Ecological and Evolutionary Science
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...
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...
Research Article | Ecological and Evolutionary ScienceRethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial BiosphereWe propose that the coral holobiont should be conceptualized as a diverse transient microbial community that is responsive to the surrounding environment and encompasses a simple, redundant, resident microbiome and a small conserved core microbiome. Most importantly, we show that the coral microbiome is comparable to the microbiomes of other organisms studied thus far. Accurately characterizing the coral-microbe interactions provides an...
- Research Article | Ecological and Evolutionary ScienceAn Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila
Erwinia tracheiphila is a virulent phytopathogen that infects two genera of cucurbit crop plants, Cucurbita spp. (pumpkin and squash) and Cucumis spp. (muskmelon and cucumber). One of the unusual ecological traits of this pathogen is that it is limited to temperate eastern North America. Here, we complete the first large-scale sequencing of an...
- Perspective | Ecological and Evolutionary ScienceBotulinum Neurotoxin-Producing Bacteria. Isn’t It Time that We Called a Species a Species?
Botulinum neurotoxins (BoNTs) are produced by a diverse set of seven clostridial species, though alternate naming systems have developed over the last 100 years. Starting in the 1950s, a single-species taxonomy where any bacterium producing BoNT would be designated Clostridium botulinum was introduced.
- Research Article | Ecological and Evolutionary ScienceParallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum
Understanding long-term patterns of microbial evolution is critical to advancing our knowledge of past and present role microbial life in driving global biogeochemical cycles. Historically, it has been challenging to study the evolution of environmental microbes due to difficulties in obtaining genome sequences from lineages that could not be cultivated, but recent advances in metagenomics and single-cell genomics have begun to obviate...