Dataset Information

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems.

ABSTRACT: Metabolic exchange mediates interactions among microbes, helping explain diversity in microbial communities. As these interactions often involve a fitness cost, it is unclear how stable cooperation can emerge. Here we use genome-scale metabolic models to investigate whether the release of "costless" metabolites (i.e. those that cause no fitness cost to the producer), can be a prominent driver of intermicrobial interactions. By performing over 2 million pairwise growth simulations of 24 species in a combinatorial assortment of environments, we identify a large space of metabolites that can be secreted without cost, thus generating ample cross-feeding opportunities. In addition to providing an atlas of putative interactions, we show that anoxic conditions can promote mutualisms by providing more opportunities for exchange of costless metabolites, resulting in an overrepresentation of stable ecological network motifs. These results may help identify interaction patterns in natural communities and inform the design of synthetic microbial consortia.

SUBMITTER: Pacheco AR

PROVIDER: S-EPMC6327061 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems.

Pacheco Alan R AR Moel Mauricio M Segrè Daniel D

Nature communications 20190109 1

Metabolic exchange mediates interactions among microbes, helping explain diversity in microbial communities. As these interactions often involve a fitness cost, it is unclear how stable cooperation can emerge. Here we use genome-scale metabolic models to investigate whether the release of "costless" metabolites (i.e. those that cause no fitness cost to the producer), can be a prominent driver of intermicrobial interactions. By performing over 2 million pairwise growth simulations of 24 species i ...[more]

PMID: 30626871

Similar Datasets

Project description:Accumulation of anthropogenic litter (i.e. garbage; AL) and its ecosystem effects in marine environments are well documented. Rivers receive AL from terrestrial habitats and represent a major source of AL to marine environments, but AL is rarely studied within freshwater ecosystems. Our objectives were to 1) quantify AL density in urban freshwaters, 2) compare AL abundance among freshwater, terrestrial, and marine ecosystems, and 3) characterize the activity and composition of AL biofilms in freshwater habitats. We quantified AL from the Chicago River and Chicago's Lake Michigan shoreline, and found that AL abundance in Chicago freshwater ecosystems was comparable to previously reported data for marine and terrestrial ecosystems, although AL density and composition differed among habitats. To assess microbial interactions with AL, we incubated AL and natural substrates in 3 freshwater ecosystems, quantified biofilm metabolism as gross primary production (GPP) and community respiration (CR), and characterized biofilm bacterial community composition via high-throughput sequencing of 16S rRNA genes. The main driver of biofilm community composition was incubation location (e.g., river vs pond), but there were some significant differences in biofilm composition and metabolism among substrates. For example, biofilms on organic substrates (cardboard and leaves) had lower GPP than hard substrates (glass, plastic, aluminum and tiles). In addition, bacterial communities on organic substrates were distinct in composition from those on hard substrates, with higher relative abundances of bacteria associated with cellulose decomposition. Finally, we used our results to develop a conceptual diagram designed to unite the study of AL in terrestrial and freshwater environments with the well-established field of marine debris research. We suggest this broad perspective will be useful for future studies which synthesize AL sources, ecosystem effects, and fate across multiple ecosystem types, and will benefit management and reduction of global AL accumulations.

Project description:The dynamics and activities of microbes colonizing organic particles (hereafter particles) greatly determine the efficiency of the aquatic carbon pump. Current understanding is that particle composition, structure and surface properties, determined mostly by the forming organisms and organic matter, dictate initial microbial colonization and the subsequent rapid succession events taking place as organic matter lability and nutrient content change with microbial degradation. We applied a transcriptomic approach to assess the role of stochastic events on initial microbial colonization of particles. Furthermore, we asked whether gene expression corroborates rapid changes in carbon-quality. Commonly used size fractionated filtration averages thousands of particles of different sizes, sources, and ages. To overcome this drawback, we used replicate samples consisting each of 3-4 particles of identical source and age and further evaluated the consequences of averaging 10-1000s of particles. Using flow-through rolling tanks we conducted long-term experiments at near in situ conditions minimizing the biasing effects of closed incubation approaches often referred to as "the bottle-effect." In our open flow-through rolling tank system, however, active microbial communities were highly heterogeneous despite an identical particle source, suggesting random initial colonization. Contrasting previous reports using closed incubation systems, expression of carbon utilization genes didn't change after 1 week of incubation. Consequently, we suggest that in nature, changes in particle-associated community related to carbon availability are much slower (days to weeks) due to constant supply of labile, easily degradable organic matter. Initial, random particle colonization seems to be subsequently altered by multiple organismic interactions shaping microbial community interactions and functional dynamics. Comparative analysis of thousands particles pooled togethers as well as pooled samples suggests that mechanistic studies of microbial dynamics should be done on single particles. The observed microbial heterogeneity and inter-organismic interactions may have important implications for evolution and biogeochemistry in aquatic systems.

Dataset Information

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems.

Publications

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets