Competitive and cooperative metabolic interactions in bacterial communities

Abstract

Revealing the ecological principles that shape communities is a major challenge of the postgenomic era. To date, a systematic approach for describing inter-species interactions has been lacking. Here we independently predict the competitive and cooperative potential between 6,903 bacterial pairs derived from a collection of 118 species ' metabolic models. We chart an intricate association between competition and cooperation indicating that the cooperative potential is maximized at moderate levels of resource overlap. Utilizing ecological data from 2,801 samples, we explore the associations between bacterial interactions and coexistence patterns. The high level of competition observed between species with mutual-exclusive distribution patterns supports the role of competition in community assembly. Cooperative interactions are typically unidirectional with no obvious benefi t to the giver. However, within their natural communities, bacteria typically form close cooperative loops resulting in indirect benefi t to all species involved. These fi ndings are important for the future design of consortia optimized towards bioremediation and bio-production applications.

Shared Metabolic Pathways in a Coevolved Insect-Bacterial Symbiosis

“…Metabolic cooperation occurs widely among microorganisms, generally in response to selection imposed by resource-poor habitats (23)(24)(25). The coevolution of shared metabolic pathways in the aphid-Buchnera symbiosis most probably has a different evolutionary basis.…”

Hypolithic and soil microbial community assembly along an aridity gradient in the Namib Desert

“…In addition, although neutral processes may result in nonrandom co-occurrence patterns (Bell 2005), deterministic processes have been shown to predominate in harsh environment and lower productivity systems, whereas stochastic processes predominate in more benign habitats and higher productivity systems (Chase 2007(Chase , 2010. There is an increasing perception of the importance of cooperative and competitive interactions between and within bacterial communities (Freilich et al 2011). Hypolithic cyanobacteria are well-known producers of exopolysaccharide (Pointing et al a major component of the extracellular matrix that protects biofilms from harsh environmental factors and may aid in water uptake and retention (Hall-Stoodley et al 2004).…”

Family-wide Structural Characterization and Genomic Comparisons Decode the Diversity-oriented Biosynthesis of Thalassospiramides by Marine Proteobacteria

“…Adenylation domain specificity was predicted using Antibiotics and Secondary Metabolite Analysis Shell (antiSMASH) (31) and NRPS predictor 2 (32), and the condensation and ketosynthase domain functions were analyzed with NaPDoS (33). Non-random co-occurrence patterns of KEGG genomes and the thalassospiramide BGCs were constructed according to methods described in a previous study (34). The statistical analyses were performed in the R studio environment (R 2.13) using the vegan, igraph, and hmisc packages.…”

“…To create the THP-1 conditioned medium, 4 l of a 2 mM fibrillar A␤ [25][26][27][28][29][30][31][32][33][34][35] (Tocris) suspension was added to 24-well plates and allowed to air-dry. THP-1 cells were subsequently plated on the A␤-coated wells at a density of 20,000/well in Neurobasal medium.…”