Biology subjects

Prabhakara, K. H.

Publications and source records attributed to Prabhakara, K. H..

4 recordsLinked to original sources

bioRxiv2025

Diverse microbial communities assemble on both recalcitrant and labile carbon sources

Microbial community assembly is shaped by the nature of available resources, with labile carbon sources such as glucose often expected to support low diversity due to rapid growth and competitive exclusion. In contrast, recalcitrant substrates like cellulose are thought to support higher diversity through slower growth and increased niche partitioning. In previous work, we showed that compost-derived microbial communities propagated on cellulose maintained high diversity over nearly a year. To determine whether such diversity is specific to recalcitrant substrates or reflects more general features of assembly, we tracked community dynamics in three environments--cellulose paper, cellulose broth, and glucose--using daily 16S rRNA profiling over eight weeks. Communities were maintained through bi-weekly serial transfers, with five replicates per treatment, yielding a high-resolution dataset of over 800 samples. Despite originating from the same inoculum, communities diverged sharply in both taxonomic and functional composition. Cellulose environments yielded stable communities enriched in specialists, while glucose environments exhibited rapid succession and dominance by generalists. Surprisingly, all environments sustained comparably high levels of taxonomic diversity. Functional inference suggested extensive cross-feeding and resource salvaging in both cases. While the mechanisms maintaining diversity on glucose remain unresolved, our results reveal distinct assembly trajectories under simple carbon regimes and provide a foundation for future mechanistic study.

ecology↗

bioRxiv2022

Algae drive convergent bacterial community assembly when nutrients are scarce

The assembly of microbial communities is a complex dynamical process that determines community structure and function. Assembly can be influenced by species-species interactions, invasions, the availability of nutrients, and microbial physiology. The interdependence of these factors presents a challenge for understanding community assembly. For example, species-species interactions can be modulated by the availability of nutrients. Here we sought to understand how nutrient supply modulated interactions to affect the assembly process. We exploited algae in association with complex bacterial consortia from soils as models for ubiquitous phototroph-heterotroph communities that play an important role in global primary production. Studying bacterial communities assembled with and without the alga in environments with varying frequency of nutrient supply allowed us to differentiate the impacts of the algae from nutrient availability on the assembly process. A statistical decomposition of community taxonomic structure revealed that it is possible to separate the effects of biotic (presence of algae) and abiotic (nutrient supply rates) factors on community assembly. We found that when the supply of external nutrients is infrequent, the algae strongly impact bacterial community assembly, driving initially diverse bacterial consortia to converge to a common structure. Analysis of sequencing data revealed that this convergence is largely mediated by algal inhibition of specific bacterial taxa. Conversely, when nutrients are supplied with high frequency, bacterial community assembly is not impacted by the presence of the alga. This study shows that complex phototroph-heterotroph communities can be powerful model systems for understanding the assembly process in a context relevant to the global ecosystem functioning.

ecology↗

bioRxiv2020

Closed microbial communities self-organize to persistently cycle carbon

Nutrient cycling is an emergent property of ecosystems at all scales, from microbial communities to the entire biosphere. Understanding how nutrient cycles emerge from the collective metabolism of ecosystems is a challenging problem. Here we use closed microbial ecosystems (CES), hermetically sealed consortia that sustain nutrient cycles when provided with only light, to learn how microbial communities cycle carbon. A new technique for quantifying carbon exchange shows that CES comprised of an alga and diverse bacteria self-organize to robustly cycle carbon. Comparing a library of CES, we find that carbon cycling does not depend strongly on the taxonomy of the bacteria present. Metabolic profiling reveals functional redundancy across CES: despite strong taxonomic differences, self-organized CES exhibit a conserved set of metabolic capabilities. SummaryClosed microbial communities of algae and bacteria self-organize to robustly cycle carbon via emergent metabolite exchange.

ecology↗

bioRxiv2017

The cooperation of the haves and the have-nots

Upon starvation, Dictyostelium discoideum (D.d.) exhibit social behavior mediated by the chemical messenger cyclic adenosine monophosphate (cAMP). Large scale cAMP waves synchronize the population of starving cells and enable them to aggregate and form a multi-cellular organism. Here, we explore the effect of cell-to-cell variability in the production of cAMP on aggregation. We create a mixture of extreme cell-to-cell variability by mixing a few cells that produce cAMP (haves) with a majority of mutants that cannot produce cAMP (have-nots). Surprisingly, such mixtures aggregate, although each population on its own cannot aggregate. We show that (1) a lack of divalent ions kills the haves at low densities and (2) the have-nots supply the cAMP degrading enzyme, phosphodiesterase, which, in the presence of divalent ions, enables the mixture to aggregate. Our results suggest that a range of degradation rates induces optimal aggregation. The haves and the have-nots cooperate by sharing complementary resources.

biophysics↗