AtlantECO-KER-AM-2

Ocean warming can affect plankton both directly, through altered metabolic activities, and indirectly, modifying the physical–chemical properties of the water column, with possible effects on ecosystem functioning. To evaluate the combined action of warming-related physiological responses and environmental changes on plankton functioning, we carried out a long-term analysis (from 1994 to 2019) of the Bermuda Atlantic Time-series Study (BATS) dataset where ocean warming and stratification have driven a decrease in the net primary production over the last decade. Using the time series of plankton observations, we assembled 1000 replicates of a food web model for each year. We observed that the total flow of matter through the model remained constant over time, despite the increased oligotrophication, due to global warming, after 2014. In fact, the plankton food web remained robust through re-modulated trophic interactions with an increased detritivory to herbivory ratio of the food web over time. However, it was problematic to re-establish the trophic connections of the food web broken by ocean warming, as remarked by the increased relative internal ascendency. Thanks to trophic plasticity, the reduced zooplankton dependence on herbivory was compensated by a significant increase in the reliance on carnivory and detritivores, highlighting the crucial role of trophic interactions in buffering significant environmental short-term changes.

While a rich history of patchiness research has explored spatial structure in the ocean, there is no consensus over the controls on biological patchiness and how physical-ecological-biogeochemical processes and patchiness relate. The prevailing thought is that physics structures biology, but this has not been tested at basin scale with consistent in situ measurements. Here we use the slope of the relationship between variance vs spatial scale to quantify patchiness and ~650,000 nearly continuous (dx ~ 200 m) measurements - representing the Atlantic, Pacific, and Southern Oceans - and find that patchiness of biological parameters and physical parameters are uncorrelated. We show variance slope is an emergent property with unique patterns in biogeochemical properties distinct from physical tracers, yet correlated with other biological tracers. These results provide context for decades of observations with different interpretations, suggest the use of spatial tests of biogeochemical model parameterizations, and open the way for studies into processes regulating the observed patterns.

Copepods are a major group of the mesozooplankton and thus a key part of marine ecosystems worldwide. Their fitness and life strategies are determined by their functional traits which allow different species to exploit various ecological niches. The range of functional traits expressed in a community defines its functional diversity (FD), which can be used to investigate how communities utilize resources and shape ecosystem processes. However, the spatial patterns of copepod FD and their relation to ecosystem functioning remain poorly understood on a global scale. Here, we use estimates of copepod community composition derived from species distribution models in combination with functional traits and indicators of ecosystem functioning to investigate the distribution of multiple facets of copepod FD, their relationships with species richness and ecosystem processes. We also project how anthropogenic climate change will impact the facets of copepod FD. We find that the facets of FD respond to species richness with variable strength and directions: functional richness, divergence, and dispersion increase with species richness whereas functional evenness and trait dissimilarity decrease. We find that primary production, mesozooplankton biomass and carbon export efficiency decrease with species richness, functional richness, divergence and dispersion. This suggests that ecosystem functioning may be disproportionally influenced by the traits of a few dominant species in line with the mass ratio hypothesis. Furthermore, climate change is projected to promote trait homogenization globally, which may decrease mesozooplankton biomass and carbon export efficiency globally. The emergent covariance patterns between copepod FD and ecosystem functions we find here strongly call for better integrating FD measurements into field studies and across scales to understand the effects of changing zooplankton biodiversity on marine ecosystem functioning.

Non-cyanobacteria diazotrophs (NCDs) are shown to dominate in surface waters shifting the long-held paradigm of cyanobacteria dominance. This raises fundamental questions on how these putative heterotrophic bacteria thrive in sunlit oceans. The absence of laboratory cultures of these bacteria significantly limits our ability to understand their behavior in natural environments and, consequently, their contribution to the marine nitrogen cycle. Here, via a multidisciplinary approach, we identify the presence of NCDs within the phycosphere of the model diatom Phaeodactylum tricornutum (Pt), which sustain the survival of Pt in nitrogen-depleted conditions. Through bacterial metacommunity sequencing and genome assembly, we identify multiple NCDs belonging to the Rhizobiales order, including Bradyrhizobium, Mesorhizobium, Georhizobium, and Methylobacterium. We demonstrate the nitrogen-fixing ability of PtNCDs through in silico identification of nitrogen fixation genes and by other experimental assays. We show the wide occurrence of this type of interactions with the isolation of NCDs from other microalgae, their identification in the environment, and their predicted associations with photosynthetic microalgae. Our study underscores the importance of microalgae interactions with NCDs to support nitrogen fixation. This work provides a unique model Pt-NCDs to study the ecology of this interaction, advancing our understanding of the key drivers of global marine nitrogen fixation.

Life history traits influence marine species dispersal and habitat colonization. Medusozoans (jellyfish and siphonophores) exhibit diverse life cycles, evolved from an ancestral cycle alternating between a benthic polyp and a pelagic medusa. Despite their ecological importance, factors shaping medusozoan distribution remain poorly understood. By integrating metabarcoding and environmental data from the Tara Oceans expedition with life history traits, we provide global evidence supporting the longstanding hypothesis that benthic polyp presence/absence is a key factor influencing the distribution and abundance of planktonic medusozoans in the surface ocean. We inferred on a time-calibrated phylogeny of Medusozoa multiple transitions to a fully planktonic (holoplanktonic) life cycle, either through polyp loss, acquisition of drifting polyps, or development of polyps parasitizing pelagic organisms. We could associate each transition with a shift toward offshore habitats and the emergence of globally dominant Operational Taxonomic Units (OTUs), whose abundance far exceeds that of any nonholoplanktonic medusozoans in the planktonic realm. The prevalence of holoplanktonic medusozoans in terms of abundance and diversity is broadly observed in coastal and offshore environments, peaking over greater bathymetric depths in tropical and subtropical regions. We show that holoplanktonic and nonholoplanktonic groups interact with distinct yet compositionally similar planktonic communities. Holoplanktonic OTUs occupy more peripheral positions in a plankton interactome, suggesting greater flexibility in biotic interactions, an adaptive trait in rapidly changing planktonic ecosystems. These findings highlight how life cycle evolution shaped the global distribution of medusozoans and suggest that variations in life history may significantly influence how medusozoans respond to global environmental changes.

Earth system models (ESMs) highly simplify their representation of biological processes, leading to major uncertainty in the impacts of climate change. Despite a growing understanding of molecular networks from genomic data, describing how changing phytoplankton physiology affects biogeochemical processes remains elusive. Here, we embed genome-scale models within a state-of-the-art ESM to deliver an integrated understanding of how gradients of nutrients modulate the molecular physiology of various plankton. In particular, when applied to Prochlorococcus, we find that glycogen and lipid management can be interpreted in terms of acclimation to different environments. Generalized to other phytoplankton such as the diatom Thalassiosira, we estimate the production of 39 metabolites that constitute hot spots of dissolved organic carbon described by their amount of carbon produced and their diversity of associated metabolites in ESMs. This modeling approach shows how genome scale–enabled ESMs have the potential to advance our understanding of microbial ecosystem functioning in ocean biogeochemical processes.

This paper presents the quantitative imaging datasets collected during the Tara Pacific expedition (2016–2018) carried out on the schooner Tara. The datasets cover a wide range of plankton sizes, from microphytoplankton (> 20 µm in size) to mesozooplankton (a few centimetres in size), and non-living particles such as plastic and detrital particles. It consists of surface samples collected across the North Atlantic and the North and South Pacific Ocean from open-ocean stations (a total of 357 samples) and from stations located in coastal waters, lagoons or reefs of 32 Pacific islands (a total of 228 samples). As this expedition involved long distances and long sailing times, we designed two sampling systems to collect plankton while sailing at speeds of up to 9 knots. To sample microplankton, surface water was pumped aboard using a customised pumping system and filtered through a 20 µm mesh size plankton net (hereafter referred to as the deck net – DN). A high-speed net (HSN; 330 µm mesh size) was developed to sample the mesoplankton. In addition, a manta net (330 µm) was also used, when possible, to collect mesoplankton and plastics simultaneously. We could not deploy these nets at the reef and lagoon stations of islands. Instead, two bongo nets (20 µm) attached to an underwater scooter were used to sample microplankton. In addition to describing and presenting the datasets, the complementary aim of this paper is to investigate and quantify the potential sampling biases associated with these two high-speed sampling systems and the different net types, in order to improve further ecological interpretations. Regarding the imaging techniques, microplankton (20–200 µm) from the DN and bongo net were imaged directly aboard Tara using a FlowCam instrument (Fluid Imaging Technologies), whereas mesoplankton (>200 µm) from the HSN and manta net were analysed in the laboratory with a ZooScan system (back on land). Organisms and other particles were taxonomically and morphologically classified using the automatic sorting tools of the EcoTaxa web application; following this, validation or correction was carried out by taxonomic experts. For microplankton smaller than 45 µm, a subsample of 30 % of the annotations was 100 % visually validated by experts. More than 300 different taxonomic and morphological groups were identified. The datasets include the metadata and the raw data from which morphological traits such as size (equivalent spherical diameter) and biovolume were calculated for each particle as well as a number of quantitative descriptors of the surface plankton communities. These descriptors include abundance, biovolumes, the Shannon diversity index and normalised biovolume size spectrum, allowing the study of their structures (e.g. taxonomic, functional, size and trophic structures) according to a wide range of environmental parameters at the basin scale.

We provide high-quality metagenome-assembled genomes (MAGs) derived from seawater and sea ice samples collected in the Southern Ocean. Several MAGs encode genes associated with dimethylsulfoniopropionate (DMSP) lyase activity and methane oxidation. This resource provides insights regarding the role of microbial communities in the production of key volatile compounds.