Biology subjects

Carlson, R. P.

Publications and source records attributed to Carlson, R. P..

4 recordsLinked to original sources

bioRxiv2022

Environment constrains fitness advantages of division of labor in microbial consortia engineered for metabolite push or pull interactions

Fitness benefits from division of labor in microbial consortia are well documented, but the dependency of the benefits on environmental context is poorly understood. Two synthetic Escherichia coli consortia were built to test the relationships between exchanged organic acid, local environment, and opportunity costs of different metabolic strategies. Opportunity costs quantify benefits not realized due to selecting one phenotype over another. The consortia catabolized glucose and exchanged either acetic or lactic acid to create producer-consumer food webs. The organic acids had different inhibitory properties and different opportunity costs associated with their positions in central metabolism. The exchanged metabolites modulated different consortial dynamics. The acetic acid-exchanging (AAE) consortium had a push interaction motif where acetic acid was secreted faster by the producer than the consumer imported it, while the lactic acid-exchanging (LAE) consortium had a pull interaction motif where the consumer imported lactic acid at a comparable rate to its production. The LAE consortium outperformed wild type (WT) batch cultures under the environmental context of weakly buffered conditions, achieving a 55% increase in biomass titer, a 51% increase in biomass per proton yield, an 86% increase in substrate conversion, and the complete elimination of byproduct accumulation all relative to the WT. However, the LAE consortium had the tradeoff of a 42% lower specific growth rate. The AAE consortium did not outperform the WT in any considered fitness metric. Fitness advantages of the LAE consortium were sensitive to environment; increasing the medium buffering capacity negated the fitness advantages compared to WT. IMPORTANCEMost naturally occurring microorganisms persist in consortia where metabolic interactions are common and often essential to ecosystem function. This study uses synthetic ecology to test how different cellular interaction motifs influence fitness properties of consortia. Environmental context ultimately controlled the division of labor fitness as shifts from weakly buffered to highly buffered conditions negated the benefits of the strategy. Understanding the limits of division of labor advances our understanding of natural community functioning which is central to nutrient cycling and provides design rules for assembling consortia used in applied bioprocessing.

synthetic biology↗

bioRxiv2021

Spatially resolved analysis of Pseudomonas aeruginosa biofilm proteomes measured by laser ablation sample transfer

Heterogeneity in the distribution of nutrients and O2 gradients during biofilm growth gives rise to changes in phenotype. There has been long term interest in identifying spatial differences during biofilm development including clues that identify chemical heterogeneity. Laser ablation sample transfer (LAST) allows site-specific sampling combined with label free proteomics to distinguish radially and axially resolved proteomes for Pseudomonas aeruginosa biofilms. Specifically, differential protein abundances on oxic vs. anoxic regions of a biofilm was observed by combining LAST with bottom up proteomics. This study reveals active metabolism in the anoxic region of the biofilm with respect to the oxic region in P. aeruginosa, an aerobe by nature. Protein abundance data related to cellular acclimations to chemical gradients include identification of glucose catabolizing proteins, high abundance of proteins from arginine and polyamine metabolism, and proteins that could also support virulence and environmental stress mediation on the anoxic region. Finally, this methodology requires only a few mm2 of biofilm area to identify hundreds of proteins.

microbiology↗

bioRxiv2020

Limitation by a shared mutualist promotes coexistence of multiple competing partners

Although mutualisms are often studied as simple pairwise interactions, they typically involve complex networks of interacting species. How multiple mutualistic partners that provide the same service and compete for resources are maintained in mutualistic networks is an open question. We use a model bacterial community in which multiple partner strains of Escherichia coli compete for a carbon source and exchange resources with a shared mutualist strain of Salmonella enterica. In laboratory experiments, competing E. coli strains readily coexist in the presence of S. enterica, despite differences in their competitive abilities. We use ecological modeling to demonstrate that a shared mutualist can create temporary resource niche differentiation by limiting growth rates, even if yield is set by a resource external to a mutualism. This mechanism can extend to maintain multiple competing partner species. Our results improve our understanding of complex mutualistic communities and aid efforts to design stable microbial communities.

ecology↗

bioRxiv2018

Flux-Balance Based Modeling of Biofilm Communities

Models of microbial community dynamics generally rely on a sub-scale model for microbial metabolisms. In systems such as distributed multispecies communities like biofilms, where it is not reasonable to simplify to a small number of limiting substrates, tracking the large number of active metabolites likely requires measurement or estimation of large numbers of kinetic and regulatory parameters. Alternatively, a largely kinetics-free methodology is proposed combining cellular level constrained, steady state metabolic flux analysis with macro scale microbial community models. The methodology easily allows coupling of macroscale information, including measurement data, with cell-scale metabolism. Illustrative examples are included.

microbiology↗