Ecological and Evolutionary Science
Research Article | Ecological and Evolutionary ScienceA New Family of DNA Viruses Causing Disease in Crustaceans from Diverse Aquatic BiomesRecent genomic and metagenomic studies have led to a dramatic expansion of the known diversity of nucleocytoplasmic large DNA viruses (NCLDVs) of eukaryotes, which include giant viruses of protists and important pathogens of vertebrates, such as poxviruses. However, the characterization of viruses from nonmodel hosts still lags behind. We sequenced the complete genomes of three viruses infecting crustaceans, the Caribbean spiny lobster...
Editor's Pick Research Article | Ecological and Evolutionary ScienceA Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness IndexIn recent decades, the taxonomy of Bacteria and Archaea, and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the average nucleotide identity. Our findings are of importance to the microbiology...
Research Article | Ecological and Evolutionary ScienceCollective Viral Spread Mediated by Virion Aggregates Promotes the Evolution of Defective Interfering ParticlesRecent insights have revealed that viruses use a highly diverse set of strategies to release multiple viral genomes into the same target cells, allowing the emergence of beneficial, but also detrimental, interactions among viruses inside infected cells. This has prompted interest among microbial ecologists and evolutionary biologists in studying how collective dispersal impacts the outcome of viral infections. Here, we have used...
Research Article | Ecological and Evolutionary SciencePangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 BacteriaThe oceans contain an estimated 662 Pg C in the form of dissolved organic matter (DOM). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria, we propose hypothetical metabolic pathways for the oxidation of organic molecules that are resistant to oxidation via common...
Editor's Pick Research Article | Ecological and Evolutionary ScienceComparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and BatsIn this comprehensive survey of microbiomes of >900 species, including 315 mammals and 491 birds, we find a striking convergence of the microbiomes of birds and animals that fly. In nonflying mammals, diet and short-term evolutionary relatedness drive the microbiome, and many microbial species are specific to a particular kind of mammal, but flying mammals and birds break this pattern with many microbes shared across different...
Research Article | Ecological and Evolutionary ScienceSingle-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in CiliatesCiliates, a eukaryotic clade that is over 1 billion years old, are defined by division of genome function between transcriptionally inactive germline micronuclei and functional somatic macronuclei. To date, most analyses of gene family evolution have been limited to cultivable model lineages (e.g., Tetrahymena, Paramecium, Oxytricha, and Stylonychia). Here, we focus on the uncultivable Karyorelictea...
Commentary | Ecological and Evolutionary ScienceHow to Train Your FungusDomestication led to profound changes in human culture. During this period, humans used breeding strategies to select for desirable traits in crops and livestock. These practices led to genetic and phenotypic changes that are trackable through archaeological and genomic records. Bacteria, yeasts, and molds also experienced domestication during the agricultural revolution, but the effects of domestication on microbes are poorly...
Research Article | Ecological and Evolutionary ScienceTime after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal CommunitiesOur findings highlight how soil fungal and bacterial communities respond to time, season, and plant species identity. We found that succession shapes the soil bacterial community, while plant species and the type of plant species that grows in the soil drive the assembly of soil fungal communities. Future research on the effects of plants on soil microbes should take into consideration the relative roles of both time and plant growth on...
Research Article | Ecological and Evolutionary ScienceIntegrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosumFungal diversity has amazed evolutionary biologists for decades. One societally important aspect of this diversity manifests in traits that enable pathogenicity. The opportunistic pathogen Chaetomium globosum is well adapted to a high-humidity environment and produces numerous secondary metabolites that defend it from predation. Many of these chemicals can threaten...
Research Article | Ecological and Evolutionary ScienceThe Emergence of Successful Streptococcus pyogenes Lineages through Convergent Pathways of Capsule Loss and Recombination Directing High Toxin ExpressionStreptococcus pyogenes is a genetically diverse pathogen, with over 200 different genotypes defined by emm typing, but only a minority of these genotypes are responsible for the majority of human infection in high-income countries. Two prevalent genotypes associated with disease rose to international dominance following recombination of a toxin locus that...