Biology subjects

Kandlikar, G. S.

Publications and source records attributed to Kandlikar, G. S..

4 recordsLinked to original sources

bioRxiv2025

Nutritional stress adaptation shapes host microbiome stability and life history dynamics

BackgroundDietary environments can shape host-microbe co-evolution by imposing selection pressures that favor host and microbial genotypes with enhanced fitness under specific nutritional conditions. However, the long-term evolutionary dynamics of these interactions after selection pressures are relaxed remain poorly understood. Here, we investigated the microbiome of Drosophila melanogaster populations that underwent long-term experimental evolution under three temporally variable nutritional regimes (constant high sugar, progressively decreasing protein, and fluctuating protein), and compared them to unselected controls. Following inbreeding of evolved populations, we examined how persistent evolutionary effects interact with aging to shape host-microbe relationships and survival. ResultsAll selected regimes exhibited reduced survival relative to controls, indicating lasting physiological costs associated with historical selection and inbreeding. Survival differed among regimes: the deteriorating-protein regime was closest to controls, the fluctuating-protein regime was intermediate, and the high-sugar regime showed the shortest lifespan. Survival effects were sex-specific: relative to control females, those from the fluctuating-protein regime exhibited reduced early-life survival, whereas females from the deteriorating-protein regime experienced greater late-life mortality. Microbiome composition varied with both selection regime and age. Although Firmicutes and Proteobacteria dominated across groups, selected lines showed increased Firmicutes and reduced Proteobacteria, especially early in life, suggesting early-life taxonomic restructuring. The decreasing-protein regime maintained more stable microbial diversity over time, whereas high-sugar and fluctuating-protein diets were associated with progressive microbiome instability with age. Core Acetobacter species (A. aceti, A. oryzifermentans) declined in abundance in selected flies, indicating persistent disruption of microbiome integrity. A random forest model predicted fly age from microbiome composition with 78.8% accuracy, reinforcing links between microbial dynamics and host aging. ConclusionHistorical dietary selection and inbreeding can leave lasting signatures on survival and microbiome composition in Drosophila. Protein restriction promoted late-life longevity and microbial stability, whereas high-sugar and fluctuating diets were associated with early-life effects followed by later-life shifts in dominant taxa. Together, these findings illustrate how nutritional history and its microbial legacies influence lifespan and aging through persistent host-microbe interactions.

evolutionary biology↗

bioRxiv2024

Realistic time-lags and litter dynamics alter predictions of plant-soil feedback across generations

Plant-soil feedback is a critical process in natural plant communities. However, it remains unclear whether greenhouse-measured microbial effects manifest in natural systems with temporally separated growing seasons as classic experiments often overlook seasonal time lags and litter dynamics. We modified the classic two-phase experiment to study plant-soil feedback for three Californian annual plant species. Our response phase used soil inoculum obtained either immediately after plant conditioning, after a six-month dry period with the conditioning plant removed, or after a dry period with the litter of the conditioning plant. We characterized soil bacterial and fungal communities in different treatments and employed recent advancement in plant-soil feedback theory to predict plant coexistence. Temporal delays and the presence of litter caused distinct responses in the fungal and bacterial communities, resulting in divergent microbial compositions at the end of the response phases. The delayed response treatments also affected microbially mediated stabilization, fitness differences, and invasion growth rates differently across species pairs, influencing predictions of plant coexistence. Our study highlights that the interplay between seasonal delays and litter dynamics prevents the direct extrapolation of plant-soil feedback measurements across multiple seasons, emphasizing the necessity of considering natural history when predicting microbially mediated plant coexistence.

ecology↗

bioRxiv2021

A quantitative synthesis of soil microbial effects on plant species coexistence

Soil microorganisms play a major role in shaping plant diversity, not only through their direct effects as pathogens, mutualists, and decomposers, but also by altering interactions between plants. In particular, previous research has shown that the soil community often generates frequency-dependent feedback loops among plants that can either destabilize species interactions, or generate stabilizing niche differences that promote species coexistence. However, recent insights from modern coexistence theory have shown that microbial effects on plant coexistence depend not only on these stabilizing or destabilizing effects, but also on the degree to which they generate competitive fitness differences. While many previous experiments have generated the data necessary for evaluating microbially mediated fitness differences, these effects have rarely been quantified in the literature. Here we present a meta-analysis of data from 50 studies, which we used to quantify the microbially mediated (de)stabilization and fitness differences derived from a classic plant-soil feedback model. Across 518 pairwise comparisons, we found that soil microbes generated both stabilization (or destabilization) and fitness differences, but also that the microbially mediated fitness differences dominated. As a consequence, if plants are otherwise equivalent competitors, the balance of soil microbe-generated (de)stabilization and fitness differences drives species exclusion much more frequently than coexistence or priority effects. Our work shows that microbially mediated fitness differences are an important but overlooked effect of soil microbes on plant coexistence. This finding paves the way for a more complete understanding of the processes that maintain plant biodiversity.

ecology↗

bioRxiv2021

EcoEvoApps: Interactive Apps for Teaching Theoretical Models in Ecology and Evolutionary Biology

O_LIThe integration of theory and data drives progress in science, but a persistent barrier to such integration in ecology and evolutionary biology (EEB) is that theory is often developed and expressed in the form of mathematical models that can feel daunting and inaccessible for students and empiricists with variable quantitative training and attitudes towards math. C_LIO_LIA promising way to make mathematical models more approachable is to embed them into interactive tools with which one can visually evaluate model structures and directly explore model outcomes through simulation. C_LIO_LITo promote such interactive learning of quantitative models, we developed EcoEvoApps, a collection of free, open-source (R/Shiny) apps that include model overviews, interactive model simulations, and code to implement these models directly in R. The package currently focuses on canonical models of population dynamics, species interaction, and landscape ecology. We also outline a vision and approach for growing the collection to include more models from across EEB. C_LIO_LIThese apps help illustrate fundamental results from theoretical ecology and can serve as valuable teaching tools in classroom settings. We present data from student surveys which show that students rate these apps as useful learning tools, and that using interactive apps leads to substantial gains in students interest and confidence in mathematical models. This points to the potential for interactive activities to make theoretical models more accessible to a wider audience, and thus facilitate the feedback between theory and data across ecology and evolutionary biology. C_LI

scientific communication and education↗