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  • Articles
    • Latest Articles
    • Special Issues
    • COVID-19 Special Collection
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    • Special Series: Sponsored Minireviews and Video Abstracts
    • Archive
  • Topics
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ecology

  • Open Access
    Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts
    Research Article | Ecological and Evolutionary Science
    Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts

    This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: “Ca. Planktophila” (acI-A), “Ca. Nanopelagicus” (acI-B), and “Ca. Fonsibacter” (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing...

    Rhiannon Mondav, Stefan Bertilsson, Moritz Buck, Silke Langenheder, Eva S. Lindström, Sarahi L. Garcia
  • Open Access
    Abundant and Diverse RNA Viruses in Insects Revealed by RNA-Seq Analysis: Ecological and Evolutionary Implications
    Research Article | Ecological and Evolutionary Science
    Abundant and Diverse RNA Viruses in Insects Revealed by RNA-Seq Analysis: Ecological and Evolutionary Implications

    Insects comprise the largest proportion of animals on earth and are frequently implicated in the transmission of vector-borne diseases. However, considerable attention has been paid to the phytophagous and hematophagous insects, with results that provide insufficient and biased information about the viruses in insects. Here, we have delivered compelling evidence for the exceptional abundance and genetic diversity of RNA viruses in a...

    Haoming Wu, Rui Pang, Tong Cheng, Liang Xue, Haiyan Zeng, Tao Lei, Moutong Chen, Shi Wu, Yu Ding, Jumei Zhang, Mang Shi, Qingping Wu
  • Open Access
    Biofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible Bacteria
    Research Article | Ecological and Evolutionary Science
    Biofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible Bacteria

    In the natural environment, bacteria most often live in communities bound to one another by secreted adhesives. These communities, or biofilms, play a central role in biogeochemical cycling, microbiome functioning, wastewater treatment, and disease. Wherever there are bacteria, there are also viruses that attack them, called phages. Interactions between bacteria and phages are likely to occur ubiquitously in biofilms. We show here,...

    Emilia L. Simmons, Matthew C. Bond, Britt Koskella, Knut Drescher, Vanni Bucci, Carey D. Nadell
  • Open Access
    Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes
    Research Article | Novel Systems Biology Techniques
    Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes

    Short-read sequencing with Illumina sequencing technology provides an accurate, high-throughput method for characterizing the metabolic potential of microbial communities. Short-read sequences can be assembled and binned into metagenome-assembled genomes, thus shedding light on the function of microbial ecosystems that are important for health, agriculture, and Earth system processes. The work presented here provides an analytical...

    Taylor M. Royalty, Andrew D. Steen
  • Open Access
    The Power of Metabolism for Predicting Microbial Community Dynamics
    Special Issue Perspective | Ecological and Evolutionary Science
    The Power of Metabolism for Predicting Microbial Community Dynamics

    Quantitative understanding and prediction of microbial community dynamics are an outstanding challenge. We test the hypothesis that metabolic mechanisms provide a foundation for accurate prediction of dynamics in microbial systems. In our research, metabolic models have been able to accurately predict species interactions, evolutionary trajectories, and response to perturbation in simple synthetic consortia.

    Jeremy M. Chacón, William R. Harcombe
  • Open Access
    Uncovering Virus-Virus Interactions by Unifying Approaches and Harnessing High-Throughput Tools
    Special Issue Perspective | Ecological and Evolutionary Science
    Uncovering Virus-Virus Interactions by Unifying Approaches and Harnessing High-Throughput Tools

    Virus-host interactions have received much attention in virology. Virus-virus interactions can occur when >1 virus infects a host and can be deemed social when one virus affects the fitness of another virus, as in the well-known case of superinfection exclusion.

    Samuel L. Díaz-Muñoz
  • Open Access
    Defining Microbiome Health through a Host Lens
    Special Issue Perspective | Host-Microbe Biology
    Defining Microbiome Health through a Host Lens

    We are walking ecosystems, inoculated at birth with a unique set of microbes that are integral to the functioning of our bodies. The physiology of our commensal microbiota is intertwined with our metabolism, immune function, and mental state.

    Sean M. Gibbons
  • Open Access
    Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research
    Special Issue Perspective | Ecological and Evolutionary Science
    Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research

    Despite increasing acknowledgment that microorganisms underpin the healthy functioning of basically all multicellular life, few cross-disciplinary teams address the diversity and function of microbiota across organisms and ecosystems. Our newly formed consortium of junior faculty spanning fields such as ecology and geoscience to mathematics and molecular biology from the University of Hawai‘i at Mānoa aims to fill this gap.

    ...
    Nicole A. Hynson, Kiana L. Frank, Rosanna A. Alegado, Anthony S. Amend, Mohammad Arif, Gordon M. Bennett, Andrea J. Jani, Matthew C. I. Medeiros, Yuriy Mileyko, Craig E. Nelson, Nhu H. Nguyen, Olivia D. Nigro, Sladjana Prisic, Sangwoo Shin, Daisuke Takagi, Samuel T. Wilson, Joanne Y. Yew
  • Open Access
    Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data
    Research Article | Host-Microbe Biology
    Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data

    Studies focusing on taxonomic compositions of the gut microbiota are plentiful, whereas its functional capabilities are still poorly understood. Specific key functions deserve detailed investigations, as they regulate microbiota-host interactions and promote host health and disease. The production of butyrate is among the top targets since depletion of this microbe-derived metabolite is linked to several emerging noncommunicable...

    Marius Vital, André Karch, Dietmar H. Pieper
  • Open Access
    Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions
    Commentary | Host-Microbe Biology
    Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions

    Understanding how microbiomes affect host resistance, parasite virulence, and parasite-associated diseases requires a collaborative effort between parasitologists, microbial ecologists, virologists, and immunologists. We hereby propose the Parasite Microbiome Project to bring together researchers with complementary expertise and to study the role of microbes in host-parasite interactions.

    Nolwenn M. Dheilly, Daniel Bolnick, Seth Bordenstein, Paul J. Brindley, Cédric Figuères, Edward C. Holmes, Joaquín Martínez Martínez, Anna J. Phillips, Robert Poulin, Karyna Rosario

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