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microbial communities

  • Open Access
    Assessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow Cytometry
    Research Article | Applied and Environmental Science
    Assessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow Cytometry

    The manifold effects of potentially toxic compounds on microbial communities are often difficult to discern. Some compounds may be transformed or completely degraded by few or multiple strains in the community, whereas others may present inhibitory effects.

    B. D. Özel Duygan, S. Rey, S. Leocata, L. Baroux, M. Seyfried, J. R. van der Meer
  • 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
    Microbial Metabolic Redundancy Is a Key Mechanism in a Sulfur-Rich Glacial Ecosystem
    Research Article | Applied and Environmental Science
    Microbial Metabolic Redundancy Is a Key Mechanism in a Sulfur-Rich Glacial Ecosystem

    A unique environment at Borup Fiord Pass is characterized by a sulfur-enriched glacial ecosystem in the low-temperature Canadian High Arctic. BFP represents one of the best terrestrial analog sites for studying icy, sulfur-rich worlds outside our own, such as Europa and Mars. The site also allows investigation of sulfur-based microbial metabolisms in cold environments here on Earth. Here, we report whole-genome sequencing data that...

    Christopher B. Trivedi, Blake W. Stamps, Graham E. Lau, Stephen E. Grasby, Alexis S. Templeton, John R. Spear
  • Open Access
    Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design
    Research Article | Applied and Environmental Science
    Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design

    One of the biggest challenges in microbial ecology is correlating the identity of microorganisms with the roles they fulfill in natural environmental systems. Studies of microbes in pure culture reveal much about their genomic content and potential functions but may not reflect an organism’s activity within its natural community. Culture-independent studies supply a community-wide view of composition and function in the context of...

    Ella T. Sieradzki, Benjamin J. Koch, Alex Greenlon, Rohan Sachdeva, Rex R. Malmstrom, Rebecca L. Mau, Steven J. Blazewicz, Mary K. Firestone, Kirsten S. Hofmockel, Egbert Schwartz, Bruce A. Hungate, Jennifer Pett-Ridge
  • Open Access
    Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function
    Research Article | Ecological and Evolutionary Science
    Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function

    Our work demonstrated that the specific microbial strains used to construct a microbiome could impact the species composition, perturbation responses, and functional outputs of that system. These findings suggest that 16S rRNA gene taxonomic profiles alone may have limited potential to predict the dynamics of microbial communities because they usually do not capture strain-level diversity. Observations from our synthetic communities...

    Brittany A. Niccum, Erik K. Kastman, Nicole Kfoury, Albert Robbat, Benjamin E. Wolfe
  • Open Access
    Emergence of Metabolite Provisioning as a By-Product of Evolved Biological Functions
    Opinion/Hypothesis | Ecological and Evolutionary Science
    Emergence of Metabolite Provisioning as a By-Product of Evolved Biological Functions

    Microbes commonly use metabolites produced by other organisms to compete effectively with others in their environment. As a result, microbial communities are composed of networks of metabolically interdependent organisms. How these networks evolve and shape population diversity, stability, and community function is a subject of active research. But how did these metabolic interactions develop initially? In particular, how and why are...

    Sebastian Gude, Gordon J. Pherribo, Michiko E. Taga
  • Open Access
    Exoenzymes as a Signature of Microbial Response to Marine Environmental Conditions
    Research Article | Applied and Environmental Science
    Exoenzymes as a Signature of Microbial Response to Marine Environmental Conditions

    Microbes release exoenzymes into the environment to break down complex organic matter and nutrients into simpler forms that can be assimilated and utilized, thereby addressing their cellular carbon, nitrogen, and phosphorus requirements. Despite its importance, the factors associated with the synthesis of exoenzymes are not clearly defined, especially for the marine environment. Here, we found that exoenzymes associated with nitrogen...

    Manoj Kamalanathan, Shawn M. Doyle, Chen Xu, Amanda M. Achberger, Terry L. Wade, Kathy Schwehr, Peter H. Santschi, Jason B. Sylvan, Antonietta Quigg
  • Open Access
    Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community
    Research Article | Molecular Biology and Physiology
    Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community

    Microorganisms in the natural world are found in communities, communicating and interacting with each other; therefore, it is essential that microbial regulatory mechanisms, such as gene regulation affected by small RNAs (sRNAs), be investigated at the community level. This work demonstrates that metatranscriptomic field experiments can link environmental variation with changes in RNA pools and have the potential to provide new insights...

    Diego R. Gelsinger, Gherman Uritskiy, Rahul Reddy, Adam Munn, Katie Farney, Jocelyne DiRuggiero
  • Open Access
    Regime Shifts in a Phage-Bacterium Ecosystem and Strategies for Its Control
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Regime Shifts in a Phage-Bacterium Ecosystem and Strategies for Its Control

    Phage-microbe communities play an important role in human health as well as natural and industrial environments. Here we show that these communities can assume several alternative species compositions separated by abrupt regime shifts. Our model predicts these regime shifts in the competition between bacterial strains protected by two different phage defense mechanisms: abortive infection/CRISPR and partial resistance. The history...

    Sergei Maslov, Kim Sneppen
  • 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

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