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soil microbiology

  • Open Access
    Siderophore-Mediated Interactions Determine the Disease Suppressiveness of Microbial Consortia
    Research Article | Ecological and Evolutionary Science
    Siderophore-Mediated Interactions Determine the Disease Suppressiveness of Microbial Consortia

    Soil-borne pathogens cause high losses in crop yields globally. The development of environmentally friendly approaches is urgently needed, but is often constrained by complex interactions between root-associated microbes and pathogens. Here, we demonstrate that the interactions within microbial consortia mediated by iron-scavenging siderophores play an important role in reducing pathogen infection and enhancing plant health. This study...

    Shaohua Gu, Tianjie Yang, Zhengying Shao, Tao Wang, Kehao Cao, Alexandre Jousset, Ville-Petri Friman, Cyrus Mallon, Xinlan Mei, Zhong Wei, Yangchun Xu, Qirong Shen, Thomas Pommier
  • Open Access
    Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil
    Research Article | Ecological and Evolutionary Science
    Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil

    Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of...

    L. V. Alteio, F. Schulz, R. Seshadri, N. Varghese, W. Rodriguez-Reillo, E. Ryan, D. Goudeau, S. A. Eichorst, R. R. Malmstrom, R. M. Bowers, L. A. Katz, J. L. Blanchard, T. Woyke
  • Open Access
    Soil Viruses: A New Hope
    Special Issue Perspective | Applied and Environmental Science
    Soil Viruses: A New Hope

    As abundant members of microbial communities, viruses impact microbial mortality, carbon and nutrient cycling, and food web dynamics. Although most of our information about viral communities comes from marine systems, evidence is mounting to suggest that viruses are similarly important in soil.

    Joanne B. Emerson
  • Open Access
    Uncovering the Metabolic Strategies of the Dormant Microbial Majority: towards Integrative Approaches
    Special Issue Perspective | Ecological and Evolutionary Science
    Uncovering the Metabolic Strategies of the Dormant Microbial Majority: towards Integrative Approaches

    A grand challenge in microbiology is to understand how the dormant majority lives. In natural environments, most microorganisms are not growing and instead exist in a spectrum of dormant states.

    Chris Greening, Rhys Grinter, Eleonora Chiri
  • Open Access
    Selection, Succession, and Stabilization of Soil Microbial Consortia
    Research Article | Ecological and Evolutionary Science
    Selection, Succession, and Stabilization of Soil Microbial Consortia

    The soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. In this study, we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for...

    Elias K. Zegeye, Colin J. Brislawn, Yuliya Farris, Sarah J. Fansler, Kirsten S. Hofmockel, Janet K. Jansson, Aaron T. Wright, Emily B. Graham, Dan Naylor, Ryan S. McClure, Hans C. Bernstein
  • Open Access
    RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids
    Research Article | Applied and Environmental Science
    RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids

    Soil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate the knowledge of soil plasmid characteristics so that the content, host associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil...

    Taylor K. Dunivin, Jinlyung Choi, Adina Howe, Ashley Shade
  • Open Access
    Proteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling <em>Bacteroidetes</em>
    Research Article | Applied and Environmental Science
    Proteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling Bacteroidetes

    Cellulose is the most abundant renewable polymer on earth, but its recalcitrance limits highly efficient conversion methods for energy-related and material applications. Though microbial cellulose conversion has been studied for decades, recent advances showcased that large knowledge gaps still exist. Bacteria of the phylum Bacteroidetes are regarded as highly efficient carbohydrate metabolizers, but most species are limited to...

    Marcel Taillefer, Magnus Ø. Arntzen, Bernard Henrissat, Phillip B. Pope, Johan Larsbrink
  • Open Access
    Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes
    Research Article | Ecological and Evolutionary Science
    Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes

    There have been many studies highlighting how plant and animal communities lag behind climate change, causing extinction and diversity debts that will slowly be paid as communities equilibrate. By virtue of their short generation times and dispersal abilities, soil bacteria might be expected to respond to climate change quickly and to be effectively in equilibrium with current climatic conditions. We found strong evidence to the...

    Joshua Ladau, Yu Shi, Xin Jing, Jin-Sheng He, Litong Chen, Xiangui Lin, Noah Fierer, Jack A. Gilbert, Katherine S. Pollard, Haiyan Chu
  • Open Access
    Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
    Research Article | Applied and Environmental Science
    Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

    This work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in these systems. This method yielded >2-fold-more viral populations (vOTUs) per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum, B. Bolduc, et al., Nat Microbiol 3:870–880, 2018,...

    Gareth Trubl, Ho Bin Jang, Simon Roux, Joanne B. Emerson, Natalie Solonenko, Dean R. Vik, Lindsey Solden, Jared Ellenbogen, Alexander T. Runyon, Benjamin Bolduc, Ben J. Woodcroft, Scott R. Saleska, Gene W. Tyson, Kelly C. Wrighton, Matthew B. Sullivan, Virginia I. Rich
  • Open Access
    Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem
    Research Article | Ecological and Evolutionary Science
    Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem

    In this study, we show how invasive plant species drive rapid shifts in the soil environment from surrounding native communities. Each of the three plant invaders had different but consistent effects on soils. Thus, there does not appear to be a one-size-fits-all strategy for how plant invaders alter grassland soil environments. This work represents a crucial step toward understanding how invaders might be able to prevent or impair...

    Sean M. Gibbons, Ylva Lekberg, Daniel L. Mummey, Naseer Sangwan, Philip W. Ramsey, Jack A. Gilbert

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