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Ecological and Evolutionary Science

  • Open Access
    A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated <em>Clostridium difficile</em> PCR Ribotype 078
    Research Article | Ecological and Evolutionary Science
    A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078

    Clostridium difficile PCR ribotype 078 (RT078) has multiple reservoirs; many are agricultural. Since 2005, this genotype has been increasingly associated with human infections in both clinical settings and the community. Investigations of RT078 whole-genome sequences revealed that tetracycline resistance had been acquired on multiple independent occasions....

    Kate E. Dingle, Xavier Didelot, T. Phuong Quan, David W. Eyre, Nicole Stoesser, Charis A. Marwick, John Coia, Derek Brown, Sarah Buchanan, Umer Z. Ijaz, Cosmika Goswami, Gill Douce, Warren N. Fawley, Mark H. Wilcox, Timothy E. A. Peto, A. Sarah Walker, Derrick W. Crook
  • Open Access
    Fungi in the Marine Environment: Open Questions and Unsolved Problems
    Minireview | Ecological and Evolutionary Science
    Fungi in the Marine Environment: Open Questions and Unsolved Problems

    Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far.

    Anthony Amend, Gaetan Burgaud, Michael Cunliffe, Virginia P. Edgcomb, Cassandra L. Ettinger, M. H. Gutiérrez, Joseph Heitman, Erik F. Y. Hom, Giuseppe Ianiri, Adam C. Jones, Maiko Kagami, Kathryn T. Picard, C. Alisha Quandt, Seshagiri Raghukumar, Mertixell Riquelme, Jason Stajich, José Vargas-Muñiz, Allison K. Walker, Oded Yarden, Amy S. Gladfelter
  • Open Access
    Changes in Intrinsic Antibiotic Susceptibility during a Long-Term Evolution Experiment with <span class="named-content genus-species" id="named-content-1">Escherichia coli</span>
    Research Article | Ecological and Evolutionary Science
    Changes in Intrinsic Antibiotic Susceptibility during a Long-Term Evolution Experiment with Escherichia coli

    Resistance to antibiotics often evolves when bacteria encounter antibiotics. However, bacterial strains and species without any known exposure to these drugs also vary in their intrinsic susceptibility. In many cases, evolved resistance has been shown to be costly to the bacteria, such that resistant types have reduced competitiveness relative to their sensitive progenitors in the absence of antibiotics. In this study, we examined...

    Otmane Lamrabet, Mikaël Martin, Richard E. Lenski, Dominique Schneider
  • Open Access
    Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior
    Research Article | Ecological and Evolutionary Science
    Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior

    The manipulation and engineering of microbiomes could lead to improved human health, environmental sustainability, and agricultural productivity. However, microbiomes have proven difficult to alter in predictable ways, and their emergent properties are poorly understood. The history of biology has demonstrated the power of model systems to understand complex problems such as gene expression or development. Therefore, a defined and...

    Gabriel L. Lozano, Juan I. Bravo, Manuel F. Garavito Diago, Hyun Bong Park, Amanda Hurley, S. Brook Peterson, Eric V. Stabb, Jason M. Crawford, Nichole A. Broderick, Jo Handelsman
  • Open Access
    Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism
    Research Article | Ecological and Evolutionary Science
    Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism

    Genomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the...

    Disa Bäckström, Natalya Yutin, Steffen L. Jørgensen, Jennah Dharamshi, Felix Homa, Katarzyna Zaremba-Niedwiedzka, Anja Spang, Yuri I. Wolf, Eugene V. Koonin, Thijs J. G. Ettema
  • Open Access
    CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes
    Research Article | Ecological and Evolutionary Science
    CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes

    The CRISPR-Cas system is one means by which bacterial and archaeal populations defend against viral infection which causes 20 to 50% of cell mortality in the ocean. We tested the hypothesis that certain viral genes are preferentially targeted for the initial attack of the CRISPR-Cas system on a viral genome. Using CASC, a pipeline for CRISPR spacer discovery, and metagenome data from oceanic microbes and viruses, we found a clear subset...

    Daniel J. Nasko, Barbra D. Ferrell, Ryan M. Moore, Jaysheel D. Bhavsar, Shawn W. Polson, K. Eric Wommack
  • Open Access
    Fitness Cost of Aflatoxin Production in <span class="named-content genus-species" id="named-content-1">Aspergillus flavus</span> When Competing with Soil Microbes Could Maintain Balancing Selection
    Research Article | Ecological and Evolutionary Science
    Fitness Cost of Aflatoxin Production in Aspergillus flavus When Competing with Soil Microbes Could Maintain Balancing Selection

    Aflatoxin, produced by the fungus Aspergillus flavus, is an extremely potent hepatotoxin that causes acute toxicosis and cancer, and it incurs hundreds of millions of dollars annually in agricultural losses. Despite the importance of this toxin to humans, it has remained unclear what the fungus gains by producing aflatoxin. In fact, not all strains of...

    Milton T. Drott, Tracy Debenport, Steven A. Higgins, Daniel H. Buckley, Michael G. Milgroom
  • Open Access
    Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen <em>Vibrio vulnificus</em>: From Genotype to Ecotype
    Research Article | Ecological and Evolutionary Science
    Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype

    Vibrio vulnificus is an emergent marine pathogen and is the cause of a deadly septicemia. However, the genetic factors that differentiate its clinical and environmental strains and its several biotypes remain mostly enigmatic. In this work, we investigated the underlying genomic properties and population dynamics of the...

    Mario López-Pérez, Jane M. Jayakumar, Jose M. Haro-Moreno, Asier Zaragoza-Solas, Geethika Reddi, Francisco Rodriguez-Valera, Orr H. Shapiro, Munirul Alam, Salvador Almagro-Moreno
  • Open Access
    Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member
    Research Article | Ecological and Evolutionary Science
    Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member

    The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat’s biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our...

    Bela Hausmann, Claus Pelikan, Thomas Rattei, Alexander Loy, Michael Pester
  • Open Access
    Competition in Biofilms between Cystic Fibrosis Isolates of <em>Pseudomonas aeruginosa</em> Is Shaped by R-Pyocins
    Research Article | Ecological and Evolutionary Science
    Competition in Biofilms between Cystic Fibrosis Isolates of Pseudomonas aeruginosa Is Shaped by R-Pyocins

    A major clinical problem caused by Pseudomonas aeruginosa, is chronic biofilm infection of the lungs in individuals with cystic fibrosis (CF). Epidemic P. aeruginosa strains dominate and displace others during CF infection, but these intraspecies interactions remain poorly understood. Here we...

    Olubukola Oluyombo, Christopher N. Penfold, Stephen P. Diggle

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