Widespread density dependence of bacterial growth under acid stress

Summary: Many microbial phenotypes are density-dependent, including group-level phenotypes emerging from cooperation. However, surveys for the presence of a particular form of density dependence across diverse species are rare, as are direct tests for the Allee effect, i.e., positive density dependence of fitness. Here, we test for density-dependent growth under acid stress in five diverse bacterial species and find the Allee effect in all. Yet social protection from acid stress appears to have evolved by multiple mechanisms. In Myxococcus xanthus, a strong Allee effect is mediated by pH-regulated secretion of a diffusible molecule by high-density populations. In other species, growth from low density under acid stress was not enhanced by high-density supernatant. In M. xanthus, high cell density may promote predation on other microbes that metabolically acidify their environment, and acid-mediated density dependence may impact the evolution of fruiting-body development. More broadly, high density may protect most bacterial species against acid stress

Data from: Less is more: selective advantages can explain the prevalent loss of biosynthetic genes in bacteria

Bacteria that have adapted to nutrient-rich, stable environments are typically characterized by reduced genomes. The loss of biosynthetic genes frequently renders these lineages auxotroph, hinging their survival on an environmental uptake of certain metabolites. The evolutionary forces that drive this genome degradation, however, remain elusive. Our analysis of 949 metabolic networks revealed auxotrophies are likely highly prevalent in both symbiotic and free-living bacteria. To unravel whether selective advantages can account for the rampant loss of anabolic genes, we systematically determined the fitness consequences that result from deleting conditionally essential biosynthetic genes from the genomes of Escherichia coli and Acinetobacter baylyi in the presence of the focal nutrient. Pairwise competition experiments with each of 20 mutants auxotrophic for different amino acids, vitamins, and nucleobases against the prototrophic wild type unveiled a pronounced, concentration-dependent growth advantage of around 13% for virtually all mutants tested. Individually deleting different genes from the same biosynthesis pathway entailed gene-specific fitness consequences and loss of the same biosynthetic genes from the genomes of E. coli and A. baylyi differentially affected the fitness of the resulting auxotrophic mutants. Taken together, our findings suggest adaptive benefits could drive the loss of conditionally essential biosynthetic genes

Cooperation and Cheating among Germinating Spores

Many microbes produce stress-resistant spores to survive unfavorable conditions [1, 2, 3, 4] and enhance dispersal [1, 5]. Cooperative behavior is integral to the process of spore formation in some species [3, 6], but the degree to which germination of spore populations involves social interactions remains little explored. Myxococcus xanthus is a predatory soil bacterium that upon starvation forms spore-filled multicellular fruiting bodies that often harbor substantial diversity of endemic origin [7, 8]. Here we demonstrate that germination of M. xanthus spores formed during fruiting-body development is a social process involving at least two functionally distinct social molecules. Using pairs of natural isolates each derived from a single fruiting body that emerged on soil, we first show that spore germination exhibits positive density dependence due to a secreted “public-good” germination factor. Further, we find that a germination defect of one strain under saline stress in pure culture is complemented by addition of another strain that germinates well in saline environments and mediates cheating by the defective strain. Glycine betaine, an osmo-protectant utilized in all domains of life, is found to mediate saline-specific density dependence and cheating. Density dependence in non-saline conditions is mediated by a distinct factor, revealing socially complex spore germination involving multiple social molecules.ISSN:0960-9822ISSN:1879-044

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities

Bacterial communities are taxonomically highly diverse, yet the mechanisms that maintain this diversity remain poorly understood. We hypothesized that an obligate and mutual exchange of metabolites, as is very common among bacterial cells, could stabilize different genotypes within microbial communities. To test this, we developed a cellular automaton to model interactions among six empirically characterized genotypes that differ in their ability and propensity to produce amino acids. By systematically varying intrinsic (i.e. benefit-to-cost ratio) and extrinsic parameters (i.e. metabolite diffusion level, environmental amino acid availability), we show that obligate cross-feeding of essential metabolites is selected for under a broad range of conditions. In spatially structured environments, positive assortment among cross-feeders resulted in the formation of cooperative clusters, which limited exploitation by non-producing auxotrophs, yet allowed them to persist at the clusters’ periphery. Strikingly, cross-feeding helped to maintain genotypic diversity within populations, while amino acid supplementation to the environment decoupled obligate interactions and favored auxotrophic cells that saved amino acid production costs over metabolically autonomous prototrophs. Together, our results suggest that spatially structured environments and limited nutrient availabilities should facilitate the evolution of metabolic interactions, which can help to maintain genotypic diversity within natural microbial populations.ISSN:1553-734XISSN:1553-735

Selective_benefits_auxotrophy_raw_data

The file contains data containing fitness (Mathusian parameters) and productivity (Max optical density at 600nm) of different auxotrophic mutants of Escherichia coli and Acinetobacter baylyi when growing in minimal medium supplemented with either amino acids, vitamins or nucleobases

Data from: Metabolic cross-feeding via intercellular nanotubes among bacteria

Bacteria frequently exchange metabolites by diffusion through the extracellular environment, yet it remains generally unclear whether bacteria can also use cell–cell connections to directly exchange nutrients. Here we address this question by engineering cross-feeding interactions within and between Acinetobacter baylyi and Escherichia coli, in which two distant bacterial species reciprocally exchange essential amino acids. We establish that in a well-mixed environment E. coli, but likely not A. baylyi, can connect to other bacterial cells via membrane-derived nanotubes and use these to exchange cytoplasmic constituents. Intercellular connections are induced by auxotrophy-causing mutations and cease to establish when amino acids are externally supplied. Electron and fluorescence microscopy reveal a network of nanotubular structures that connects bacterial cells and enables an intercellular transfer of cytoplasmic materials. Together, our results demonstrate that bacteria can use nanotubes to exchange nutrients among connected cells and thus help to distribute metabolic functions within microbial communities

Population dynamics in environments without amino acid supplementation.

<p>Repeated simulations (n = 100) are plotted for varying benefit-to-cost ratios (BCR) and degrees of amino acid diffusion (bold line: mean, shaded ribbon: standard deviation). All simulations start with a random distribution of all genotypes and undergo a specific dynamic alternation of genotype frequencies. Depending on the genotype’s strategy, it can repress, facilitate, or even outcompete others (see text for more details). Legend: red = wild type, blue = overproducing genotype, yellow = auxotroph (2 types), green = cross-feeder (2 types).</p