Biology subjects

Hwa, T.

Publications and source records attributed to Hwa, T..

17 recordsLinked to original sources

bioRxiv2026

Minimizing co-growth as a broad predictor of community robustness

Microbial communities rarely remain in a fixed physiological state. Instead, they progress through internal life cycles in which changing metabolites, spatial organization, and physiological states reshape ecological interactions over time. Despite extensive theory on coexistence with fixed interactions, we lack simple quantitative predictors of robustness for communities undergoing repeated growth and dispersal cycles. Here we show that a single quantity, the temporal co-growth of community members, predicts robustness across several models of community maturation, including chemotactic spatial patterning, cross-feeding with toxicity, and a phenomenological many-species model with prescribed growth trajectories. Communities in which different species grow at distinct times persist far longer under stochastic reseeding than communities with overlapping growth, with average community lifetime increasing approximately exponentially as co-growth decreases. Across the systems studied here, diverse mechanisms such as spatial organization, metabolic cascades, and physiological programs promote robustness insofar as they reduce the temporal overlap of rapid growth across species. These results identify co-growth as a common quantitative feature of robust dynamically maturing communities and suggest that minimizing co-growth may provide a broader organizing principle for ecological robustness.

ecology↗

bioRxiv2025

Extrusion-modulated DnaA activity oscillations coordinate DNA replication with biomass growth

Robust control of DNA replication is fundamental to bacterial proliferation. In Escherichia coli, replication initiation is thought to be regulated by oscillations in DnaA activity, driven by DnaA-chromosome interactions that differ among leading models. However, direct evidence linking these oscillations to replication initiation has been lacking, and existing models fail to explain the observed decoupling of replication initiation from dnaA expression. Here, we establish a direct link between DnaA activity and replication initiation by demonstrating robust oscillations in DnaA activity, which peak precisely at replication initiation across diverse growth conditions and genetic perturbations. Notably, these oscillations persist even when dnaA transcription remains constant, suggesting a regulatory mechanism that modulates DnaA activity independently of its expression. Additionally, we propose an extrusion model in which DNA-binding proteins sense biomass-DNA imbalance and extrude DnaA from the chromosome to trigger replication, overcoming limitations of existing models. Consistent with this model, perturbation of the nucleoid-associated protein H-NS modulates DnaA activity and replication timing, supporting its mechanistic validity.

microbiology↗

bioRxiv2025

Growth in Low Carbon Conditions Reveals Amino-Acid-Coupled Iron Uptake

Bacteria in nature encounter substrates at widely varying concentrations, yet studies of bacterial physiology have focused more on nutrient type than concentration, partly due to challenges in maintaining low concentrations. We developed a Millifluidic Continuous Culture Device (MCCD) to culture bacteria under precisely controlled nutrient conditions, including very low concentrations, in a manner suitable for proteomic analysis. Using the MCCD, we cultured Escherichia coli with a mixture of amino acids as the sole carbon source at three concentrations supporting growth rates spanning a fivefold range. Surprisingly, at the lowest concentration, cells exhibited proteomic signatures of iron shortage despite equal iron levels across conditions. We observed the uptake of labeled iron-histidine and iron-cysteine complexes, indicating that amino acids facilitated iron acquisition and that amino-acid-bound iron is bioavailable to E. coli. These findings reveal a previously unknown mechanism of bacterial iron acquisition that emerged under the flow imposed by the MCCD, which likely diluted the siderophore pool and reduced their efficacy. This work highlights the importance of studying bacterial physiology under low nutrient concentrations and demonstrates how physical conditions, such as flow, shape microbial nutrient acquisition strategies.

microbiology↗

bioRxiv2024

Competition strategies driving resource partitioning in chitin degrading communities

Resource competition strongly shapes microbial community dynamics and function. In polysaccharide-degrading communities, primary degraders secrete monomer-releasing enzymes and exploiters consume released products without investing in enzymes. By investigating competitive strategies between chitin degraders and N-acetylglucosamine (GlcNAc) exploiters, we uncover several interacting factors, including GlcNAc liberation rates, diffusive loss, and resource partitioning between competitors, which determine community viability and growth dynamics at early stages of degradation. Aside from cases involving antibiotic secretion or aggregation on particles to privatize degrading enzymes, exploiters also inhibit degraders by siphoning away limiting GlcNAc flux during early stages of particle degradation, when degraders must overcome diffusive GlcNAc loss to sustain chitinase production. Analogous to the Allee effect in population biology, these effects lead to sensitive dependences on initial species densities for a community to thrive. This study elucidates how metabolic competition at early stages of particle degradation shapes species interactions, resource partitioning, and ultimately community viability.

microbiology↗

bioRxiv2024

Dynamic coexistence driven by physiological transitions in microbial communities

AO_SCPLOWBSTRACTC_SCPLOWMicrobial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into stressed or non-growing states. Such dynamics are typical of ecological succession in nature and serial-dilution cycles in the laboratory. Here, we introduce a phenomenological model, the Community State model, to gain insight into the dynamic coexistence of microbes due to changes in their physiological states. Our model bypasses specific interactions (e.g., nutrient starvation, stress, aggregation) that lead to different combinations of physiological states, referred to collectively as "community states", and modeled by specifying the growth preference of each species along a global ecological coordinate, taken here to be the total community biomass density. We identify three key features of such dynamical communities that contrast starkly with steady-state communities: increased tolerance of community diversity to fast growth rates of species dominating different community states, enhanced community stability through staggered dominance of different species in different community states, and increased requirement on growth dominance for the inclusion of late-growing species. These features, derived explicitly for simplified models, are proposed here to be principles aiding the understanding of complex dynamical communities. Our model shifts the focus of ecosystem dynamics from bottom-up studies based on idealized inter-species interaction to top-down studies based on accessible macroscopic observables such as growth rates and total biomass density, enabling quantitative examination of community-wide characteristics.

ecology↗

bioRxiv2024

Marine Bacteria Alteromonas spp. Require UDP-glucose-4-epimerase for Aggregation and Production of Sticky Exopolymer

The physiology and ecology of particle-associated marine bacteria are of growing interest, but our knowledge of their aggregation behavior and mechanisms controlling their association with particles remains limited. We have found that a particle-associated isolate, Alteromonas sp. ALT199 strain 4B03, and the related type-strain A. macleodii 27126 both form large (>500 m) aggregates while growing in rich medium. A non-clumping variant (NCV) of 4B03 spontaneously arose in the lab, and whole genome sequencing revealed a partial deletion in the gene encoding UDP-glucose-4-epimerase (galE{Delta}308-324). In 27126, a knock-out of galE ({Delta}galE::kmr) resulted in a loss of aggregation, mimicking the NCV. Microscopic analysis shows that both 4B03 and 27126 rapidly form large aggregates, whereas their respective galE mutants remain primarily as single planktonic cells or clusters of a few cells. Strains 4B03 and 27126 also aggregate chitin particles, but their galE mutants do not. Alcian Blue staining shows that 4B03 and 27126 produce large transparent exopolymer particles (TEP), but their galE mutants are deficient in this regard. This study demonstrates the capabilities of cell-cell aggregation, aggregation of chitin particles, and production of TEP in strains of Alteromonas, a widespread particle-associated genus of heterotrophic marine bacteria. A genetic requirement for galE is evident for each of the above capabilities, expanding the known breadth of requirement for this gene in biofilm-related processes. ImportanceHeterotrophic marine bacteria have a central role in the global carbon cycle. Well-known for releasing CO2 by decomposition and respiration, they may also contribute to particulate organic matter (POM) aggregation, which can promote CO2 sequestration via the formation marine snow. We find that two members of the prevalent particle-associated genus Alteromonas can form aggregates comprising cells alone or cells and chitin particles, indicating their ability to drive POM aggregation. In line with their multivalent aggregation capability, both strains produce TEP, an excreted polysaccharide central to POM aggregation in the ocean. We demonstrate a genetic requirement for galE in aggregation and large TEP formation, building our mechanistic understanding of these aggregative capabilities. These findings point toward a role for heterotrophic bacteria in POM aggregation in the ocean and support broader efforts to understand bacterial controls on the global carbon cycle based on microbial activities, community structure, and meta-omic profiling.

microbiology↗

bioRxiv2023

Spatiotemporal development of growth and death zones in expanding bacterial colonies driven by emergent nutrient dynamics

Bacterial colony growth on hard agar is commonplace in microbiology; yet, what occurs inside a growing colony is complex even in the simplest cases. Robust colony expansion kinetics featuring a linear radial growth and a saturating vertical growth indicates a common developmental program which is elucidated here for Escherichia coli cells using a combination of modeling and experiments. Radial colony expansion is found to be limited by mechanical factors rather than nutrients as commonly assumed. In contrast, vertical expansion is limited by glucose depletion inside the colony, an effect compounded by reduced growth yield due to anaerobiosis. Carbon starvation in the colony interior results in substantial cell death within 1-2 days, with a distinct death zone that expands with the growing colony. Overall, the development of simple colonies lacking EPS production and differentiation is dictated by an interplay of mechanical constraints and emergent nutrient gradients arising from obligatory metabolic processes.

microbiology↗

bioRxiv2023

Sustained growth and rapid dispersal of chitin-associated marine bacteria

Many biogeochemical functions involve bacteria utilizing solid substrates. However, little is known about the coordination of bacterial growth with the kinetics of attachment to and detachment from such substrates. In this quantitative study of Vibrio sp. 1A01 growing on chitin particles, we reveal the heterogeneous nature of the exponentially growing culture, comprised of two co-existing subpopulations: a minority replicating on chitin particles and a non-replicating majority which was planktonic. This partition resulted from a high rate of cell detachment from particles. Despite high detachment, sustained exponential growth of cells on particles was enabled by the enrichment of extra-cellular chitinases excreted and left behind by detached cells. The "inheritance" of these chitinases sustains the colonizing subpopulation despite its reduced density. This simple mechanism helps to circumvent a tradeoff between growth and dispersal, allowing particle-associated marine heterotrophs to explore new habitats without compromising their fitness on the habitat they have already colonized.

microbiology↗

bioRxiv2022

Functional Decomposition of Metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions

Quantifying the contribution of individual molecular components to complex cellular processes is a grand challenge in systems biology. Here we establish a general theoretical framework (Functional Decomposition of Metabolism, FDM) to quantify the contribution of every metabolic reaction to metabolic functions, e.g. the biosynthesis of metabolic building blocks such as amino acids. This allows us to obtain a plethora of results for E. coli growing in different conditions. A detailed quantification of energetic costs for biosynthesis and biomass growth on glucose shows that ATP generated during de novo biosynthesis of building blocks almost balances the ATP costs of peptide chain polymerization, the single largest energy expenditure for growing cells. This leaves the bulk of energy generated by fermentation and respiration (consuming 1/3 of the glucose intake) during aerobic growth unaccounted for. FDM also enabled the quantification of protein allocated towards each metabolic function, unveiling linear enzyme-flux relations for biosynthesis. These results led us to derive a function-based coarse-grained model to capture global protein allocation and overflow metabolism, without relying on curated pathway annotation or clustering of gene expression data.

systems biology↗

bioRxiv2022

A Metabolic Sum Rule Dictates Bacterial Response to Short-Chain Fatty Acid Stress

Short-chain fatty acids (SCFAs) such as acetate accumulate in fermentative environments, inhibiting many types of bacteria. While it is known that cells accumulate SCFAs to high concentrations internally, the cause of SCFA toxicity is not understood. By forcing Escherichia coli cells to accumulate a variety of "useless metabolites", we establish via extensive omic analysis a metabolic sum rule, by which the accumulation of exogenous metabolites such as acetate forces the depletion of endogenous metabolites. The latter leads to bottlenecks in biosynthesis, manifested as a simple linear relation between useless metabolite accumulation and growth reduction. Guided by quantitative models, we show that acetate-stressed cells optimize growth by partially acidifying their own cytoplasm, which reduces acetate accumulation, restoring the endogenous metabolites as allowed by the sum rule.

microbiology↗

bioRxiv2022

A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus sp. 1A01

While the Vibrio splendidus species is best known as an opportunistic pathogen in oysters, the Vibrio splendidus sp. 1A01 strain was first identified as an early colonizer of synthetic chitin particles incubated in seawater. To gain a better understanding of its metabolism, a genome-scale metabolic model (GSMM) of V. splendidus sp. 1A01 was reconstructed. GSMMs enable us to simulate all metabolic reactions in a bacterial cell using Flux Balance Analysis. A draft model was built using an automated pipeline from BioCyc. Manual curation was then performed based on experimental data, in part by gap-filling metabolic pathways and tailoring the models biomass reaction to V. splendidus sp. 1A01. The challenges of building a metabolic model for a marine microorganism like V. splendidus sp. 1A01 are described.

microbiology↗

bioRxiv2021

Cellular perception of growth rate and the mechanistic origin of bacterial growth laws

Bacteria organize many activities according to their grow rate via the ppGpp signaling system. Yet it is not clear how this signaling system "knows" how fast cells grow. Through quantitative experiments, we show that ppGpp responds inversely to the rate of translational elongation in E. coli. Together with its roles in inhibiting ribosome biogenesis and activity, ppGpp closes a key regulatory circuit that enables the cell to perceive and control the rate of its growth across conditions. The celebrated linear growth law relating the ribosome content and growth rate emerges as a consequence of keeping a supply of ribosome reserves while maintaining elongation rate in slow growth conditions. Further analysis suggests the elongation rate itself is detected by sensing the ratio of dwelling and translocating ribosomes, a strategy employed to collapse the complex, high-dimensional dynamics of the molecular processes underlying cell growth to perceive the physiological state of the whole.

systems biology↗

bioRxiv2021

Stress-induced cross-feeding of internal metabolites provides a dynamic mechanism of microbial cooperation

Metabolic cross-feeding plays vital roles in promoting ecological diversity. While some microbes depend on exchanges of essential nutrients for growth, forces driving the extensive cross-feeding needed to support the coexistence of free-living microbes are poorly understood. Here we characterize bacterial physiology under self-acidification, and establish that extensive excretion of key metabolites following acidification provides a collaborative, inter-species mechanism of stress resistance. This collaboration occurs not only between species isolated from the same community, but also between unrelated species with complementary (glycolytic vs. gluconeogenic) modes of metabolism. Cultures of such communities cycle through different phases in growth-dilution experiments, comprising of exponential growth, growth arrest upon acidification, collaborative stress relief, and growth recovery, with each phase involving distinct physiological states of individual species. Our findings challenge the static view of ecosystems commonly portrayed in ecological models, and offer an alternative dynamical view based on growth advantages of different species in different phases.

microbiology↗

bioRxiv2021

Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

Bacteria allocate their proteome to cellular functions differently in different growth conditions. It is largely unknown how such allocation arises from known mechanisms of gene regulation while constrained by limited translation capacity and fixed protein density. Here, we performed absolute transcriptomic and proteomic analysis for E. coli across many conditions, obtaining a plethora of results on promoters and mRNAs characteristics that clash with conventional expectations: the majority of mRNAs exhibit similar translational efficiencies, while the promoter strengths are vastly different across genes. These characteristics prescribe two principles of gene regulation guiding bacteria to attain the desired protein allocation under global constraints: Total transcriptional output is tightly coordinated with ribosomal activity, and the concentrations of individual proteins are largely set by transcription. These two principles lead to a quantitative formulation of Central Dogma which unravels the complex relationship between gene regulatory activities and mRNA/protein concentrations across conditions. The knowledge obtained will be invaluable for accurately inferring gene regulatory interactions from omics data, as well as for guiding the design of genetic circuits for synthetic biology applications in E. coli and other organisms.

systems biology↗

bioRxiv2021

Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions

To swim and navigate, motile bacteria synthesize a complex motility machinery involving flagella, motors, and a sensory system. A myriad of studies has elucidated the molecular processes involved, but less is known about the coordination of motility expression with cellular physiology: In Escherichia coli, motility genes are strongly upregulated in nutrient-poor conditions compared to nutrient-replete conditions; yet a quantitative link to cellular motility has not been developed. Here, we systematically investigate gene expression, swimming behavior, and cell growth across a broad spectrum of exponential growth condition. We establish that E. coli up-regulates the expression of motility genes at slow growth to compensate for reduction in cell size, such that the number of flagella per cell is maintained across conditions. The observed 4-5 flagella per cell is the minimum number needed to keep the majority of cells motile. This simple regulatory objective allows E. coli cells to remain motile across a broad range of growth conditions while keeping the biosynthetic and energetic demands to establish and drive the motility machinery at the minimum needed. Given the strong reduction in flagella synthesis resulting from cell size increases at fast growth, our findings also provide a novel physiological perspective on bacterial cell size control: A larger cell-size at fast growth is an efficient strategy to increase the allocation of cellular resources to the synthesis of those proteins required for fast growth, while maintaining processes such as motility which are only needed on a per-cell basis.

microbiology↗

bioRxiv2021

Suboptimal proteome allocation during changing environments constrains bacterial response and growth recovery

To sustain growth in fluctuating environments microbial organisms must respond appropriately. The response generally requires the synthesis of novel proteins, but this synthesis can be impeded due to the depletion of biosynthetic precursors when growth conditions vary. Microbes must thus devise effective response strategies to manage depleting precursors. To better understand these strategies, we here investigate the active response of Escherichia coli to changes in nutrient conditions, connecting transient gene-expression behavior to growth phenotypes. By synthetically modifying the gene expression during changing growth conditions, we show how the competition by genes for the limited protein synthesis capacity constrains the cellular response. Despite this constraint, cells substantially express genes that are not required, severely slowing down the response. These findings highlight that cells do not optimize growth and recovery in every encountered environment but rather exhibit hardwired response strategies that may have evolved to promote growth and fitness in their native environment and include the regulation of multiple genes. The constraint and the suboptimality of the cellular response uncovered in this study provides a conceptual framework relevant for many research applications, from the prediction of evolution and adaptation to the improvement of gene circuits in biotechnology.

microbiology↗

bioRxiv2019

A general quantitative relation linking bacterial cell growth and the cell cycle

The foundation of bacterial cell cycle studies has long resided in two interconnected dogmas between biomass growth, DNA replication, and cell division during exponential growth: the SMK growth law that relates cell mass (a measure of cell size) to growth rate1, and Donachies hypothesis of a growth-rate-independent initiation mass2. These dogmas have spurred many efforts to understand their molecular bases and physiological consequences3-12. Most of these studies focused on fast-growing cells, with doubling times shorter than 60 min. Here, we systematically studied the cell cycle of E. coli for a broad range of doubling times (24 min to over 10 hr), with particular attention on steady-state growth. Surprisingly, we observed that neither dogma held across the range of growth rates examined. In their stead, a new linear relation unifying the slow- and fast-growth regimes was revealed between the cell mass and the number of cell divisions it takes to replicate and segregate a newly initiated pair of replication origins. This and other findings in this study suggest a single-cell division model, which not only reproduces the bulk relations observed but also recapitulates the adder phenomenon established recently for stochastically dividing cells13-15. These results allowed us to develop quantitative insight into the bacterial cell cycle, providing a firm new foundation for the study of bacterial growth physiology.

microbiology↗