Jenny A. Huggett

DNA metabarcoding of zooplankton samples is well suited to surveys of marine pelagic ecosystems; however, consistent amplification across zooplankton groups cannot be assumed when using “universal” miniCOI primers. Under-representation of some groups may result from primer bias or inadequate coverage in barcode reference libraries. We designed taxon-specific mini-barcode primers to improve the representation of copepods, euphausiids, chaetognaths, and hydrozoans in metabarcoding outputs of mixed zooplankton samples from the Southwest (SW) Indian Ocean. In silico analyses of downloaded sequences per group identified the most informative mini-barcode region, and barcode gap analyses confirmed that the selected regions could distinguish among species within each group. In vitro analyses of DNA extracts from individual specimens per group showed that the new mini-barcode primers outperformed the standard and universal miniCOI primers by consistently recovering higher Phred quality scores. Metabarcoding of four in situ mixed zooplankton samples collected with plankton tow nets and processed with a combination of taxon-specific and universal primers identified 220 species. Use of the primer cocktails increased the proportionate representation of the target groups by three- to five-fold compared to a previous study. Read counts were dominated by copepods and euphausiids, implying that they had the highest relative biomass in samples. We conclude that a combination of universal and taxon-specific primers in metabarcoding assays will achieve a more comprehensive assessment of biodiversity by enhancing species richness estimates across different groups.

Plankton, a diverse group of aquatic organisms, make Earth livable, regulate aquatic life, and provide benefits to human societies such as access to clean water, food security, and well-being. They also support economies and inspire biotechnological innovations. This article aims to raise awareness of the value of plankton to humanity and serves as an informative guide for aquatic professionals, policymakers, and anyone interested in plankton. We present the value of plankton across six themes of human interest: biogeochemistry; ecology; climate; the evolution of science; economy; and culture, recreation, and well-being. Guided by the 2022 Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services values assessment, we introduce the six themes under the Life Framework of Values to offer a comprehensive summary of the significance of plankton to humanity. In addition, we provide examples of plankton variables used in policy frameworks and recommendations for enhancing understanding of their value through long-term sustainable research and monitoring.

In marine ecosystems, most physiological, ecological, or physical processes are size dependent. These include metabolic rates, the uptake of carbon and other nutrients, swimming and sinking velocities, and trophic interactions, which eventually determine the stocks of commercial species, as well as biogeochemical cycles and carbon sequestration. As such, broad-scale observations of plankton size distribution are important indicators of the general functioning and state of pelagic ecosystems under anthropogenic pressures. Here, we present the first global datasets of the Pelagic Size Structure database (PSSdb), generated from plankton imaging devices. This release includes the bulk particle normalized biovolume size spectrum (NBSS) and the bulk particle size distribution (PSD), along with their related parameters (slope, intercept, and R ² ) measured within the epipelagic layer (0–200 m) by three imaging sensors: the Imaging FlowCytobot (IFCB), the Underwater Vision Profiler (UVP), and benchtop scanners. Collectively, these instruments effectively image organisms and detrital material in the 7–10 000 µm size range. A total of 92 472 IFCB samples, 3068 UVP profiles, and 2411 scans passed our quality control and were standardized to produce consistent instrument-specific size spectra averaged to 1° × 1° latitude and longitude and by year and month. Our instrument-specific datasets span most major ocean basins, except for the IFCB datasets we have ingested, which were exclusively collected in northern latitudes, and cover decadal time periods (2013–2022 for IFCB, 2008–2021 for UVP, and 1996–2022 for scanners), allowing for a further assessment of the pelagic size spectrum in space and time. The datasets that constitute PSSdb's first release are available at https://doi.org/10.5281/zenodo.11050013 (Dugenne et al., 2024b). In addition, future updates to these data products can be accessed at https://doi.org/10.5281/zenodo.7998799.

In marine ecosystems, most physiological, ecological, or physical processes are size-dependent. These include metabolic rates, uptake of carbon and other nutrients, swimming and sinking velocities, and trophic interactions, which eventually determine the stocks of commercial species, as well as biogeochemical cycles and carbon sequestration. As such, broad scale observations of plankton size distribution are important indicators of the general functioning and state of pelagic ecosystems under anthropogenic pressures. Here, we present the first global datasets of the Pelagic Size Structure database (PSSdb), generated from plankton imaging devices. This release includes the bulk particle Normalized Biovolume Size Spectrum (NBSS) and bulk Particle Size Distribution (PSD), along with their related parameters (slope, intercept, and R²) measured within the epipelagic layer (0–200 m) by three imaging sensors: the Imaging FlowCytobot (IFCB), the Underwater Vision Profiler (UVP) and benchtop scanners. Collectively, these instruments effectively image organisms and detrital material in the 7–10,000 μm size range. A total of 92,472 IFCB samples, 3,068 UVP profiles, and 2,411 scans passed our quality control and were standardized to produce consistent instrument-specific size spectra averaged in 1x1° latitude/longitude, and by year and month. Our instrument-specific datasets span all major ocean basins, except for the IFCB which was exclusively deployed in northern latitudes, and cover decadal time periods (2013–2022 for IFCB, 2008–2021 for UVP, and 1996–2022 for scanners), allowing for a further assessment of the pelagic size spectrum in space and time. The datasets that constitute PSSdb’s first release are available at https://doi.org/10.5281/zenodo.10150020 (Dugenne et al., 2023).

In marine ecosystems, most physiological, ecological, or physical processes are size-dependent. These include metabolic rates, uptake of carbon and other nutrients, swimming and sinking velocities, and trophic interactions, which eventually determine the stocks of commercial species, as well as biogeochemical cycles and carbon sequestration. As such, broad scale observations of plankton size distribution are important indicators of the general functioning and state of pelagic ecosystems under anthropogenic pressures. Here, we present the first global datasets of the Pelagic Size Structure database (PSSdb), generated from plankton imaging devices. This release includes the bulk particle Normalized Biovolume Size Spectrum (NBSS) and bulk Particle Size Distribution (PSD), along with their related parameters (slope, intercept, and R2) measured within the epipelagic layer (0–200 m) by three imaging sensors: the Imaging FlowCytobot (IFCB), the Underwater Vision Profiler (UVP) and benchtop scanners. Collectively, these instruments effectively image organisms and detrital material in the 7–10,000 μm size range. A total of 92,472 IFCB samples, 3,068 UVP profiles, and 2,411 scans passed our quality control and were standardized to produce consistent instrument-specific size spectra averaged in 1x1° latitude/longitude, and by year and month. Our instrument-specific datasets span all major ocean basins, except for the IFCB which was exclusively deployed in northern latitudes, and cover decadal time periods (2013–2022 for IFCB, 2008–2021 for UVP, and 1996–2022 for scanners), allowing for a further assessment of the pelagic size spectrum in space and time. The datasets that constitute PSSdb’s first release are available at https://doi.org/10.5281/zenodo.10150020 (Dugenne et al., 2023).

Zooplankton play a key role in marine food webs and carbon cycling and are useful indicators of climaterelated changes and ocean health in pelagic ecosystems. Zooplankton are traditionally identified to species through microscopy, but new molecular techniques have enabled the identification of individual specimens (DNA barcoding) or multiple species in the same sample (DNA metabarcoding). Metabarcoding has been tested and refined using zooplankton collected in South African waters for the first time. Challenges to the implementation of DNA-based methods to measure zooplankton biodiversity easily and routinely include an incomplete DNA barcode reference library, logistical complexity and uptake of the new technology by environmental management agencies. These challenges call for a national effort to intensify zooplankton barcoding initiatives and to effectively engage stakeholders in developing a roadmap towards application of DNA-based methods in marine environmental management. Significance: Metabarcoding has been successfully applied to marine zooplankton for the first time in South Africa, demonstrating its potential as a tool to generate ecosystem indicators during routine ocean observations. National barcoding efforts must be intensified to provide a comprehensive reference library of zooplankton DNA. Effective engagement with stakeholders is required to overcome logistical and policy challenges, and to provide a roadmap towards application of DNA-based methods in marine environmental management.

For over 50 years, the conceptualisation of low-nutrient oligotrophic systems having longer food chains and thus lower energy transfer to fish than their high-nutrient eutrophic counterparts¹ has achieved the status of an ecological paradigm. However, recent global assessments indicate global fish biomass could be much higher than previously thought^2–4, suggesting that our traditional understanding of food webs may need to be revisited. Here, we challenge the classical paradigm by exploring the role of zooplankton in food webs across the world’s oceans. Using observed zooplankton size spectra, and output from a size-spectrum model that resolves nine zooplankton groups, we conclude that food chains in oligotrophic (low-nutrient) and eutrophic (high-nutrient) systems have similar lengths. We offer a compelling hypothesis to explain this emergent pattern: self-organisation of zooplankton groups across the global productivity gradient regulates food chain length. We find that in oligotrophic systems the increased carnivory and longer food chains are offset by relatively large gelatinous filter feeders eating the dominant small phytoplankton, resulting in shorter-than-expected food chains, but decreasing food quality for fish. Our findings highlight the pivotal role zooplankton play in regulating energy transfer. Better resolution of zooplankton groups, their feeding relationships and carbon content in models will increase our ability to estimate current global fish biomass ⁵, project future fish biomass under climate change^6–8, and provide more-robust forecasts of nutrient⁹ and carbon cycling¹⁰.

The Indian Ocean presents two distinct climate regimes. The north Indian Ocean is dominated by the monsoons, whereas the seasonal reversal is less pronounced in the south. The prevailing wind pattern produces upwelling along different parts of the coast in both hemispheres during different times of the year. Additionally, dynamical processes and eddies either cause or enhance upwelling. This paper reviews the phenomena of upwelling along the coast of the Indian Ocean extending from the tip of South Africa to the southern tip of the west coast of Australia. Observed features, underlying mechanisms, and the impact of upwelling on the ecosystem are presented. In the Agulhas Current region, cyclonic eddies associated with Natal pulses drive slope upwelling and enhance chlorophyll concentrations along the continental margin. The Durban break-away eddy spun up by the Agulhas upwells cold nutrient-rich water. Additionally, topographically induced upwelling occurs along the inshore edges of the Agulhas Current. Wind-driven coastal upwelling occurs along the south coast of Africa and augments the dynamical upwelling in the Agulhas Current. Upwelling hotspots along the Mozambique coast are present in the northern and southern sectors of the channel and are ascribed to dynamical effects of ocean circulation in addition to wind forcing. Interaction of mesoscale eddies with the western boundary, dipole eddy pair interactions, and passage of cyclonic eddies cause upwelling. Upwelling along the southern coast of Madagascar is caused by the Ekman wind-driven mechanism and by eddy generation and is inhibited by the Southwest Madagascar Coastal Current. Seasonal upwelling along the East African coast is primarily driven by the northeast monsoon winds and enhanced by topographically induced shelf breaking and shear instability between the East African Coastal Current and the island chains. The Somali coast presents a strong case for the classical Ekman type of upwelling; such upwelling can be inhibited by the arrival of deeper thermocline signals generated in the offshore region by wind stress curl. Upwelling is nearly uniform along the coast of Arabia, caused by the alongshore component of the summer monsoon winds and modulated by the arrival of Rossby waves generated in the offshore region by cyclonic wind stress curl. Along the west coast of India, upwelling is driven by coastally trapped waves together with the alongshore component of the monsoon winds. Along the southern tip of India and Sri Lanka, the strong Ekman transport drives upwelling. Upwelling along the east coast of India is weak and occurs during summer, caused by alongshore winds. In addition, mesoscale eddies lead to upwelling, but the arrival of river water plumes inhibits upwelling along this coast. Southeasterly winds drive upwelling along the coast of Sumatra and Java during summer, with Kelvin wave propagation originating from the equatorial Indian Ocean affecting the magnitude and extent of the upwelling. Both El Niño–Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) events cause large variability in upwelling here. Along the west coast of Australia, which is characterized by the anomalous Leeuwin Current, southerly winds can cause sporadic upwelling, which is prominent along the southwest, central, and Gascoyne coasts during summer. Open-ocean upwelling in the southern tropical Indian Ocean and within the Sri Lanka Dome is driven primarily by the wind stress curl but is also impacted by Rossby wave propagations. Upwelling is a key driver enhancing biological productivity in all sectors of the coast, as indicated by enhanced sea surface chlorophyll concentrations. Additional knowledge at varying levels has been gained through in situ observations and model simulations. In the Mozambique Channel, upwelling simulates new production and circulation redistributes the production generated by upwelling and mesoscale eddies, leading to observations of higher ecosystem impacts along the edges of eddies. Similarly, along the southern Madagascar coast, biological connectivity is influenced by the transport of phytoplankton from upwelling zones. Along the coast of Kenya, both productivity rates and zooplankton biomass are higher during the upwelling season. Along the Somali coast, accumulation of upwelled nutrients in the northern part of the coast leads to spatial heterogeneity in productivity. In contrast, productivity is more uniform along the coasts of Yemen and Oman. Upwelling along the west coast of India has several biogeochemical implications, including oxygen depletion, denitrification, and high production of CH₄ and dimethyl sulfide. Although weak, wind-driven upwelling leads to significant enhancement of phytoplankton in the northwest Bay of Bengal during the summer monsoon. Along the Sumatra and Java coasts, upwelling affects the phytoplankton composition and assemblages. Dissimilarities in copepod assemblages occur during the upwelling periods along the west coast of Australia. Phytoplankton abundance characterizes inshore edges of the slope during upwelling season, and upwelling eddies are associated with krill abundance. The review identifies the northern coast of the Arabian Sea and eastern coasts of the Bay of Bengal as the least observed sectors. Additionally, sustained long-term observations with high temporal and spatial resolutions along with high-resolution modelling efforts are recommended for a deeper understanding of upwelling, its variability, and its impact on the ecosystem.

Macroecological relationships provide insights into rules that govern ecological systems. Bergmann's rule posits that members of the same clade are larger at colder temperatures. Whether temperature drives this relationship is debated because several other potential drivers covary with temperature. We conducted a near‐global comparative analysis on marine copepods (97 830 samples, 388 taxa) to test Bergmann's rule, considering other potential drivers. Supporting Bergmann's rule, we found temperature better predicted size than did latitude or oxygen, with body size decreasing by 43.9% across the temperature range (‐1.7 to 30ºC). Body size also decreased by 26.9% across the range in food availability. Our results provide strong support for Bergman's rule in copepods, but emphasises the importance of other drivers in modifying this pattern. As the world warms, smaller copepod species are likely to emerge as ‘winners', potentially reducing rates of fisheries production and carbon sequestration.