Ecological and Evolutionary Science
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.
Special Issue Perspective | Ecological and Evolutionary ScienceMicrobial Metazoa Are Microbes TooMicrobial metazoa inhabit a certain “Goldilocks zone,” where conditions are just right for the continued ignorance of these taxa. These microscopic animal species have body sizes of <1 mm and include diverse groups such as nematodes, tardigrades, kinorhynchs, loriciferans, and platyhelminths.
Special Issue Perspective | Ecological and Evolutionary ScienceUncovering Virus-Virus Interactions by Unifying Approaches and Harnessing High-Throughput ToolsVirus-host interactions have received much attention in virology. Virus-virus interactions can occur when >1 virus infects a host and can be deemed social when one virus affects the fitness of another virus, as in the well-known case of superinfection exclusion.
Special Issue Perspective | Ecological and Evolutionary ScienceTowards a Better Understanding of Microbial Community Dynamics through High-Throughput Cultivation and Data IntegrationThe investigation of microbial community dynamics is hampered by low resolution, a lack of control, and a small number of replicates. These deficiencies can be tackled with defined communities grown under well-controlled conditions in high-throughput automated cultivation devices.
Special Issue Perspective | Ecological and Evolutionary ScienceExploring the Evolution of Virulence Factors through Bioinformatic Data MiningThe molecular evolution of virulence factors is a central theme in our understanding of bacterial pathogenesis and host-microbe interactions. Using bioinformatics and genome data mining, recent studies have shed light on the evolution of important virulence factor families and the mechanisms by which they have adapted and diversified in function.
Research Article | Ecological and Evolutionary ScienceElemental Composition, Phosphorous Uptake, and Characteristics of Growth of a SAR11 Strain in Batch and Continuous CultureWhile SAR11 bacteria contribute a significant fraction to the total picoplankton biomass in the ocean and likely are major players in organic C and nutrient cycling, the cellular characteristics and metabolic features of most lineages have either only been hypothesized from genomes or otherwise not measured in controlled laboratory experimentation. The dearth of data on even the most basic characteristics for what is arguably the most...