Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture

Abstract

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized – and confirmed – that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.

Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow?

“…Dynamic changes in nutrient concentrations have been shown to influence bacterial interactions with ramifications for microbial community structure and function (Friedman and Gore, 2017; Khan et al, 2018). In these pure culture studies, either cooperation or competition was the dominant interaction strategy depending on the nutrients considered and their concentrations (Brockhurst et al, 2008, 2010, Lambert et al, 2011, 2014; Ravindran, 2017).…”

Lactobacillus acidophilusdisrupts collaborative multispecies bile acid metabolism

“…It was not intended to inform clinical practice. However, the results and conclusions presented establish an important idea related to broader microbiome sciences; microbial interactions are context dependent 64,65 and the presence or absence of select species and/or metabolites can have a strong effect on the overall community-level function.…”

“…In particular, simplified model consortia gaining interest in microbiome research because they enable experimentalists to manage complexity by controlling multiple system components under defined treatments. The utility of simplified consortia, or bench-top microbiomes, has been demonstrated for a variety of human-associated communities 61,62 and other complex microbial ecosystems related to plants 63 , sediment/biofilms 64-66 and marine habitats 67,68 . Here, we developed a simple model microbial consortium that was specifically designed to investigate how the addition of a common probiotic ( L. acidophilus ) effects microbial interactions mediated through bile acid transformations.…”

Reconciling Ecological and Engineering Design Principles for Building Microbiomes

“…There are two common approaches—within the current state of the science—for developing model microbial communities: top-down selection of natural microbiomes toward representative consortia with reduced complexity (7) and bottom-up construction of consortia, which are predesigned assemblages based on hypotheses or specific engineering design principles (8–10). These approaches have been discussed and compared in a number of review and perspective articles (2–4, 11) and hence will not be covered in more detail here.…”