Biology subjects

Chavhan, Y.

Publications and source records attributed to Chavhan, Y..

6 recordsLinked to original sources

bioRxiv2026

Phenotypic plasticity segregates antagonistic species but undermines their coexistence

Environmental change often induces novel phenotypes in multiple cohabiting species, yet how such common-cue-induced plasticity shapes their coexistence is largely unknown. Testing this link requires disentangling inducing-environment effects from induced-phenotype effects, which remains elusive. We address this gap using two mutually antagonistic bacterial species, Staphylococcus aureus (Sa) and Pseudomonas aeruginosa (Pa). In habitual salinity, where both bacteria show unicellularity, Pa severely diminished Sa. In contrast, high salinity induced macroscopic cell clustering that spatially segregated Sa and Pa (Sa: bottom-dwelling vertical filament; Pa: top-dwelling horizontal mat), and led to >10-fold higher coexistence than habitual salinity. Counterintuitively, physically inhibiting cell clustering (abolishing segregation) in high salinity led to a further >100-fold higher coexistence (Sa:Pa::~1:1). This was because salinity-induced clustering was adaptive for Pa, but not for Sa: such adaptive plasticity enabled killer Pa to proliferate by monopolizing oxygen, which diminished Sa in a correlated manner, thereby weakening coexistence (mechanistically explained by diffusion-based killing). Hence, although the inducing environment promoted overall coexistence, the induced phenotype undermined it. Community-wide genomics revealed that the high level of coexistence achieved by abolishing segregation in high salinity allowed rapid coculture-specific evolution. Taken together, we uncover how plasticity can appear to promote antagonistic coexistence despite causally undermining it.

evolutionary biology↗

bioRxiv2023

Population size shapes trade-off dilution and adaptation to a marginal niche unconstrained by sympatric habitual conditions

Niche expansion remains significantly understudied in sympatric scenarios where marginal and habitual niches are simultaneously available. Devoid of spatial constraints, such conditions impose selection to maintain fitness in habitual (high-productivity) niches while adapting to marginal (low-productivity) niches. Hence, habitual niche composition should constrain adaptation to marginal niches. This remains untested. Similarly, it is unknown if larger populations expand their niches better. We tested these hypotheses using experimental evolution with Escherichia coli and found that larger populations consistently adapted better to both marginal and habitual niches. Whereas the habitual niche composition (constant versus fluctuating environments; environmental fluctuations varying in both predictability and speed) significantly shaped fitness in habitual niches, surprisingly, it failed to constrain adaptation to the marginal niche. Curiously, two negatively correlated habitual niches can still each be positively correlated with the marginal niche. This allows the marginal niche to dilute trade-offs between habitual niches, thereby enabling costless niche expansion.

evolutionary biology↗

bioRxiv2022

Bacteria evolve macroscopic multicellularity via the canalization of phenotypically plastic cell clustering

The evolutionary transition from unicellular to multicellular life was a key innovation in the history of life. Given scarce fossil evidence, experimental evolution has been an important tool to study the likely first step of this transition, namely the formation of undifferentiated cellular clusters. Although multicellularity first evolved in bacteria, the extant experimental evolution literature on this subject has primarily used eukaryotes. Moreover, it focuses on mutationally driven (and not environmentally induced) phenotypes. Here we show that both Gram-negative and Gram-positive bacteria exhibit phenotypically plastic (i.e., environmentally induced) cell clustering. Under high salinity, they grow as elongated ~ 2 cm long clusters (not as individual planktonic cells). However, under habitual salinity, the clusters disintegrate and grow planktonically. We used experimental evolution with Escherichia coli to show that such clustering can be canalized successfully: the evolved bacteria inherently grow as macroscopic multicellular clusters, even without environmental induction. Highly parallel mutations in genes linked to cell wall assembly formed the genomic basis of canalized multicellularity. While the wildtype also showed cell shape plasticity across high versus low salinity, it was either canalized or reversed after evolution. Interestingly, a single mutation could canalize multicellularity by modulating plasticity at multiple levels of organization. Taken together, we show that phenotypic plasticity can prime bacteria for evolving undifferentiated macroscopic multicellularity.

evolutionary biology↗

bioRxiv2020

An interplay of population size and environmental heterogeneity explains why fitness costs are rare

Theoretical models of ecological specialization commonly assume that adaptation to one environment leads to fitness reductions (costs) in others. However, empirical studies often fail to detect such costs. We addressed this conundrum using experimental evolution with Escherichia coli in several homogeneous and heterogeneous environments at multiple population sizes. We found that in heterogeneous environments, smaller populations paid significant costs, but larger ones avoided them altogether. Contrastingly, in homogeneous environments, larger populations paid more costs than the smaller ones. Overall, large population sizes and heterogeneous environments led to cost avoidance when present together but not on their own. Whole-genome whole-population sequencing revealed that the enrichment of multiple mutations within the same lineage (and not subdivision into multiple distinct specialist subpopulations) was the mechanism of cost avoidance. Since the conditions revealed by our study for avoiding costs are widespread, it explains why the costs expected in theory are rarely detected in experiments.

evolutionary biology↗

bioRxiv2020

Larger bacterial populations evolve heavier fitness trade-offs and undergo greater ecological specialization

Evolutionary studies over the last several decades have invoked fitness trade-offs to explain why species prefer some environments to others. However, the effects of population size on trade-offs and ecological specialization remain largely unknown. To complicate matters, trade-offs themselves have been visualized in multiple ways in the literature. Thus, it is not clear how population size can affect the various aspects of trade-offs. To address these issues, we conducted experimental evolution with Escherichia coli populations of two different sizes in two nutritionally limited environments and studied fitness trade-offs from three different perspectives. We found that larger populations evolved greater fitness trade-offs, regardless of how trade-offs are conceptualized. Moreover, although larger populations adapted more to their selection conditions, they also became more maladapted to other environments, ultimately paying heavier costs of adaptation. To enhance the generalizability of our results, we further investigated the evolution of ecological specialization across six different environmental pairs and found that larger populations specialized more frequently and evolved consistently steeper reaction norms of fitness. This is the first study to demonstrate a relationship between population size and fitness trade-offs and the results are important in understanding the population genetics of ecological specialization and vulnerability to environmental changes.

evolutionary biology↗

bioRxiv2019

Adapting in larger numbers can increase the vulnerability of Escherichia coli populations to environmental changes

Larger populations generally adapt faster to their existing environment. However, it is unknown if the population size experienced during evolution influences the ability to face sudden environmental changes. To investigate this issue, we subjected replicate Escherichia coli populations of different sizes to experimental evolution in an environment containing a cocktail of three antibiotics. In this environment, the ability to actively efflux molecules outside the cell is expected to be a major fitness-affecting trait. We found that all the populations eventually reached similar fitness in the antibiotic cocktail despite adapting at different speeds, with the larger populations adapting faster. Surprisingly, whereas efflux activity enhanced in the smaller populations, it decayed in the larger ones. The evolution of efflux activity was largely shaped by pleiotropic responses to selection and not by drift. This demonstrates that quantitative differences in population size can lead to qualitative differences (decay/enhancement) in the fate of a character during adaptation to identical environments. Furthermore, the larger populations showed inferior fitness upon sudden exposure to several alternative stressful environments. These observations provide a novel link between population size and vulnerability to environmental changes. Counter-intuitively, adapting in larger numbers can render bacterial populations more vulnerable to abrupt environmental changes.

evolutionary biology↗