Ecological and Evolutionary Science
Research Article | Ecological and Evolutionary ScienceImpact of Homologous Recombination on the Evolution of Prokaryotic Core GenomesMicrobial populations exchange genetic material through a process called homologous recombination. Although this process has been studied in particular organisms, we lack an understanding of its differential impact over the genome and across microbes with different life-styles. We used a common analytical framework to assess this process in a representative set of microorganisms. Our results uncovered important trends. First, microbes...
Research Article | Ecological and Evolutionary ScienceTrophic Specialization Results in Genomic Reduction in Free-Living Marine Idiomarina BacteriaThe streamlining hypothesis is usually used to explain the genomic reduction events in free-living bacteria like SAR11. However, we find that the genomic reduction phenomenon in the bacterial genus Idiomarina is different from that in SAR11. Therefore, we propose a new hypothesis to explain genomic reduction in this genus based on trophic specialization that could result in genomic reduction, which would be not uncommon in...
Editor's Pick Research Article | Ecological and Evolutionary ScienceThe Transcriptional Cycle Is Suited to Daytime N2 Fixation in the Unicellular Cyanobacterium “Candidatus Atelocyanobacterium thalassa” (UCYN-A)The symbiotic N2-fixing cyanobacterium UCYN-A, which is closely related to Braarudosphaera bigelowii, and its eukaryotic algal host have been shown to be globally distributed and important in open-ocean N2 fixation. These unique cyanobacteria have reduced metabolic capabilities, even lacking genes for oxygenic photosynthesis and carbon fixation....
Research Article | Ecological and Evolutionary ScienceOrigins and Evolution of the Global RNA ViromeThe majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than was attainable previously. This reconstruction reveals the relationships between different...
Research Article | Ecological and Evolutionary ScienceSalmonella enterica Phylogeny Based on Whole-Genome Sequencing Reveals Two New Clades and Novel Patterns of Horizontally Acquired Genetic ElementsRapid improvements in nucleotide sequencing access and affordability have led to a drastic increase in availability of genetic information. This information will improve the accuracy of molecular descriptions, including serovars, within S. enterica. Although the concept of serovars continues to be useful, it may have more significant limitations than previously...
Opinion/Hypothesis | Ecological and Evolutionary ScienceHypothesis: a Plastically Produced Phenotype Predicts Host Specialization and Can Precede Subsequent Mutations in BacteriophageThe role of phenotypic plasticity in the evolution of new traits is controversial due to a lack of direct evidence. Phage host range becomes plastic in the presence of restriction-modification (R-M) systems in their hosts.
Research Article | Ecological and Evolutionary ScienceLeishmania Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric AmplificationProtozoan parasites of the genus Leishmania cause severe human and veterinary diseases worldwide, termed leishmaniases. A hallmark of Leishmania biology is its capacity to adapt to a variety of unpredictable fluctuations inside its human host, notably pharmacological interventions, thus, causing...
Research Article | Ecological and Evolutionary ScienceThe Transferable Resistome of ProduceProduce is one of the most popular food commodities. Unfortunately, leafy greens can be a reservoir of transferable antibiotic resistance genes. We found that IncF and IncI plasmids were the most prevalent plasmid types in E. coli isolates from produce. This study highlights the importance of the rare microbiome associated with produce as a source of antibiotic...
Research Article | Ecological and Evolutionary ScienceEcological Analyses of Mycobacteria in Showerhead Biofilms and Their Relevance to Human HealthBacteria thrive in showerheads and throughout household water distribution systems. While most of these bacteria are innocuous, some are potential pathogens, including members of the genus Mycobacterium that can cause nontuberculous mycobacterial (NTM) lung infection, an increasing threat to public health. We found that showerheads in households across the United States and Europe often harbor abundant mycobacterial communities...
Research Article | Ecological and Evolutionary ScienceStructural and Nonstructural Genes Contribute to the Genetic Diversity of RNA VirusesWith the advent of advanced sequencing technology, studies of RNA viruses have shown that genetic diversity can contribute to both attenuation and virulence and the paradigm is that this is controlled by the error-prone RNA-dependent RNA polymerase (RdRp). Since wild-type yellow fever virus (YFV) strain Asibi has genetic diversity typical of a wild-type RNA virus, while 17D virus vaccine has limited diversity, it provides a unique...