Ecological and Evolutionary Science
Research Article | Ecological and Evolutionary ScienceLying in Wait: Modeling the Control of Bacterial Infections via Antibiotic-Induced ProvirusesAntibiotic resistance is a growing concern for management of common bacterial infections. Here, we show that antibiotics can be effective at subinhibitory levels when bacteria carry latent phage. Our findings suggest that specific treatment strategies based on the identification of latent viruses in individual bacterial strains may be an effective personalized medicine approach to antibiotic stewardship.
Research Article | Ecological and Evolutionary ScienceCharacteristics and Evolutionary Analysis of Photosynthetic Gene Clusters on Extrachromosomal Replicons: from Streamlined Plasmids to ChromidsThe evolution of photosynthesis was a significant event during the diversification of biological life. Aerobic anoxygenic photoheterotrophic bacteria (AAPB) share physiological characteristics with chemoheterotrophs and represent an important group associated with bacteriochlorophyll-dependent phototrophy in the environment. Here, characterization and evolutionary analyses were conducted for 13 bacterial strains that contained...
Research Article | Ecological and Evolutionary ScienceBioinformatics Identification of Anti-CRISPR Loci by Using Homology, Guilt-by-Association, and CRISPR Self-Targeting Spacer ApproachesAs a naturally occurring adaptive immune system, CRISPR-Cas (clustered regularly interspersed short palindromic repeats–CRISPR-associated genes) systems are widely found in bacteria and archaea to defend against viruses. Since 2013, the application of various bacterial CRISPR-Cas systems has become very popular due to their development into targeted and programmable genome engineering tools with the ability to edit almost any genome. As...
Editor's Pick Research Article | Ecological and Evolutionary ScienceA Genome-Based Species Taxonomy of the Lactobacillus Genus ComplexThe Lactobacillus genus complex is a group of bacteria that constitutes an important source of strains with medical and food applications. The number of bacterial whole-genome sequences available for this taxon has been increasing rapidly in recent years. Despite this wealth of information, the species within this group are still largely defined by older techniques. Here, we constructed a completely new species-level taxonomy...
Editor's Pick Research Article | Ecological and Evolutionary ScienceStrategies for Building Computing Skills To Support Microbiome Analysis: a Five-Year Perspective from the EDAMAME WorkshopHigh-throughput sequencing and related statistical and bioinformatic analyses have become routine in microbiology in the past decade, but there are few formal training opportunities to develop these skills. A weeklong workshop can offer sufficient time for novices to become introduced to best computing practices and common workflows in sequence analysis. We report our experiences in executing such a workshop targeted to professional...
Commentary | Ecological and Evolutionary ScienceMaking Workshops Work: Insights from EDAMAMEMicrobiology, like many areas of life science research, is increasingly data-intensive. As such, bioinformatics and data science skills have become essential to leverage microbiome sequencing data for discovery. Short intensive courses have sprung up as formal computational training opportunities at individual institutions fail to meet demands. In this issue, Shade et al. (A. Shade, T. K. Dunivin, J. Choi, T. K.
Research Article | Ecological and Evolutionary ScienceMechanistic Model for the Coexistence of Nitrogen Fixation and Photosynthesis in Marine TrichodesmiumTrichodesmium is a major nitrogen-fixing cyanobacterium and exerts a significant influence on the oceanic nitrogen cycle. It is also a widely used model organism in laboratory studies. Since the nitrogen-fixing enzyme nitrogenase is extremely sensitive to oxygen, how these surface-dwelling plankton manage the two conflicting processes of nitrogen fixation and photosynthesis has been a long-standing question. In this study, we...
Perspective | Ecological and Evolutionary ScienceExperimental Microbiomes: Models Not to ScaleLow-cost, high-throughput nucleic acid sequencing ushered the field of microbial ecology into a new era in which the microbial composition of nearly every conceivable environment on the planet is under examination. However, static “screenshots” derived from sequence-only approaches belie the underlying complexity of the microbe-microbe and microbe-host interactions occurring within these systems.
Research Article | Ecological and Evolutionary ScienceProteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic AlphaproteobacteriumAmmonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have...
Special Issue Perspective | Ecological and Evolutionary ScienceThe Power of Metabolism for Predicting Microbial Community DynamicsQuantitative understanding and prediction of microbial community dynamics are an outstanding challenge. We test the hypothesis that metabolic mechanisms provide a foundation for accurate prediction of dynamics in microbial systems. In our research, metabolic models have been able to accurately predict species interactions, evolutionary trajectories, and response to perturbation in simple synthetic consortia.