Biology subjects

Talmy, D.

Publications and source records attributed to Talmy, D..

6 recordsLinked to original sources

bioRxiv2026

The diel light cycle modulates microcystin content in continuous cultures and natural communities of Microcystis: Implications for bloom monitoring

Harmful algal blooms dominated by Microcystis spp. threaten fisheries, recreation, and drinking-water supplies because many strains produce the hepatotoxin microcystin. Monitoring programs compare microcystin concentrations among samples collected at different times of day, yet the extent that diel variation affects these estimates remains poorly resolved. We tested whether microcystin concentrations varied over a diel cycle under laboratory conditions and evaluated the effect of short-term sunlight exposure on a natural bloom community. Axenic Microcystis aeruginosa PCC 7806 was maintained in cyclostats with controlled nutrients and temperature under a 16 h light:8 h dark cycle. Microcystin concentrations normalized to culture volume (g L-1) and biovolume (ag m-E-3 were significantly higher (p [≤] 0.05) at the end of the dark period (64 {+/-} 8 g MC L-1; 630 {+/-} 40 ag MC m-3) than at the end of the light period (45 {+/-} 7 g MC L-1; 390 {+/-} 60 ag MC m-3), and this pattern was reproducible across consecutive days. Cell abundance and photosynthetic efficiency remained constant, indicating variation was not explained by changes in growth or photosynthetic performance. In parallel, water from a Lake Erie Microcystis bloom was exposed to sunlight or paired dark controls, and microcystin concentrations declined ~19% after just 60 min of sunlight exposure (p = 0.048). Together, these results demonstrate that microcystin measurements can vary predictably across the diel cycle and that light contributes to daytime declines. Although the underlying mechanism(s) remain unresolved, time of day should be considered, or standardized, when monitoring microcystins.

microbiology↗

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

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

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

Coastal bacteria and protists assimilate viral carbon and nitrogen

Free viruses are the most abundant type of biological particles in the biosphere, but the lack of quantitative knowledge about their consumption by heterotrophic protists and bacterial degradation has hindered the inclusion of virovory in biogeochemical models. Here, using isotope-labeled viruses added to three independent microcosm experiments with natural microbial communities followed by isotope measurements with single-cell resolution and flow cytometry, we quantified the flux of viral C and N into virovorous protists and bacteria and compared the loss of viruses due to abiotic vs biotic factors. We found that some protists can obtain most of their C and N requirements from viral particles and that viral C and N get incorporated into bacterial biomass. We found that bacteria and protists were responsible for increasing the daily removal rate of viruses by 33% to 85%, respectively, compared to abiotic processes alone. Our laboratory incubation experiments showed that abiotic processes removed roughly 50% of the viruses within a week, and adding biotic processes led to a removal of 83% to 91%. Our data provide direct evidence for the transfer of viral C and N back into the microbial loop through protist grazing and bacterial breakdown, representing a globally significant flux that needs to be investigated further to better understand and predictably model the C and N cycles of the hydrosphere.

ecology↗

bioRxiv2021

Enhancing Quantitative and Data Science Education for Graduate Students in Biomedical Science

Substantial guidance is available on undergraduate quantitative training for biologists, including reports focused on biomedical science, but far less attention has been paid to the graduate curriculum. In this setting, we propose an innovative approach to quantitative education that goes beyond recommendations of a course or set of courses or activities. Due to the diversity of quantitative methods, it is infeasible to expect that biomedical PhD students can be exposed to more than a minority of the quantitative concepts and techniques employed in modern biology. We developed a novel prioritization approach in which we mined and analyzed quantitative concepts and skills from publications that faculty in relevant units deemed central to the scientific comprehension of their field. The analysis provides a prioritization of quantitative skills and concepts and could represent an effective method to drive curricular focus based upon program-specific faculty input for biological science programs of all types. Our results highlight the disconnect between typical undergraduate quantitative education for life science students, focused on continuous mathematics, and the concepts and skills in graphics, statistics, and discrete mathematics that arise from priorities established by biomedical science faculty. One Sentence SummaryWe developed a novel approach to prioritize quantitative concepts and methods for inclusion in a graduate biomedical science curriculum based upon approaches included in faculty-identified key publications.

scientific communication and education↗