Interchanging species of similar function: Under natural conditions, bacteria form mixed, interacting communities. Understanding how such communities assemble and stabilize is important in a range of contexts, from biotechnological applications to what happens in our guts. Goldford et al. sampled the microbial communities from soil and plants containing hundreds to thousands of sequence variants. The organisms were passaged after culture in low concentrations of single carbon sources and were cross-fed with each other's metabolites; then, the resulting communities were sequenced using 16S ribosomal RNA, and the outcomes were modeled mathematically. The mix of species that survived under steady conditions converged reproducibly to reflect the experimentally imposed conditions rather than the mix of species initially inoculated—although at coarse phylogenetic levels, taxonomic patterns persisted. Science , this issue p. 469

Phosphate is essential for all living systems, serving as a building block of genetic and metabolic machinery. However, it is unclear how phosphate could have assumed these central roles on primordial Earth, given its poor geochemical accessibility. We used systems biology approaches to explore the alternative hypothesis that a protometabolism could have emerged prior to the incorporation of phosphate. Surprisingly, we identified a cryptic phosphate-independent core metabolism producible from simple prebiotic compounds. This network is predicted to support the biosynthesis of a broad category of key biomolecules. Its enrichment for enzymes utilizing iron-sulfur clusters, and the fact that thermodynamic bottlenecks are more readily overcome by thioester rather than phosphate couplings, suggest that this network may constitute a "metabolic fossil" of an early phosphate-free nonenzymatic biochemistry. Our results corroborate and expand previous proposals that a putative thioester-based metabolism could have predated the incorporation of phosphate and an RNA-based genetic system. PAPERCLIP.

A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a “resource-limited” regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species’ consumption preferences. These two regimes have distinct species abundance patterns, different functional profiles, and respond differently to environmental perturbations. Our model reproduces large-scale ecological patterns observed across multiple experimental settings such as nestedness and differential beta diversity patterns along energy gradients. We discuss the experimental implications of our results and possible connections with disorder-induced phase transitions in statistical physics. The diversity, stability and functional structure of microbial communities have dramatic effects on the health of humans and of ecosystems. The complexity of these communities has so far precluded the development of a general predictive model that would capture the dependence of these features on environmental conditions. We confronted this challenge by constructing a flexible simulation framework, and randomly sampling parameters under a variety of modeling assumptions to identify generic patterns. We found two qualitatively distinct regimes of community structure, which reproduce observed patterns of biodiversity, and make new predictions about stability and function.

Significance: In the microbial world, it is common for previously isolated communities to come in contact with one another. This phenomenon is known as community coalescence. Despite it being a key process in the assembly of microbial communities, little is known about the mechanisms that determine its outcomes. Here we present an experimental system that allowed us to study over 100 coalescence events between previously segregated microbiomes. Our results, predicted by a mathematical model, provide direct evidence of ecological coselection: the situation where members of a community recruit one another during coalescence. Our combined experimental and theoretical framework represents a powerful tool to predict the outcomes and interrogate the mechanisms of community coalescence.

Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of a genome-scale atlas of small molecule-enzyme regulatory interactions. Here, we develop a framework leveraging the vast, but fragmented, biochemical literature to reconstruct and analyze the small molecule regulatory network (SMRN) of the model organism Escherichia coli, including the primary metabolite regulators and enzyme targets. Using metabolic control analysis, we prove a fundamental trade-off between regulation and enzymatic activity, and we combine it with metabolomic measurements and the SMRN to make inferences on the sensitivity of enzymes to their regulators. Generalizing the analysis to other organisms, we identify highly conserved regulatory interactions across evolutionarily divergent species, further emphasizing a critical role for small molecule interactions in the maintenance of metabolic homeostasis.

Summary: In the oceans and seas, environmental conditions change over multiple temporal and spatial scales. Here, we ask what factors affect the bacterial community structure across time, depth and size fraction during six seasonal cruises (2 years) in the ultra‐oligotrophic Eastern Mediterranean Sea. The bacterial community varied most between size fractions (free‐living (FL) vs. particle‐associated), followed by depth and finally season. The FL community was taxonomically richer and more stable than the particle‐associated (PA) one, which was characterized by recurrent ‘blooms’ of heterotrophic bacteria such as Alteromonas and Ralstonia . The heterotrophic FL and PA communities were also correlated with different environmental parameters: the FL population correlated with depth and phytoplankton, whereas PA bacteria were correlated primarily with the time of sampling. A significant part of the variability in community structure could, however, not be explained by the measured parameters. The metabolic potential of the PA community, predicted from 16S rRNA amplicon data using PICRUSt, was enriched in pathways associated with the degradation and utilization of biological macromolecules, as well as plastics, other petroleum products and herbicides. The FL community was enriched in predicted pathways for the metabolism of inositol phosphate, a potential phosphorus source, and of polycyclic aromatic hydrocarbons.