Biology subjects

Lennon, J. T.

Publications and source records attributed to Lennon, J. T..

At least 19 recordsLinked to original sources

bioRxiv2026

Metabolic inequality in microbial communities

How metabolic activity is partitioned among individuals determines the scaling of cellular physiology to higher levels of biological organization. Yet the mechanisms that generate this heterogeneity and shape its distribution remain largely unresolved. We quantified single-cell metabolism in microbial communities spanning aquatic, terrestrial, and host-associated ecosystems. Across more than one million cells, metabolic activity followed a long-tailed distribution best described by a lognormal model, with a small subset of individuals contributing disproportionately to community metabolism. In some cases, the most active 20% of cells accounted for over 90% of metabolic output, but this pattern became less pronounced in more productive environments. To assess the consequences of metabolic inequality, we developed a stochastic simulation model linking single-cell activity to community respiration via enzyme kinetics. Because respiration responds nonlinearly to enzyme activity, variation among cells does not translate proportionally into ecosystem-level fluxes. As a result, ignoring metabolic heterogeneity can bias estimates of community respiration by up to 60%. Our findings reveal a general pattern of metabolic inequality in microbial communities that holds across a wide range of habitats. Accounting for this structure is critical for understanding how microorganisms regulate ecosystem processes and for improving predictions of large-scale biogeochemical dynamics. SignificanceInequality and disparity are common features of social, economic, and physical systems. Such patterns also arise in nature, where a small fraction of individuals accounts for an outsized share of biological output, including reproduction, immunity, and diversity. Here, we show that metabolic activity in microbial communities follows a characteristic right-skewed distribution across diverse ecosystems, including lakes, soils, ocean plankton, marine sediments, and mammalian guts. Instead of the rich getting richer, metabolism becomes more evenly distributed among cells in more productive environments. By explicitly representing metabolic inequality, we can reduce bias in estimates of microbial activity and improve the scaling of cellular processes to ecosystem-level fluxes.

ecology↗

bioRxiv2026

Microbe-mediated plant acclimation to drought may be rare in agriculture

Microbial communities can shift under drought in ways that enhance plant performance during drought ("microbe-mediated acclimation"). However, it is also possible for microbial communities to shift in ways that worsen the effects of drought ("mal-acclimation"). It is unclear how and where microbe-mediated acclimation vs. mal-acclimation occurs, or if there are types of soils or microbial communities that are more likely to harbor microbes that enhance plant acclimation and limit mal-acclimation. We tested for microbe-mediated plant acclimation/mal-acclimation to drought in soils from 21 maize farms in the midwestern United States, spanning a range of climate, soil types, and management practices. We first conditioned soil microbial communities to drought vs. well-watered conditions in a greenhouse and then tested for microbe-mediated acclimation by growing maize in soils inoculated with the conditioned microbial communities under drought and well-watered conditions. Drought-conditioned soils did not enhance plant performance under drought. In fact, one third of the farms exhibited mal-acclimation, especially under well-watered conditions where wet-conditioned soils reduced plant performance in well-watered contemporary conditions. Farm management practices, climate, soil texture, and microbial diversity generally did not predict when this microbe-mediated mal-acclimation occurred. Overall, these results suggest that in agricultural soils, microbes may frequently impede-rather than facilitate-plant acclimation to soil moisture levels. Open research statementThe plant and soil data used in this study are available via the Environmental Data Initiative repository at https://doi.org/10.6073/pasta/f4a0db3a076cf6d8cef908947f82736e. The bacterial and fungal amplicon sequence data are available via the European Nucleotide Archive under accessions PRJEB110071 and PRJEB109827, respectively.

ecology↗

bioRxiv2025

Evolutionary bioenergetics of sporulation

Energy is required for the expression and maintenance of complex traits. In many habitats, however, free energy available to support biosynthesis is in vanishingly short supply. As a result, many taxa have evolved persistence strategies that support survival in unfavorable environments. Among these is sporulation, an ancient bacterial program governed by a large genetic network that requires energy for both regulation and execution. Yet sporulation is a last resort, initiated when cellular energy is nearly exhausted. To resolve this paradox, we quantified the energetic cost of sporulation in units of ATP by integrating time-resolved genome, transcriptome, and proteome profiles. The full cost of the spore cycle, including both formation and revival, ranks among the most energy-intensive processes in the bacterial cell, requiring almost 1010 ATP and consuming about 10% of the total energy budget. The majority of this cost arises from translation, membrane synthesis, and protein turnover. Despite its considerable upfront investment, sporulation enables long-term survival and becomes optimal when harsh conditions extend over timescales of months or longer. This trade-off between immediate cost and delayed benefit helps explain when sporulation is maintained or replaced by alternative strategies. By incorporating our estimates into mechanistic models, we show how metabolic constraints shape sporulation efficiency, while genome-wide mutation accumulation data reveal that even modest energetic burdens can become visible to selection, influencing the evolutionary fate of this complex and widespread trait.

evolutionary biology↗

bioRxiv2025

The Enterostat: a 3D-printed bioreactor for simulating gut microbiome dynamics

While the gut microbiome is central to host fitness, research in animal systems is limited by challenges in scalability and experimental control. Engineered bioreactors provide a valuable tool for studying microbiome dynamics, but many fail to capture the full anatomical and functional complexity of the gastrointestinal tract. Most existing models focus on either micro-scale features, such as villi and mucosal folds, or macro-scale parameters, such as fluid flow and volume, without integrating both. To address this gap, we introduce the Enterostat, a gut bioreactor platform designed to incorporate structural detail across scales while remaining adaptable to the dimensions and structural complexity of different hosts. We describe the modeling, fabrication, and operation of the Enterostat, and highlight its potential applications in microbiome research. The physical design of the Enterostat gives rise to oxygen gradients and particle retention, conditions that support the establishment and stability of microbial communities. The Enterostat also captures eco-evolutionary responses to antibiotic perturbations, demonstrating its utility for both applied and basic research. Overall, the Enterostat provides a versatile platform for pharmaceutical testing and for investigating how gastrointestinal architecture shapes microbiome composition and function.

microbiology↗

bioRxiv2025

Simple, rapid, and sensitive assay for the quantification of total polysaccharides to estimate extracellular polymeric substances (EPS) in soil

Current methods for quantifying total polysaccharides in soil are expensive or require prolonged incubation of hazardous reagents at 100{degrees}C in glass vessels. We present a fast, sensitive, and inexpensive spectrophotometric assay quantifying polysaccharides in aqueous solution, featuring an instant reaction of room-temperature reagents using disposable tubes and cuvettes.

molecular biology↗

bioRxiv2024

Nitrogen enrichment alters selection on rhizobial genes

1Mutualisms evolve over time when individuals belonging to different species derive fitness benefits through the exchange of resources and services. Although prevalent in natural and managed ecosystems, mutualisms can be destabilized by environmental fluctuations that alter the costs and benefits of maintaining the symbiosis. In the rhizobia-legume mutualism, bacteria provide reduced nitrogen to the host plant in exchange for photosynthates that support bacterial metabolism. However, this relationship can be disrupted by the addition of external nitrogen sources to the soil, such as fertilizers. While the molecular mechanisms underpinning the rhizobia-legume symbiosis are well-characterized, the genome-wide fitness effects of nitrogen enrichment on symbiotic rhizobia are less clear. Here, we inoculated a randomly barcoded transposon-site sequencing (RB-TnSeq) library of the bacterium Ensifer (Sinorhizobium) meliloti into soils containing a host plant, alfalfa (Medicago sativa), under conditions of low and high nitrogen availability. Although plant performance remained robust to fertilization, nitrogen enrichment altered gene fitness for specific traits and functions in the rhizobial partner. Genes involved in carbohydrate metabolism showed increased fitness irrespective of soil nutrient content, whereas fitness gains in quorum-sensing genes were only observed in high-nitrogen environments. We also documented reductions in the fitness of nucleotide metabolism and cell-growth genes, while genes from oxidative phosphorylation and various amino-acid biosynthesis pathways were detrimental to fitness under elevated soil nitrogen, underscoring the complex trade-offs in rhizobial responses to nutrient enrichment. Our experimental functional genomics approach identified gene functions and pathways across all E. meliloti replicons that may be associated with the disruption of an agronomically important mutualism. 2 ImportanceUnderstanding the evolutionary dynamics of the rhizobia-legume mutualism is important for elucidating how plant-soil-microbe interactions operate in natural and managed ecosystems. Legumes constitute a significant portion of global food production and generate 25% of all terrestrially fixed nitrogen. The application of chemical fertilizers can disrupt the mutualism by altering the selective pressures experienced by symbiotic rhizobia, potentially affecting gene fitness throughout the microbial genome and leading to the evolution of less productive or cooperative mutualists. To investigate how exogenous nitrogen inputs influence gene fitness during the complex rhizobial lifecycle, we used a barcoded genome-wide mutagenesis screen to quantify gene-level fitness across the rhizobial genome during symbiosis and identify metabolic functions affected by nitrogen enrichment. Our findings provide genomic insight into potential eco-evolutionary mechanisms by which symbioses are maintained or degraded over time in response to changing environmental conditions.

evolutionary biology↗

bioRxiv2024

Resuscitation-promoting factor (Rpf) terminates dormancy among diverse soil bacteria

Microorganisms often inhabit environments that are suboptimal for growth and reproduction. To survive when challenged by such conditions, individuals may engage in dormancy where they enter a metabolically inactive state. For this persistence strategy to confer an evolutionary advantage, microorganisms must be able to resuscitate and reproduce when conditions improve. Among bacteria in the phylum Actinomycetota, dormancy can be terminated by resuscitation-promoting factor (Rpf), an exoenzyme that hydrolyzes glycosidic bonds in the peptidoglycan of the cell wall. We characterized Rpf from Micrococcus KBS0714, a bacterium isolated from agricultural soil. Compared to previous studies, the Rpf elicited activity at relatively high concentrations, yet demonstrated high substrate affinity. Site-directed mutations at conserved catalytic sites significantly reduced or abolished resuscitation, as did the deletion of repeating motifs in a lectin-encoding linker region. We then tested the effects of recombinant Rpf from Micrococcus KBS0714 on a diverse set of dormant soil bacteria. Patterns of resuscitation mapped onto strain phylogeny, which reflected core features of the cell envelope. Additionally, the direction and magnitude of the Rpf effect were associated with functional traits, in particular, aspects of the moisture niche and biofilm production, which are critical for understanding persistence and resuscitation during dormancy. These findings expand our understanding of how Rpf may affect seed-bank dynamics and have implications for the diversity and functioning of soil ecosystems.

microbiology↗

bioRxiv2024

Residence time structures microbial communities through niche partitioning

Much of life on Earth is at the mercy of currents and flow. Residence time ({tau}) estimates how long organisms and resources stay within a system based on the ratio of volume (V) to flow rate (Q). Short residence times promote immigration but may prevent the establishment of species that cannot quickly reproduce, or resist being washed out. In contrast, long residence times reduce resource input, selecting for species that can survive on a low supply of energy and nutrients. Theory suggests that these opposing forces shape the abundance, diversity, and function of flowing systems. In this study, we subjected chemostats inoculated with a complex lake microbial community to a residence time gradient spanning seven orders of magnitude. Microbial abundance, richness, and evenness increased with residence time, while functions like productivity and resource consumption decreased along the gradient. Microbial taxa were non- randomly distributed, forming distinct clusters of short-{tau} and long-{tau} specialists, reflecting a pattern of niche partitioning. Consistent with theoretical predictions, we demonstrate that residence time shapes assembly processes with direct implications for biodiversity and community function. These insights are crucial for understanding and managing flowing environments, such as animal gut microbiomes, soil litter invertebrate communities, and plankton in freshwater and marine ecosystems.

ecology↗

bioRxiv2024

Phage infection fronts trigger early sporulation and collective defense in bacterial populations

I.Bacteriophage (phage) infect, lyse, and propagate within bacterial populations. However, physiological changes in bacterial cell state can protect against infection even within genetically susceptible populations. One such example is the generation of endospores by Bacillus and its relatives, characterized by a reversible state of reduced metabolic activity that protects cells against stressors including desiccation, energy limitation, antibiotics, and infection by phage. Here we tested how sporulation at the cellular scale impacts phage dynamics at population scales when propagating amongst B. subtilis in spatially structured environments. Initially, we found that plaques resulting from infection and lysis were approximately 3-fold smaller on lawns of sporulating wild-type bacteria vs. non-sporulating bacteria. Notably, plaque size was reduced due to an early termination of expanding phage plaques rather than the reduction of plaque growth speed. Microscopic imaging of the plaques revealed sporulation rings, i.e., spores enriched around plaque edges relative to phage-free regions. We developed a series of mathematical models of phage, bacteria, spore, and small molecules that recapitulate plaque dynamics and identify a putative mechanism: sporulation rings arise in response to lytic activity. In aggregate, sporulation rings inhibit phage from accessing susceptible cells even when sufficient resources are available for further infection and lysis. Together, our findings identify how dormancy can self-limit phage infections at population scales, opening new avenues to explore the entangled fates of phages and their bacterial hosts in environmental and therapeutic contexts.

microbiology↗

bioRxiv2024

Bacterium secretes chemical inhibitor that sensitizes competitor to bacteriophage infection

To overtake competitors, microbes produce and secrete secondary metabolites that kill neighboring cells and sequester nutrients. This natural product-mediated competition likely evolved in complex microbial communities that included viral pathogens. From this ecological context, we hypothesized that microbes secrete metabolites that "weaponize" natural pathogens (i.e., bacteriophages) to lyse their competitors. Indeed, we discovered a bacterial secondary metabolite that sensitizes other bacteria to phage infection. We found that this metabolite provides the producer (a Streptomyces sp.) with a fitness advantage over its competitor (Bacillus subtilis) by promoting phage infection. The phage-promoting metabolite, coelichelin, sensitized B. subtilis to a wide panel of lytic phages, and it did so by preventing the early stages of sporulation through iron sequestration. Beyond coelichelin, other natural products may provide phage-mediated competitive advantages to their producers--either by inhibiting sporulation or through yet-unknown mechanisms.

microbiology↗

bioRxiv2023

Coevolution with a seed bank

Dormancy is as an adaptation to living in fluctuating environments. It can also influence species interactions, for example, by providing organisms with a refuge from predators and parasites. Here we test the hypothesis that dormancy generates a seed bank of protected individuals that can modify antagonistic coevolutionary dynamics. We experimentally evolved a spore-forming bacterial host along with a phage parasite that can infect active but not dormant cells. Seed banks buffered population dynamics against phage infection and retained phenotypic diversity that was otherwise lost to directional selection. By storing genetic diversity, seed banks also altered the distribution of host alleles, which contributed to dampened coevolutionary dynamics. Our findings demonstrate that dormancy generates a seed bank that can modify the eco-evolutionary outcomes of host-parasite systems.

evolutionary biology↗

bioRxiv2023

Human-gut phages harbor sporulation genes

Spore-forming bacteria are prevalent in mammalian guts and have implications for host health and nutrition. The production of dormant spores is thought to play an important role in the colonization, persistence, and transmission of these bacteria. Spore formation also modifies interactions among microorganisms such as infection by phages. Recent studies suggest that phages may counter dormancy-mediated defense through the expression of phage-encoded sporulation genes during infection, which can alter the transitions between active and inactive states. By mining genomes and gut-derived metagenomes, we identified sporulation genes that are preferentially encoded by phages that infect spore-forming bacteria. These included genes involved in chromosome partitioning, DNA damage repair, and cell wall-associated functions. In addition, phages contained homologs of sporulation-specific transcription factors, notably spo0A, the master regulator of sporulation, which could allow phages to control the complex genetic network responsible for spore development. Our findings suggest that phages could influence the formation of bacterial spores with implications for the health of the human gut microbiome, as well as bacterial communities in other environments. SIGNIFICANCEPhages acquire bacterial genes and use them to alter host metabolism in ways that enhance their fitness. To date, most auxiliary genes replace or modulate enzymes that are used by the host for nutrition or energy production. However, phage fitness is affected by all aspects of host physiology, including decisions that reduce metabolic activity of the cell. Here we focus on endosporulation, a complex and ancient form of dormancy found among the Bacillota that involves hundreds of genes. By coupling homology searches with host classification, we identify 31 phage-encoded homologs of sporulation genes that are mostly limited to phages infecting spore-forming bacteria. Nearly one-third the homologs recovered were regulatory genes suggesting that phages may manipulate host genetic networks by tapping into their control elements. Our findings also suggest a mechanism by which phages can overcome the defensive strategy of dormancy, which may be involved in coevolutionary dynamics of spore-forming bacteria.

microbiology↗

bioRxiv2022

Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching

Organisms have evolved different mechanisms in response to periods of environmental stress, including dormancy - a reversible state of reduced metabolic activity. Transitions to and from dormancy can be random or induced by changes in environmental conditions. Prior theoretical work has shown that stochastic transitioning between active and dormant states at the individual level can maximize fitness at the population level. However, such theories of bet-hedging strategies typically neglect certain physiological features of transitions to dormancy, including time lags to gain protective benefits. Here, we construct and analyze a dynamic model that couples stochastic changes in environmental state with the population dynamics of organisms that can initiate dormancy after an explicit time delay. Stochastic environments are simulated using a multi-state Markov chain through which the mean and variance of environmental residence time can be adjusted. In the absence of time lags (or in the limit of very short lags), we find that bet-hedging strategy transition probabilities scale inversely with the mean environmental residence times, consistent with prior theory. We also find that increasing delays in dormancy decreases optimal transitioning probabilities, an effect that can be influenced by the correlations of environmental noise. When environmental residence times - either good or bad - are uncorrelated, the maximum population level fitness is obtained given low levels of transitioning between active and dormant states. However when environmental residence times are correlated, optimal dormancy initiation and termination probabilities increase insofar as the mean environmental persistent time is longer than the delay to reach dormancy. We also find that bet hedging is no longer advantageous when delays to enter dormancy exceed the mean environmental residence times. Altogether, these results show how physiological limits to dormancy and environmental dynamics shape the evolutionary benefits and even viability of bet hedging strategies at population scales.

ecology↗

bioRxiv2022

Macroevolutionary constraints on global microbial diversity

Biologists have long sought to quantify the number of species on Earth. Often missing from these efforts is the contribution of microorganisms. Despite recent large-scale sampling efforts, estimates of global microbial diversity span many orders of magnitude. To reconcile this uncertainty, it is important to consider how speciation and extinction over the last four billion years constrain inventories of biodiversity. We parameterized macroevolutionary and mass-extinction event models to determine how diversification limits present-day microbial diversity. We find that while 106-107 taxa is most probable, much larger values ([≥]1012) are feasible. Allowing for mass extinction events does not greatly alter these conclusions. Along with empirical predictions, our models provide support for a massive global-scale microbiome while shedding light on the upper limits of life on Earth.

ecology↗

bioRxiv2022

Traits of soil bacteria predict plant responses to soil moisture

Microbes can promote beneficial plant and animal responses to abiotic environments, but the ecological drivers of this benefit remain elusive. Here we investigated byproduct benefits, which occur when traits that increase the fitness of one species provide incidental benefits to another species with no direct cost to the provider species. In experimental mesocosms, microbial traits predicted plant responses to soil moisture such that bacteria with self-beneficial traits in drought increased plant early growth, size at reproduction, and chlorophyll concentration under drought, while bacteria with self-beneficial traits in well-watered environments increased these same plant traits in well-watered environments. Thus, microbial traits that promote microbial success in different soil moisture environments also promote plant success in these same environments. Our results show that the concept of byproduct benefits, originally conceived to explain the evolution of cooperation in pairwise mutualisms, also applies to interactions between plants and non-symbiotic soil microbes.

ecology↗

bioRxiv2021

Phage-encoded sigma factors alter bacterial dormancy

By entering a reversible state of reduced metabolic activity, dormant microorganisms are able to tolerate suboptimal conditions that would otherwise reduce their fitness. Dormancy may also benefit bacteria by serving as a refuge from parasitic infections. Here we focus on dormancy in the Firmicutes, where endospore development is transcriptionally regulated by the expression of sigma factors. A disruption of this process could influence the survivorship and reproduction of phages that infect spore-forming hosts with implications for coevolutionary dynamics. Here, we characterized the distribution and diversity of sigma factors in nearly 3,500 phage genomes. Homologs of sporulation-specific sigma factors were identified in phages that infect spore-forming hosts. Unlike sigma factors required for phage reproduction, the sporulation-like sigma factors were non-essential for lytic infection. However, when expressed in the spore-forming Bacillus subtilis, sigma factors from phages activated the bacterial sporulation gene network and reduced spore yield. Our findings suggest that the acquisition of host-like transcriptional regulators may allow phages to manipulate a complex and ancient trait in one of the most abundant cell types on Earth.

microbiology↗

bioRxiv2021

Seed Banks Alter the Rate and Direction of Molecular Evolution in Bacillus subtilis

Fluctuations in the availability of resources constrains the growth and reproduction of individuals, which subsequently effects the evolution of their respective populations. Many organisms contend with such fluctuations by entering a reversible state of reduced metabolic activity, a phenomenon known as dormancy. This pool of dormant individuals (i.e., a seed bank) does not reproduce and is expected to act as an evolutionary buffer, though it is difficult to observe this effect directly over an extended evolutionary timescale. Through genetic manipulation, we analyze the molecular evolutionary dynamics of Bacillus subtilis populations in the presence and absence of a seed bank over 700 days. The ability of these bacteria to enter a dormant state increased the accumulation of genetic diversity over time and altered the trajectory of mutations, findings that were recapitulated using simulations based on a mathematical model of evolutionary dynamics. While the ability to form a seed bank did not alter the degree of negative selection, we found that it consistently altered the direction of molecular evolution across genes. Together, these results show that the ability to form a seed bank can affect the direction and rate of molecular evolution over an extended evolutionary timescale.

evolutionary biology↗

bioRxiv2021

Quantifying microbial associations of dissolved organic matter under global change

Microbes play a critical role in regulating the size, composition, and turnover of dissolved organic matter (DOM), which is one of the largest pools of carbon in aquatic ecosystems. Global change may alter DOM-microbe associations with implications for biogeochemical cycles, although disentangling these complex interactions remains a major challenge. Here we develop a framework called Energy-Diversity-Trait integrative Analysis (EDTiA) to examine the associations between DOM and bacteria along temperature and nutrient gradients in a manipulative field experiment on mountainsides in contrasting subarctic and subtropical climates. In both study regions, the chemical composition of DOM correlated with bacterial communities, and was primarily controlled by nutrients and to a lesser degree by temperature. At a molecular-level, DOM-bacteria associations depended strongly on the molecular traits of DOM, with negative associations indicative of decomposition as molecules are more biolabile. Using bipartite networks, we further demonstrated that negative associations were more specialized than positive associations indicative of DOM production. Nutrient enrichment promoted specialization of positive associations, but decreased specialization of negative associations particularly at warmer temperatures in subtropical climate. These global change drivers influenced specialization of negative associations most strongly via molecular traits, while both molecular traits and bacterial diversity similarly affected positive associations. Together, our framework provides a quantitative approach to understand DOM-microbe associations and wider carbon cycling across scales under global change.

ecology↗