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Ecological and Evolutionary Science

  • Open Access
    Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria
    Research Article | Ecological and Evolutionary Science
    Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria

    Soil microbes respond to environmental change by altering how they allocate carbon to growth versus respiration—or carbon use efficiency (CUE). Ecosystem and Earth System models, used to project how global soil C stocks will continue to respond to the climate crisis, often assume that microbes respond homogeneously to changes in the environment. In this study, we quantified how CUE varies with changes in temperature and substrate...

    Grace Pold, Luiz A. Domeignoz-Horta, Eric W. Morrison, Serita D. Frey, Seeta A. Sistla, Kristen M. DeAngelis
  • Open Access
    A Genus Definition for <em>Bacteria</em> and <em>Archaea</em> Based on a Standard Genome Relatedness Index
    Editor's Pick Research Article | Ecological and Evolutionary Science
    A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index

    In 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...

    R. A. Barco, G. M. Garrity, J. J. Scott, J. P. Amend, K. H. Nealson, D. Emerson
  • Open Access
    A New Family of DNA Viruses Causing Disease in Crustaceans from Diverse Aquatic Biomes
    Research Article | Ecological and Evolutionary Science
    A New Family of DNA Viruses Causing Disease in Crustaceans from Diverse Aquatic Biomes

    Recent 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...

    Kuttichantran Subramaniam, Donald C. Behringer, Jamie Bojko, Natalya Yutin, Abigail S. Clark, Kelly S. Bateman, Ronny van Aerle, David Bass, Rose C. Kerr, Eugene V. Koonin, Grant D. Stentiford, Thomas B. Waltzek
  • Open Access
    Collective Viral Spread Mediated by Virion Aggregates Promotes the Evolution of Defective Interfering Particles
    Research Article | Ecological and Evolutionary Science
    Collective Viral Spread Mediated by Virion Aggregates Promotes the Evolution of Defective Interfering Particles

    Recent 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...

    Iván Andreu-Moreno, Rafael Sanjuán
  • Open Access
    Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria
    Research Article | Ecological and Evolutionary Science
    Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria

    The 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...

    Jimmy H. W. Saw, Takuro Nunoura, Miho Hirai, Yoshihiro Takaki, Rachel Parsons, Michelle Michelsen, Krista Longnecker, Elizabeth B. Kujawinski, Ramunas Stepanauskas, Zachary Landry, Craig A. Carlson, Stephen J. Giovannoni
  • Open Access
    Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats

    In 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...

    Se Jin Song, Jon G. Sanders, Frédéric Delsuc, Jessica Metcalf, Katherine Amato, Michael W. Taylor, Florent Mazel, Holly L. Lutz, Kevin Winker, Gary R. Graves, Gregory Humphrey, Jack A. Gilbert, Shannon J. Hackett, Kevin P. White, Heather R. Skeen, Sarah M. Kurtis, Jack Withrow, Thomas Braile, Matthew Miller, Kevin G. McCracken, James M. Maley, Vanessa O. Ezenwa, Allison Williams, Jessica M. Blanton, Valerie J. McKenzie, Rob Knight
  • Open Access
    Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates
    Research Article | Ecological and Evolutionary Science
    Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates

    Ciliates, 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...

    Ying Yan, Xyrus X. Maurer-Alcalá, Rob Knight, Sergei L. Kosakovsky Pond, Laura A. Katz
  • Open Access
    How to Train Your Fungus
    Commentary | Ecological and Evolutionary Science
    How to Train Your Fungus

    Domestication 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...

    John G. Gibbons
  • Open Access
    Time after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal Communities
    Research Article | Ecological and Evolutionary Science
    Time after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal Communities

    Our 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...

    S. Emilia Hannula, Anna M. Kielak, Katja Steinauer, Martine Huberty, Renske Jongen, Jonathan R. De Long, Robin Heinen, T. Martijn Bezemer
  • Open Access
    Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of <span class="named-content genus-species" id="named-content-1">Chaetomium globosum</span>
    Research Article | Ecological and Evolutionary Science
    Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum

    Fungal 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...

    Zheng Wang, Francesc López-Giráldez, Junrui Wang, Frances Trail, Jeffrey P. Townsend

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