greatest on interannual scales, intermediate on seasonal scales, and smallest across regions, in contrast to abundance patterns, suggesting that zooplankton diversity may be a more sensitive indicator of ecosystem response to inter annual climate variation than zoo plankton abundance. Local factors such as bathymetry, proximity of the coast, and advection probably drive zooplankton and pelagic nekton diversity patterns in the GoMA, while ocean-basin scale diversity patterns probably contribute to the increase in diversity at the Scotian Shelf break, a zone of mixing between the cold-temperate community of the shelf and the warm-water community offshore. Pressing research needs include establishment of a comprehensive system for observing change in zooplankton and pelagic nekton diversity, enhanced observations of "underknown" but important functional components of the ecosystem, population and metapopulation studies, and development of analytical modeling tools to enhance understanding of diversity patterns and drivers. Ultimately, sustained observations and modeling analysis of biodiversity must be effectively communicated to managers and incorporated into ecosystem approaches for management of GoMA living marine resources.

From sea to sea: Canada's three oceans of biodiversity

Evaluating and understanding biodiversity in marine ecosystems are both necessary and challenging for conservation. This paper compiles and summarizes current knowledge of the diversity of marine taxa in Canada's three oceans while recognizing that this compilation is incomplete and will change in the future. That Canada has the longest coastline in the world and incorporates distinctly different biogeographic provinces and ecoregions (e.g., temperate through ice-covered areas) constrains this analysis. The taxonomic groups presented here include microbes, phytoplankton, macroalgae, zooplankton, benthic infauna, fishes, and marine mammals. The minimum number of species or taxa compiled here is 15,988 for the three Canadian oceans. However, this number clearly underestimates in several ways the total number of taxa present. First, there are significant gaps in the published literature. Second, the diversity of many habitats has not been compiled for all taxonomic groups (e.g., intertidal rocky shores, deep sea), and data compilations are based on short-term, directed research programs or longer-term monitoring activities with limited spatial resolution. Third, the biodiversity of large organisms is well known, but this is not true of smaller organisms. Finally, the greatest constraint on this summary is the willingness and capacity of those who collected the data to make it available to those interested in biodiversity meta-analyses. Confirmation of identities and intercomparison of studies are also constrained by the disturbing rate of decline in the number of taxonomists and systematists specializing on marine taxa in Canada. This decline is mostly the result of retirements of current specialists and to a lack of training and employment opportunities for new ones. Considering the difficulties encountered in compiling an overview of biogeographic data and the diversity of species or taxa in Canada's three oceans, this synthesis is intended to serve as a biodiversity baseline for a new program on marine biodiversity, the Canadian Healthy Ocean Network. A major effort needs to be undertaken to establish a complete baseline of Canadian marine biodiversity of all taxonomic groups, especially if we are to understand and conserve this part of Canada's natural heritage.

Marine biodiversity, ecosystem functioning, and carbon cycles

Although recent studies suggest that climate change may substantially accelerate the rate of species loss in the biosphere, only a few studies have focused on the potential consequences of a spatial reorganization of biodiversity with global warming. Here, we show a pronounced latitudinal increase in phytoplanktonic and zooplanktonic biodiversity in the extratropical North Atlantic Ocean in recent decades. We also show that this rise in biodiversity paralleled a decrease in the mean size of zooplanktonic copepods and that the reorganization of the planktonic ecosystem toward dominance by smaller organisms may influence the networks in which carbon flows, with negative effects on the downward biological carbon pump and demersal Atlantic cod (Gadus morhua). Our study suggests that, contrary to the usual interpretation of increasing biodiversity being a positive emergent property promoting the stability/resilience of ecosystems, the parallel decrease in sizes of planktonic organisms could be viewed in the North Atlantic as reducing some of the services provided by marine ecosystems to humans.