Biology subjects

Iudicone, D.

Publications and source records attributed to Iudicone, D..

9 recordsLinked to original sources

bioRxiv2026

Particle-based representation of phytoplankton modulates emergent coexistence and biogeography in a model ocean

Phytoplankton communities sustain the marine food web through primary productivity. These communities sustain a high diversity of species, all of which must draw from the same finite nutrient supply. The mechanisms driving phytoplankton biogeography and succession, as well as those enabling high diversity, remain incompletely understood. Here, we compare emerging patterns of biogeography, richness, and diversity in a size-structured phytoplankton community as it is advected and diffused within an idealized North Atlantic double-gyre circulation, using both Eulerian and Lagrangian (particle-based) modeling (PBM) frameworks. When a sufficient number of particles is modeled, the PBM, which resolves mortality at the particle level, produces stronger seasonal variability in biomass in the northern gyre and less stable and higher biomass in the southern gyre, while reproducing large-scale chlorophyll patterns observed by satellite. These contrasting dynamics are accompanied by distinct regional diversity patterns: local richness and diversity are generally higher in the PBM than in the Eulerian model in the northern gyre, with differences depending on the mortality threshold, whereas in the oligotrophic southern gyre, PBM local richness increases with particle number, while Eulerian richness is more sensitive to the mortality threshold. The PBM also produces a dynamic and emergent biogeographical structure that is more robust to the mortality threshold than the Eulerian model. Finally, Lagrangian variability in environmental conditions experienced by particles shows a stronger impact compared to the local Eulerian variability in the Northern gyre and stresses variable sensitivity to environmental histories. Together, these results suggest that the discrete representation of biomass fundamentally alters mortality, biogeography, and emergent coexistence patterns in model plankton ecosystems.

ecology↗

bioRxiv2025

Deviation from Power-Law Distribution when Scaling the Distribution of Marine Plankton Folds from Genomes to Communities

At different scales of living systems, biological entities appear to follow scaling laws, such as power laws, which are often explained from stochastic mechanisms. This is the case for the number of species in a community and the number of genes or protein folds in a genome. Resulting from evolutionary processes combining gene family duplications and expansions with selective pressures, the distribution of protein folds systematically follows a power law in all individually observed genomes. A small number of folds are highly prevalent, while the majority of folds appear only once per genome. However, previous studies on fold occurrence have focused on individual genomes, isolated from their community contexts. In the oceans, plankton communities consist of complex assemblages of species, each exhibiting variable relative abundances. We investigated the consequences of this variability on the composition and distribution of folds by considering the relative abundance of species. By annotating folds to genes of environmental genomes of plankton collected by the Tara Oceans expedition, we show that the relative abundance of folds deviates from the classical power law and instead follows a Type II Pareto distribution. This model, typically observed in other complex organizations such as economics, allows us to classify different categories of folds that exhibit biogeographical differences. Our results show that scaling fold distributions from individual genomes to species communities lead to a deviation from the expected behavior of simple power-law relationship towards a more complex model. This phenomenon could be linked with the variable complexity of marine planktonic ecosystems.

genomics↗

bioRxiv2025

Planetary-scale marine community modeling predicts metabolic synergy and viral impacts

The oceans buffer against climate change via biogeochemical cycles underpinned by microbial metabolic activities. While planetary-scale surveys provide baseline microbiome data, inferring metabolic and biogeochemical impacts remains challenging. Genome-scale modeling has addressed analogous issues at the cellular level, highlighting key metabolic reactions contingent upon specific environmental conditions. Here we adapt this mechanistic modeling framework towards analyzing global ocean microbial communities to reveal metabolic processes predicted to maintain ecosystem functioning. To achieve this, we developed a genome-scale superorganism metabolic model for each TARA Ocean metagenome or metatranscriptome (i.e., limited to reactions known from heterotrophic prokaryotes and viruses), and evaluated these models to establish a community-wide metabolic phenotype for each sample. To validate, we showed that even with reaction-mappable genes only ([~]1/4 of the total genes), model composition revealed metabolism-inferred ecological zones that matched taxonomy-inferred zones. Model inferred metabolic phenotypes revealed reaction cooperation associated with microbial metabolism and organism diversity. These phenotypes also suggest elevated ecological roles for viruses as model predictions suggest they genomically target community-critical metabolic reactions that underpin metabolic phenotype stability, and also demonstrate that, as metabolites are better understood, immediate estimates could be made for where viruses remineralize versus sink carbon. While this new constraints-based, agile, and mechanistic modeling framework is highly upgradable, it already begins to convert molecular-scale environmental omics data to ecological and even planetary-scale biogeochemical features that will better bring microbes and their viruses into Earth system and climate models.

systems biology↗

bioRxiv2022

Changes in functional composition and gene expression in eukaryotic plankton at the Atlantic-Arctic Polar front

In the Arctic Ocean, phytoplankton communities, dominated by eukaryotes, sustain the marine food web and influence biogeochemical cycles. While many are endemic, some are transported by currents from the Atlantic Ocean along an environmental gradient that steepens at the polar front. Despite these distinct biogeographies, the functional characteristics of these communities remain poorly characterized. Here, we analyzed twenty metatranscriptomes from a North Atlantic-Arctic environmental gradient considering ocean currents transport times. Functions related to the regulation of gene expression and cold acclimation were more abundant in Arctic metatranscriptomes. Using the PHATE dimensionality reduction algorithm, reconstructed transcriptomes of Bacillariophyta, Mamiellales, Pelagophyceae, and Phaeocystales revealed different gene expression patterns, including photosynthesis regulation. All groups showed upregulation of numerous key temperature-associated functions and a subset of shared functions, supporting a convergence in transcriptomic changes under polar conditions. This study, based on a new resource of reconstructed transcriptomes, addressed the functional differentiation of eukaryotic phytoplankton across the North Atlantic and Arctic Ocean. It evidenced both differential and convergent changes in gene expression across the polar front in widespread phytoplankton types. These results advance our understanding of the functional dynamics of phytoplankton along environmental gradients.

genomics↗

bioRxiv2022

Global observation of plankton communities from space

Satellite remote sensing from space is a powerful way 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 representative communities from a global plankton network that included both zooplankton and phytoplankton and using global satellite observations to predict their biogeography. Six representative plankton communities were identified from a global co-occurrence network inferred using a novel rDNA 18S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to train a model that predicted these representative communities from satellite data. The model showed an overall 67% accuracy in the prediction of the representative communities. The prediction based on 17 satellite-derived parameters showed better performance than based only on temperature and/or the concentration of chlorophyll a. The trained model allowed to predict the global spatiotemporal distribution of communities over 19-years. Our model exhibited strong seasonal changes in the community compositions in the subarctic-subtropical boundary regions, which were consistent with previous field observations. This network-oriented approach can easily be extended to more comprehensive models including prokaryotes as well as viruses.

ecology↗

bioRxiv2021

Insights into biotic and abiotic modulation of ocean mesopelagic communities

For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO - and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities.

ecology↗

bioRxiv2020

Environmental vulnerability of the global ocean plankton community interactome

Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles, and help regulate climate. Though 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 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.

ecology↗

bioRxiv2020

Restructuring of genomic provinces of surface ocean plankton under climate change

The impact of climate change on diversity, functioning and biogeography of marine plankton remains a major unresolved issue. Here, niche theory is applied to plankton metagenomes of 6 size fractions, from viruses to meso-zooplankton, sampled during the Tara Oceans expedition. Niches are used to derive plankton size-dependent structuring of the oceans south of 60{degrees}N in climato-genomic provinces characterized by signature genomes. By 2090, assuming the RCP8.5 high warming scenario, provinces would be reorganized over half of the considered ocean area and quasi-systematically displaced poleward. Particularly, tropical provinces would expand at the expense of temperate ones. Sea surface temperature is identified as the main driver of changes (50%) followed by phosphate (11%) and salinity (10%). Compositional shifts among key planktonic groups suggest impacts on the nitrogen and carbon cycles. Provinces are linked to estimates of carbon export fluxes which are projected to decrease on average by 4% in response to biogeographical restructuring.

ecology↗

bioRxiv2020

Global drivers of eukaryotic plankton biogeography in the sunlit ocean

Eukaryotic plankton are a core component of marine ecosystems with exceptional taxonomic and ecological diversity. Yet how their ecology interacts with the environment to drive global distribution patterns is poorly understood. Here, we use Tara Oceans metabarcoding data covering all the major ocean basins combined with a probabilistic model of taxon co-occurrence to compare the biogeography of 70 major groups of eukaryotic plankton. We uncover two main axes of biogeographic variation. First, more diverse groups display stronger biogeographic structure. Second, large-bodied consumers are structured by oceanic basins, mostly via the main currents, while small-bodied phototrophs are structured by latitude, with a comparatively stronger influence of environmental conditions. Our study highlights striking differences in biogeographies across plankton groups and investigates their determinants at the global scale. One-sentence summaryEukaryotic plankton biogeography and its determinants at global scale reflect differences in ecology and body size.

ecology↗