Biology subjects

Zakem, E.

Publications and source records attributed to Zakem, E..

9 recordsLinked to original sources

bioRxiv2025

Facilitation-competition tradeoffs structure microbial niches and nitrogen cycling

The marine nitrogen cycle is regulated by ecological interactions among diverse microbial populations, especially in oxygen minimum zones where populations carrying out anaerobic metabolisms, mainly denitrification and anammox, drive fixed nitrogen loss. While competition for limiting resources is well studied, the combined effects of competition and facilitation, where a "feeder" population supplies a required resource to a "recipient", remain poorly understood. Here we develop a trait-based consumer-resource framework to test how recipient populations reshape the ecological niches of their feeders and competitors. Invasion analysis shows that recipients expand either their feeders or the feeders competitors niche, depending on the populations relative competitive abilities on limiting resources. In terms of biogeochemistry, ecological outcomes result in diverse N-loss pathways; specifically, when growth is limited by both organic matter and nitrate, we observe increased nitrous oxide production. Additionally, the model suggests that anammox bacteria occupy a wider range of organic matter and nitrate supply regimes than denitrifying populations, consistent with their more frequent detection across diverse marine environments. The results link microbial interaction networks to biogeochemical fluxes relevant at global scales, and extend ecological theory to multi-resource systems with nested competitive and facilitative interactions.

microbiology↗

bioRxiv2025

On Copiotrophy and Temperature: Controls on Microbial Maximum Growth Rate Versus Translation Rate Optimization

Maximum growth rate is often used as a primary axis of functional variation in studies of microorganisms because it is key parameter in models of microbial growth, because it is closely conceptually related to the "copiotrophy-oligotrophy" axis used to organize microbial functional roles within ecosystems, and because emerging tools make it straightforward to estimate from genomic and metagenomic data. However, temperature, via its influence on reaction kinetics, may act as a confounder in studies that measure genomic signatures of growth optimization across environments by decoupling the cellular optimization for relatively fast growth from absolute growth rates. Observations suggest that growth optimization need not always indicate rapid growth. For example, strong temperature gradients are the norm across much of the worlds oceans, where slow-growing deep-ocean microbes show elevated signals of genomic growth optimization relative to the faster-growing communities at the surface. Looking across environments, we find a negative relationship between genomic growth optimization and optimal growth temperature, indicating the potential decoupling of genomic traits associated with copiotrophy from maximum growth rate, particularly when measured in the presence of a strong temperature gradient. Our results suggest that, as a result of temperatures confounding effects, genomic signatures of growth optimization better predict the ecological roles and functional genomic content of microorganisms than do growth rates themselves. Finally, we suggest reframing copiotrophy as a set of traits that allow an organism to escape from a thermodynamic baseline maximum growth rate, rather than in relation to a specific rate cutoff.

microbiology↗

bioRxiv2025

Density dependence promotes species coexistence and provides a unifying explanation for distinct productivity-diversity relationships

Understanding diversity patterns in complex communities, such as microbial consortia, requires a mechanistic framework appropriate for many species. Negative density dependence is often utilized in complex ecosystem models, typically as a density-dependent mortality term for a population, but its full impact on community structure remains unclear. Here we use mechanistic population models of resource consumption to examine the effects of negative density dependence and develop a tractable framework for understanding diversity patterns in complex systems. To provide mechanistic grounding, we quantify how density-dependent mortality expands coexistence zones along resource gradients in simple communities using graphical analysis. We then derive an analytical, ecologically insightful formula predicting species abundances in subsets (guilds) of complex communities, in which many species share a resource or predator. Finally, we use the formula to explain how distinct relationships between productivity and diversity emerge from the resulting mechanistic framework, providing insights into previously unreconciled observed patterns.

ecology↗

bioRxiv2025

Redox-constrained microbial ecology dictates nitrogen loss versus retention

Microorganisms drive biogeochemical cycling. Therefore, examining environmental change through the lens of microbial ecology is particularly useful for developing a mechanistic understanding of the biogeochemical consequences and feedbacks of perturbations to ecosystems. When aquatic systems with deep anoxic waters undergo eutrophication, the resulting surface productivity impacts the anaerobic microbial community below. The increase in sinking organic carbon can shift the anaerobic community function from inorganic nitrogen (N) loss to N retention, amplifying eutrophication as a positive feedback. However, we lack a mechanistic understanding of this transition, which is critical for anticipating these impacts in aquatic environments where microbial community composition is unknown. Here, we provide a first-principles, quantitative model of this transition from N loss to retention by linking ecological dynamics to the energetics underlying microbial metabolisms. We develop and analyze an ecosystem model in which redox chemistry constrains the traits of key anaerobic N-cycling microbial functional types: denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and anaerobic ammonium oxidation (anammox). The model captures the transition from N loss to N retention with increasing organic carbon supply, consistent with previous observations for specific systems and species. Results identify characteristics of the microbial community composition at the net zero N loss point at which N loss balances N retention, providing testable hypotheses for sequencing data and other observations. By tying microbial ecological dynamics to environmental chemical potential, results provide a broadly applicable framework for improving predictions of the biogeochemical impacts of eutrophication alongside deoxygenation and other ecosystem perturbations.

ecology↗

bioRxiv2024

Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information

Microbial maximum growth rates vary widely across species and are key parameters for ecosystem modeling. Measuring these rates is challenging, but genomic features like codon usage statistics provide useful signals for predicting growth rates for as-yet uncultivated organisms, though current predictors often show high variance. To improve accuracy, we integrate phylogenetic signals, leveraging the evolutionary relationships among species to refine trait predictions. We present Phydon, which combines codon statistics and phylogenetic information to enhance the precision of maximum growth rate estimates, especially when a close relative with a known growth rate is available. We construct the largest and most taxonomically broad database of temperature-corrected growth rate estimates for 111,349 microbial species. The results reveal a bimodal distribution of maximum growth rates, resolving distinct groups of fast and slow growers. Our hybrid approach advances the accuracy of genome-based growth rate predictions and presents a new framework for accurate genome-based trait prediction.

microbiology↗

bioRxiv2024

Ecological dynamics explain modular denitrification in the ocean

Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is the multi-step denitrification, the dominant pathway for bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain only subsets ("modules") of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the observed prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when growth is limited by organic matter (OM), explaining the viability of populations respiring nitrite and N2O in a nitrate-filled ocean. Results predict denitrifier community succession along environmental gradients: shorter versus longer modules are favored when OM versus N limits growth, respectively, suggesting a niche for the NO3-{longrightarrow}NO2- module in free-living communities and for the complete pathway in organic particles, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO3-{longrightarrow}NO2- module. Results also capture observations that nitrate is the dominant source of N2O. These results advance the mechanistic understanding of the relationship between microbial ecology and N loss, which is essential for accurately predicting the oceans future.

ecology↗

bioRxiv2023

Oxygen intrusions sustain aerobic nitrite oxidation in anoxic marine zones

Anaerobic metabolisms are thought to dominate nitrogen cycling in anoxic marine zones (AMZs). However, thriving populations of aerobic nitrite-oxidizing bacteria (NOB) in AMZs challenge this assumption and remain unexplained. Using theory and modelling, we show how periodic oxygen intrusions sustain aerobic NOB in AMZs alongside more competitive aerobic heterotrophs. Ecological theory, supported by numerical simulations and genomics, frames NOB as opportunists exploiting a fleeting supply of oxygen. Consistent with in situ observations, simulated NOB contribute substantially to total oxygen consumption at AMZ boundaries, which implies that NOB may provide a major stabilizing feedback to AMZs. Fine-scale ocean currents increase the metabolic diversity in AMZs, which could stabilize AMZ volume under climate change. One-Sentence SummaryWhiffs of oxygen to the oceans anoxic zones increase microbial diversity and alter biogeochemical cycling.

systems biology↗

bioRxiv2020

A unified theory for organic matter accumulation

Organic matter constitutes a key reservoir in global elemental cycles. However, our understanding of the dynamics of organic matter and its accumulation remains incomplete. Seemingly disparate hypotheses have been proposed to explain organic matter accumulation: the slow degradation of intrinsically recalcitrant substrates, the depletion to concentrations that inhibit microbial consumption, and a dependency on the consumption capabilities of nearby microbial populations. Here, using a mechanistic model, we develop a theoretical framework that explains how organic matter predictably accumulates in natural environments due to biochemical, ecological, and environmental factors. The new framework subsumes the previous hypotheses. Changes in the microbial community or the environment can move a class of organic matter from a state of functional recalcitrance to a state of depletion by microbial consumers. The model explains the vertical profile of dissolved organic carbon in the ocean and connects microbial activity at subannual timescales to organic matter turnover at millenial timescales. The threshold behavior of the model implies that organic matter accumulation may respond nonlinearly to changes in temperature and other factors, providing hypotheses for the observed correlations between organic carbon reservoirs and temperature in past earth climates.

ecology↗

bioRxiv2019

Systematic variation in marine dissolved organic matter stoichiometry and remineralization ratios as a function of lability

Remineralization of organic matter by heterotrophic organisms regulates the biological sequestration of carbon, thereby mediating atmospheric CO2. While surface nutrient supply impacts the elemental ratios of primary production, stoichiometric control by remineralization remains unclear. Here we develop a mechanistic description of remineralization and its stoichiometry in a marine microbial ecosystem model. The model simulates the observed elemental plasticity of phytoplankton and the relatively constant, lower C:N of heterotrophic biomass. In addition, the model captures the observed decreases in DOC:DON and the C:N remineralization ratio with depth for more labile substrates, which are driven by a switch in the dominant source of labile DOM from phytoplankton to heterotrophic biomass. Only a model version with targeted remineralization of N-rich components is able to simulate the observed profiles of preferential remineralization of DON relative to DOC and the elevated C:N of bulk DOM. The model suggests that more labile substrates are associated with C-limited heterotrophic growth and not with preferential remineralization, while more recalcitrant substrates are associated with growth limited by processing rates and with preferential remineralization. The resulting patterns of variable remineralization stoichiometry mediate the extent to which a proportional increase in carbon production resulting from changes in phytoplankton stoichiometry can increase the efficiency of the biological pump. Results emphasize the importance of understanding the physiology of both phytoplankton and heterotrophs for anticipating changes in biologically driven ocean carbon storage.

ecology↗