Biology subjects

Dutkiewicz, S.

Publications and source records attributed to Dutkiewicz, S..

12 recordsLinked to original sources

bioRxiv2026

Invariant scaling of the Species Abundance Distribution in observed and simulated marine plankton communities

Marine plankton are functionally diverse and span over five orders of magnitude in diameter, with important consequences for marine biogeochemical cycles. Marine ecosystem simulations are beginning to resolve this diversity; however, major uncertainties persist regarding the structure and function of planktonic ecosystems. Here we diagnosed plankton Species Abundance Distributions (SADs) in large-scale surveys and in a global, mechanistic plankton community simulation. The fitted slopes of the SADs vary by less than 10% across latitude, season, and biome in both observations and the simulation. Fitting parametric SADs further reveals spatial structure in the shape and functional form of the SAD aligned with established biogeographic provinces. Together, these results demonstrate a largely invariant structure of marine plankton communities that persists despite strong environmental gradients and taxonomic turnover. These findings suggest that the emergent shape and scaling of plankton SADs reflect fundamental constraints on community assembly and provide a compact quantitative diagnostic for planktonic ecosystem structure.

ecology↗

bioRxiv2026

Implicit representation of viruses fails to capture impacts of virus-induced mortality in global marine ecosystem models

Virus-induced mortality influences plankton biogeography, community structure, and ocean elemental cycles. However, quantification of virus-induced impacts remains challenging and often limited in scope. An alternative to explicit inclusion of viral dynamics in biogeochemical models is to represent viral effects implicitly, by assuming that mortality increases quadratically with cell or biomass density. Using 1D and 3D configurations of a nutrient-phytoplankton-zooplankton-virus-detritus (NPZVD) model, we ask whether the implicit quadratic mortality assumption captures patterns of virus-induced mortality, and its impact on biomass and primary production. The 1D water-column configuration shows that, at the onset of the spring bloom, the quadratic, implicit representation imposes viral losses on phytoplankton density instantaneously, which limits spring bloom formation. This is in contrast to the explicit representation, which allows initial bloom formation to proceed unhampered initially, but imposes a far stronger viral mortality later in the year driven by high rates of host-virus contact due to high phytoplankton and viral densities that take time to accumulate. By comparison to the implicit model, explicit resolution of viruses within the 3D global model shows strong potential for viruses to prematurely terminate phytoplankton blooms. Biogeochemical models would therefore benefit from explicit representation of viral infection insofar as models can be developed that adequately recapitulate in situ observations. Key PointsO_LIGlobal model reveals significant spatial heterogeneity arising from explicit, rather than implicit, representation of viruses C_LIO_LIImplicit representation of viral dynamics fails to capture the potential for viruses to terminate phytoplankton blooms C_LIO_LIBiogeochemical models require explicit representation of viruses to adequately simulate their effect on marine systems C_LI

microbiology↗

bioRxiv2026

Estimating absolute microbial abundances from metabarcoding anchored to cytometry data

Over the past decades, metabarcoding and automated cell-counting approaches have greatly advanced our understanding of marine microbial communities. Metabarcoding provides high taxonomic resolution and comprehensive community characterization, typically as relative gene abundances, whereas flow cytometry provides absolute cell abundances but lower taxonomic coverage. Here, we assess whether concurrent flow-cytometry observations can calibrate metabarcoding data to derive absolute gene abundances across four basin-scale Atlantic and Pacific Ocean transects. We first show that flow-cytometry-anchored calibration reproduces absolute abundances of Prochlorococcus and Synechococcus with performance comparable (R2 = 0.87) to internal DNA standard-based quantification. For datasets lacking internal standards, the choice of cytometric "anchor" species introduces systematic offsets in absolute abundance estimates, although spatial patterns remain robust. These offsets may reflect underestimation of cytometric counts or variation in rRNA gene copy numbers among actively dividing cells. We therefore recommend the use of multiple anchors where possible to diagnose systematic uncertainty. Applying this framework, we derive absolute gene concentrations for diverse plankton taxa from compositional metabarcoding data. For taxa with known rRNA gene copy numbers, calibration further enables estimation of absolute cell concentrations. We also resolve ecotype-level absolute abundances of Prochlorococcus along a longitudinal temperature gradient, revealing ecological patterns not apparent from compositional or cytometric data alone. Our results demonstrate that calibrated metabarcoding provides a practical quantitative bridge between molecular and cytometric observations, yielding high taxonomic resolution together with absolute gene concentrations and quantified uncertainties.

ecology↗

bioRxiv2026

Seasonal patterns in Synechococcus pigment diversity at two temperate sites with contrasting oceanic regimes

Competition for light has driven extensive pigment diversification among phytoplankton species, yet how this diversity shapes their spatiotemporal distribution in the field has been little studied so far. The cyanobacterium Synechococcus is an ideal model for addressing this issue, since this group has colonized most light spectral niches in marine environments. Here, we used an approach based on marker read recruitment from metagenomes to analyze the seasonal succession of Synechococcus pigment types (PTs) at two time-series stations off French coasts exhibiting contrasting oceanic regimes. Marked seasonality was observed at both sites. The shallow, permanently mixed English Channel site SOMLIT-Astan was characterized by an alternation between green-light specialists (PT 3a) peaking in spring, and chromatic acclimaters type A (PT 3dA) accounting for most of the Synechococcus community in winter. In contrast, the pigment diversity was much higher at the deep Mediterranean station BOUSSOLE. In the upper layer, the two main PTs were the blue light specialists (PT 3c), which dominated the community in summer and fall, and PT 3dA cells, which were more abundant in spring. The third most abundant PT was chromatic acclimaters type B (PT 3dB), which accounted for up to 15% of the surface community in late fall. Strikingly, PT 3dA was dominant at depth during most of the year. Multivariate analyses between PT abundances, clade abundances and environmental factors, notably water color indexes, suggested new associations between PTs to specific clades and ecological niches. This study provides novel insights for refining distribution models of Synechococcus PTs and phytoplankton groups in general.

microbiology↗

bioRxiv2026

Viral impacts on plankton standing stocks, primary productivity, and biogeochemistry in a model ocean

Viral lysis fuels the microbial loop by enhancing organic matter recycling (via the viral shunt) and can redirect organic matter toward export (via the viral shuttle). However, the global impact of viral infection mediated by shunt and shuttle pathways remains unclear. Here, we implemented viral infection and lysis processes in a global ocean ecosystem model, including a single phytoplankton (representing Prochlorococcus), virus (representing cyanophage), and nanozooplankton. Despite low but plausible levels of viral infection, high shunt efficiencies generated enhanced-productivity regions covering up to approximately one-half of the global ocean. For lower viral shunt efficiencies, the enhanced-productivity regions contracted abruptly, accompanied by steady declines in productivity. Viral-mediated increases in primary productivity reduced the extent of tropical oligotrophic regions at high shunt efficiencies, while lower efficiencies expanded oligotrophic areas. These results provide a path forward to developing predictive models of how viral infection and the fate of cellular lysates shape global ocean ecosystems.

ecology↗

bioRxiv2025

Cellular-level control on global ocean deoxygenation driven by phytoplankton ecophysiology

Phytoplankton elemental composition shapes the distribution of dissolved nutrient concentrations and thus plays a key role in ocean biogeochemistry. While the carbon-to-nitrogen-to-phosphorus ratio (C:N:P) in marine phytoplankton has been extensively studied, the hydrogen (H) and oxygen (O) content have received less attention despite their critical role in determining dissolved oxygen (O2) consumption rates in the ocean. Here, we estimated the elemental composition of marine phytoplankton, including the H and O content, from first principles, using a cellular allocation model embedded in a global ocean model. We estimated that an average phytoplankton cell has a chemical formula of C107H190N16O53P, with an O2 demand of 149 mol O2/mol P and respiration quotients of 1.40 mol O2/mol C, suggesting a lower H and O content, and higher O2 demand than commonly assumed. We found global variations in the O2 demand of organic matter respiration driven by population structure and cellular reorganisation under different environmental conditions. By testing how shifts in the macromolecular composition of phytoplankton cells affect the oceans O2 budget, we found that O2 consumption increases significantly when shifting cell composition from carbohydrate-rich to protein- or lipid-rich cells. As a result, low-O2 (hypoxic) zones in the ocean expanded by 75%. These findings demonstrate that cellular-level processes in marine phytoplankton shape the global O2 cycle and large-scale patterns of ocean biogeochemistry.

ecology↗

bioRxiv2025

Coexistence of Photosynthetic Marine Microorganisms, Viruses, and Grazers: Toward Integration in Ocean Ecosystem Models

Photosynthetic microorganisms are responsible for primary production at the base of the marine food web that impacts ocean biogeochemistry and ecological interactions. The growth of these microorganisms is balanced by mortality processes, including top-down losses from zooplankton grazing and infection and lysis by viruses. Multiple types of grazers and viruses often coexist despite apparent competition for the same (or similar) microorganisms. Here, we develop a community model of photosynthetic microorganisms, grazers, and viruses that accounts for molar cell and virion elemental quotas suitable for incorporation into ocean ecosystem models. Our aim is to investigate mechanisms that enable coexistence of a virus and a grazer with a single phytoplankton type. To do so, we evaluate the extent to which coexistence is facilitated by: (i) infected phytoplankton, potentially subject to non-preferential intraguild predation, where grazers feed on virally infected microorganisms; (ii) heterogeneity in susceptibility to infection, where microorganisms vary in their resistance to the virus either intracellularly or extracellularly; and (iii) the inclusion of higher-order mortality terms for the predators. We find evidence for a trade-off between the virus latent period and virulence in facilitating a coexistence regime. The inclusion of an explicit latent period can generate oscillations of all populations that facilitate coexistence by reducing the growth rate of the free virus, or lead to system collapse when oscillations become too large. Heterogeneity in phage susceptibility promotes coexistence through resource partitioning between the predators, while higher-order mortality terms widen the coexistence regime by stabilizing the system. We observe strong sensitivity of model outcomes to viral life history traits, including shifts in infected cell percentages and the balance between virally and zooplankton-induced mortality. Finally, taking advantage of algebraic calculation of model equilibria, we identify life history trait parameter combinations that yield realistic ecological properties in simplified oligotrophic and mesotrophic epipelagic environments. Importantly, our ecological models suggest that ongoing efforts to embed virus dynamics in large-scale ocean ecosystem models should likely include phytoplankton types that are moderately to strongly resistant to viral infection and lysis.

ecology↗

bioRxiv2024

Intraspecific diversity in thermal performance determines phytoplankton ecological niche

Temperature has a primary influence on phytoplankton physiology and affects biodiversity and ecology. To examine how intraspecific diversity and temperature shape plankton populations, we grew 12 strains of the ecologically-important coccolithophore Gephyrocapsa huxleyi isolated from regions of different temperature for [~]45 generations (2 months), each at 6-8 temperatures, and characterized the acclimated thermal response curve of each strain. Even with virtually identical temperature optima and overlapping cell size, strain growth rates varied between 0.45 and 1 day-1. While some thermal curves were effectively symmetrical, others had more slowly declining growth rates above the "thermal optimum," and thermal niche widths varied between 16.7 and 24.8 {degrees}C. This suggests that different strains use distinct thermal response mechanisms. We investigated the ecological implications of such intraspecific diversity on thermal response using an ocean ecosystem simulation resolving distinct phytoplankton thermal phenotypes. Resolving model analogs of thermal "generalists" and "specialists" (similar to those observed in G. huxleyi) resulted in a distinctive global biogeography of preferred thermal niche widths with a nonlinear latitudinal pattern. We leveraged the model output to predict the ranges of the 12 strains we studied in the laboratory and demonstrated how this approach could refine predictions of phytoplankton thermal geographic range in situ. Our combination of observed thermal traits and modeled biogeography highlights the capacity of diverse groups to persist through temperature shifts. Significance StatementIntraspecific diversity in the phytoplankton may underpin their distribution. We show that within a single coccolithophore species, thermal response curves have diverse trait parameters. For example, many strains had a variable range of temperatures at which they could survive (thermal niche width). Adding this thermal niche width diversity to an ecosystem model simulation impacted phytoplankton coexistence and overall biomass. These observations show that thermal niche width is a gap in phytoplankton representation in ecosystem models that impacts modeled phytoplankton biogeography and concomitant carbon cycle dynamics. Including thermal tolerance is crucial to predictive modeling as ocean temperature dynamics change.

ecology↗

bioRxiv2024

Predictable functional biogeography of marine microbial heterotrophs

Heterotrophic bacteria and archaea ( heteroprokaryotes) drive global carbon cycling, but how to quantitatively organize their functional complexity remains unclear. We generated a global-scale understanding of marine heteroprokaryotic functional biogeography by synthesizing genetic sequencing data with a mechanistic marine ecosystem model. We incorporated heteroprokaryotic diversity into the trait-based model along two axes: substrate lability and growth strategy. Using genetic sequences along three ocean transects, we compiled 21 heteroprokaryotic guilds and estimated their degree of optimization for rapid growth (copiotrophy). Data and model consistency indicated that gradients in grazing and substrate lability predominantly set biogeographical patterns, and identified deep-ocean slow copiotrophs whose ecological interactions control the surface accumulation of dissolved organic carbon.

ecology↗

bioRxiv2023

DAR1 - An Easy to Use, Single-Box, Configuration of a Global Scale Biogeochemical Ecosystem Model

Global scale biogeochemical ocean models, such as the MIT-Darwin model, are important tools to help us understand the mechanisms which drive elemental cycles and marine planktonic ecosystems. However, these models are difficult to use and their complex outputs can make them tricky to interpret. Here we present DAR1, an easy-to-use framework written in Julia that maintains all of the ecological and chemical complexity present in the MIT-Darwin model while removing the computational and physical complexity. We provide three studies to showcase DAR1 features: a framework for nutrient amendment bottle experiments; a test of steady state assumptions on plankton community structure at the global scale; and a test of theoretical predictions for the niche space of nitrogen-fixing plankton. DAR1 is ideal for model based testing of ecological predictions from field and experimental observations while also providing access to modeling tools for the non-expert.

ecology↗

bioRxiv2023

Assessing the potential of backscattering as a proxy for phytoplankton carbon biomass

Despite phytoplankton contributing roughly half of the photosynthesis on earth and fueling marine food-webs, field measurements of phytoplankton biomass remain scarce. The particulate backscattering coefficient (bbp) has often been used as an optical proxy to estimate phytoplankton carbon biomass (Cphyto). However, total observed bbp is impacted by phytoplankton size, cell composition, and non-algal particles. The lack of phytoplankton field data has prevented the quantification of uncertainties driven by these factors. Here, we first review and discuss existing bbp algorithms by applying them to bbp data from the BGC-Argo array in surface waters (<10m). We find a bbp threshold where estimated Cphyto differs by more than an order of magnitude. Next, we use a global ocean circulation model (the MITgcm Biogeochemical and Optical model) that simulates plankton dynamics and associated inherent optical properties to quantify and understand uncertainties from bbp-based algorithms in surface waters. We do so by developing and calibrating an algorithm to the model. Simulated error-estimations show that bbp-based algorithms overestimate/underestimate Cphyto between 5% and 100% in surface waters, depending on the location and time. This is achieved in the ideal scenario where Cphyto and bbp are known precisely. This is not the case for algorithms derived from observations, where the largest source of uncertainty is the scarcity of phytoplankton biomass data and related methodological inconsistencies. If these other uncertainties are reduced, the model shows that bbp could be a relatively good proxy for phytoplankton carbon biomass, with errors close to 20% in most regions. Plain Language SummaryPhytoplankton contribute roughly half of the photosynthesis on earth and fuel fisheries around the globe. Yet, few direct measurements of phytoplankton concentration are available. Frequently, concentrations of phytoplankton are instead estimated using the optical properties of water. Backscattering is one of these optical properties, representing the light being scattered backwards. Previous studies have suggested that backscattering could be a good method to estimate phytoplankton concentration. However, other particles that are present in the ocean also contribute to backscattering. In this paper we examine how well backscattering can be used to estimate phytoplankton. To address this question, we use data from drifting instruments that are spread across the ocean and a computer model that simulates phytoplankton and backscattering over the global oceans. We find that by using backscattering, phytoplankton can be overestimated/underestimated on average by [~]20%. This error differs between regions, and can be larger than 100% at high latitudes. Computer simulations allowed us to quantify spatial and temporal variability in backscattering signal composition, and thereby understand potential errors in inferring phytoplankton with backscattering, which could not have been done before due to the lack of phytoplankton data. Key PointsO_LIPhytoplankton carbon bbp-based algorithms can differ up to an order of magnitude at low bbp values. C_LIO_LIAn algorithm fitted to a global model output shows biases ranging between 15% and 40% in most regions. C_LIO_LIMost uncertainties are due to the relative contribution of phytoplankton to total bbp. C_LI

ecology↗

bioRxiv2021

Diel light cycles affect phytoplankton competition in the global ocean

Light, essential for photosynthesis, is present in two periodic cycles in nature: seasonal and diel. Although seasonality of light is typically resolved in ocean ecosystem and biogeochemistry models because of its significance for seasonal succession and biogeography of phytoplankton, the diel light cycle is generally not resolved. Here we use a three-dimensional global ocean model and compare high temporal resolution simulations with and without diel light cycles. The model simulates 15 phytoplankton types of different cell size, encompassing two broad ecological strategies: small cells with high nutrient affinity (gleaners) and larger cells with high maximal growth rate (opportunists). Both are grazed by zooplankton and limited by nitrogen, phosphorus and iron. Simulations show that diel cycles of light induce diel cycles in phytoplankton populations and limiting nutrients in the global ocean. Diel nutrient cycles are associated with higher concentration of limiting nutrients by up to 200% at low latitudes (-40{degrees} to 40{degrees}), a process that increases opportunists biomass by up to 50%. Size classes with the highest maximal growth rates from both gleaner and opportunist groups are favored the most by diel light cycles. This mechanism weakens as latitude increases because the effects of the seasonal cycle dominate over those of the diel cycle. The present work shows that resource competition under diel light cycles has a significant impact on phytoplankton biogeography, indicating the necessity of resolving diel processes in global ocean models.

ecology↗