Metabolic constraints on the evolution of antibiotic resistance

Despite our continuous improvement in understanding antibiotic resistance, the interplay between natural selection of resistance mutations and the environment remains unclear. To investigate the role of bacterial metabolism in constraining the evolution of antibiotic resistance, we evolved Escherichia coli growing on glycolytic or gluconeogenic carbon sources to the selective pressure of three different antibiotics. Profiling more than 500 intracellular and extracellular putative metabolites in 190 evolved populations revealed that carbon and energy metabolism strongly constrained the evolutionary trajectories, both in terms of speed and mode of resistance acquisition. To interpret and explore the space of metabolome changes, we developed a novel constraint‐based modeling approach using the concept of shadow prices. This analysis, together with genome resequencing of resistant populations, identified condition‐dependent compensatory mechanisms of antibiotic resistance, such as the shift from respiratory to fermentative metabolism of glucose upon overexpression of efflux pumps. Moreover, metabolome‐based predictions revealed emerging weaknesses in resistant strains, such as the hypersensitivity to fosfomycin of ampicillin‐resistant strains. Overall, resolving metabolic adaptation throughout antibiotic‐driven evolutionary trajectories opens new perspectives in the fight against emerging antibiotic resistance.ISSN:1744-429

Life at the Micro-Scale - Marine Microbial Ecology on Model Particulate Organic Matter

Microbes play a crucial role in global-scale ecosystem processes such as marine carbon cycling. Bridging the gap between the micro-scale at which ecological interactions between bacteria unfold and the orders-of-magnitude larger ecosystem-scale is one of the major challenges in microbial ecology. Here, we address this gap by investigating how communities of bacteria assemble on and degrade model particulate organic matter, a crucial process in biological carbon cycling in the marine environment. We aim to answer a central question in microbial ecology: how microbial communities reproducibly self-organize and if those dynamics can be predicted. We first track the taxon dynamics of bacteria attached to different types of model marine particles and demonstrate that particle-attached communities undergo reproducible successions. Moreover, we discover two ecological strategies of particle attached bacteria: in one, bacteria attach to all particle types alike and, in the other, they selectively colonize one particle type. The partitioning into ecological strategies reveals simple, modular design principles in community assembly dynamics during particulate organic matter decomposition. We next link micro-scale ecology –the interactions between microbes that coexist in close proximity– of model marine microbial communities to community function, in this case turnover of particulate organic matter. We find that interactions between two major functional classes of bacteria, primary particle degraders and secondary, non-degrading consumers, regulate particulate organic matter turnover. Secondary consumers decrease particle degradation rates as they compete for available resources such as carbon or physical space, thereby altering the dynamics of carbon cycling and remineralization in the ocean. The demonstrated regulation of particulate organic matter turnover by ecological interactions between two major groups of bacteria and the observed taxonomic shifts during the successional transitions that shape particle attached microbial communities contribute to our understanding of the effect of microbial ecology at the micro-scale on global-scale ecosystem processes

Strain-level diversity drives alternative community types in millimetre-scale granular biofilms

Microbial communities are often highly diverse in their composition, both at a coarse-grained taxonomic level, such as genus, and at a highly resolved level, such as strains, within species. This variability can be driven by either extrinsic factors such as temperature and or by intrinsic ones, for example demographic fluctuations or ecological interactions. The relative contributions of these factors and the taxonomic level at which they influence community composition remain poorly understood, in part because of the difficulty in identifying true community replicates assembled under the same environmental parameters. Here, we address this problem using an activated granular sludge reactor in which millimetre-scale biofilm granules represent true community replicates. Differences in composition are then expected to be driven primarily by biotic factors. Using 142 shotgun metagenomes of single biofilm granules we found that, at the commonly used genus-level resolution, community replicates varied much more in their composition than would be expected from neutral assembly processes. This variation did not translate into any clear partitioning into discrete community types, that is, distinct compositional states, such as enterotypes in the human gut. However, a strong partition into community types did emerge at the strain level for the dominant organism: genotypes of Candidatus Accumulibacter that coexisted in the metacommunity (the reactor) excluded each other within community replicates (granules). Individual granule communities maintained a significant lineage structure, whereby the strain phylogeny of Accumulibacter correlated with the overall composition of the community, indicating a high potential for co-diversification among species and communities. Our results suggest that due to the high functional redundancy and competition between close relatives, alternative community types are most probably observed at the level of recently differentiated genotypes but not at higher orders of genetic resolution.Swiss National Science Foundation (Grant 162251)Human Frontier Science Program (Strasbourg, France) (Grant LT000643/2016-L)Simons Foundation (Grant 542395

Physics-based prediction of biopolymer degradation

In the natural environment, insoluble biomatter provides a preeminent source of carbon for bacteria. Its degradation by microbial communities thus plays a major role in the global carbon-cycle. The prediction of degradation processes and their sensitivity to changes in environmental conditions can therefore provide critical insights into globally occurring environmental adaptations. To elucidate and quantify this macro-scale phenomenon, we conduct micro-scale experiments that examine the degradation of isolated biopolymer particles and observe highly nonlinear degradation kinetics. Since conventional scaling arguments fail to explain these observations, it is inferred that the coupled influence of both the physical and biochemical processes must be considered. Hence, we develop a theoretical model that accounts for the bio-chemo-mechanically coupled kinetics of polymer degradation, by considering the production of bio-degraders and their ability to both dissociate the material from its external boundaries and to penetrate it to degrade its internal mechanical properties. This change in mechanical properties combined with the intake of solvent or moisture from the environment leads to chemo-mechanically coupled swelling of the material and, in-turn, influences the degradation kinetics. We show that the model quantitatively captures our experimental results and reveals distinct signatures of different bacteria that are independent of the specific experimental conditions (i.e. particle volume and initial concentrations). Finally, after validating our model against the experimental data we extend our predictions for degradation processes across various length and time scales that are inaccessible in a laboratory setting

Towards High Surface Area α-Al₂O₃–Mn-Assisted Low Temperature Transformation

When impregnated with manganiferous precursors, γ-Al2O3 may be converted into α-Al2O3 under relatively mild and energy-saving conditions. In this work, a manganese assisted conversion to corundum at temperatures as low as 800 °C is investigated. To observe the alumina phase transition, XRD and solid-state 27Al-MAS-NMR are applied. By post-synthetical treatment in concentrated HCl, residual manganese is removed up to 3 wt.-%. Thereby, α-Al2O3 with a high specific surface area of 56 m2 g−1 is obtained after complete conversion. Just as for transition alumina, thermal stability is an important issue for corundum. Long-term stability tests were performed at 750 °C for 7 days. Although highly porous corundum was synthesized, the porosity decreased with time at common process temperatures

Microscale ecology regulates particulate organic matter turnover in model marine microbial communities

The degradation of particulate organic matter in the ocean is a central process in the global carbon cycle, the mode and tempo of which is determined by the bacterial communities that assemble on particle surfaces. Here, we find that the capacity of communities to degrade particles is highly dependent on community composition using a collection of marine bacteria cultured from different stages of succession on chitin microparticles. Different particle degrading taxa display characteristic particle half-lives that differ by ~170 h, comparable to the residence time of particles in the ocean’s mixed layer. Particle half-lives are in general longer in multispecies communities, where the growth of obligate cross-feeders hinders the ability of degraders to colonize and consume particles in a dose dependent manner. Our results suggest that the microscale community ecology of bacteria on particle surfaces can impact the rates of carbon turnover in the ocean.ISSN:2041-172

Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities

Understanding the principles that govern the assembly of microbial communities across earth's biomes is a major challenge in modern microbial ecology. This pursuit is complicated by the difficulties of mapping functional roles and interactions onto communities with immense taxonomic diversity and of identifying the scale at which microbes interact [1]. To address this challenge, here, we focused on the bacterial communities that colonize and degrade particulate organic matter in the ocean [2–4]. We show that the assembly of these communities can be simplified as a linear combination of functional modules. Using synthetic polysaccharide particles immersed in natural bacterioplankton assemblages [1, 5], we showed that successional particle colonization dynamics are driven by the interaction of two types of modules: a first type made of narrowly specialized primary degraders, whose dynamics are controlled by particle polysaccharide composition, and a second type containing substrate-independent taxa whose dynamics are controlled by interspecific interactions—in particular, cross-feeding via organic acids, amino acids, and other metabolic byproducts. We show that, as a consequence of this trophic structure, communities can assemble modularly—i.e., by a simple sum of substrate-specific primary degrader modules, one for each complex polysaccharide in the particle, connected to a single broad-niche range consumer module. Consistent with this model, a linear combination of the communities on single-polysaccharide particles accurately predicts community composition on mixed-polysaccharide particles. Our results suggest that the assembly of heterotrophic communities that degrade complex organic materials follows simple design principles that could be exploited to engineer heterotrophic microbiomes. Enke et al. show that particle-attached marine microbial communities assemble by recruiting functional groups of taxa in an additive manner. Specialist groups degrade specific polysaccharides, whereas generalist byproduct utilizers invade independently of particle substrate. This simple organization allows prediction of community structure.Simons Foundation. Simons Early Career Award (410104)Alfred P. Sloan Foundation. Fellowship (FG-20166236)National Science Foundation (U.S.) (Grant OCE-1658451)Simons Collaboration: Principles of Microbial Ecosystems (PriME) (Award 542395

Microscale ecology regulates particulate organic matter turnover in model marine microbial communities

The degradation of particulate organic matter in the ocean is a central process in the global carbon cycle, the mode and tempo of which is determined by the bacterial communities that assemble on particle surfaces. Here, we find that the capacity of communities to degrade particles is highly dependent on community composition using a collection of marine bacteria cultured from different stages of succession on chitin microparticles. Different particle degrading taxa display characteristic particle half-lives that differ by ~170 h, comparable to the residence time of particles in the ocean's mixed layer. Particle half-lives are in general longer in multispecies communities, where the growth of obligate cross-feeders hinders the ability of degraders to colonize and consume particles in a dose dependent manner. Our results suggest that the microscale community ecology of bacteria on particle surfaces can impact the rates of carbon turnover in the ocean.NSF grant OCE-1658451European Starting Grant no. 336938Simons Early Career Award 410104Alfred P Sloan fellowship FG-20166236Swiss National Science Foundation (162251)Human Frontiers Science Program (LT000643/2016-L

Turnover in Life-Strategies Recapitulates Marine Microbial Succession Colonizing Model Particles

Particulate organic matter (POM) in the ocean sustains diverse communities of bacteria that mediate the remineralization of organic complex matter. However, the variability of these particles and of the environmental conditions surrounding them present a challenge to the study of the ecological processes shaping particle-associated communities and their function. In this work, we utilize data from experiments in which coastal water communities are grown on synthetic particles to ask which are the most important ecological drivers of their assembly and associated traits. Combining 16S rRNA amplicon sequencing with shotgun metagenomics, together with an analysis of the full genomes of a subset of isolated strains, we were able to identify two-to-three distinct community classes, corresponding to early vs. late colonizers. We show that these classes are shaped by environmental selection (early colonizers) and facilitation (late colonizers) and find distinctive traits associated with each class. While early colonizers have a larger proportion of genes related to the uptake of nutrients, motility, and environmental sensing with few pathways enriched for metabolism, late colonizers devote a higher proportion of genes for metabolism, comprising a wide array of different pathways including the metabolism of carbohydrates, amino acids, and xenobiotics. Analysis of selected pathways suggests the existence of a trophic-chain topology connecting both classes for nitrogen metabolism, potential exchange of branched chain amino acids for late colonizers, and differences in bacterial doubling times throughout the succession. The interpretation of these traits suggests a distinction between early and late colonizers analogous to other classifications found in the literature, and we discuss connections with the classical distinction between r- and K-strategists.ISSN:1664-302