soil microbiology
Research Article | Ecological and Evolutionary ScienceComplementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest SoilMicrobial 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...
Special Issue Perspective | Applied and Environmental ScienceSoil Viruses: A New HopeAs 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.
Special Issue Perspective | Ecological and Evolutionary ScienceUncovering the Metabolic Strategies of the Dormant Microbial Majority: towards Integrative ApproachesA 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.
Research Article | Ecological and Evolutionary ScienceSelection, Succession, and Stabilization of Soil Microbial ConsortiaThe 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...
Research Article | Applied and Environmental ScienceRefSoil+: a Reference Database for Genes and Traits of Soil PlasmidsSoil-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...
Research Article | Applied and Environmental ScienceProteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling BacteroidetesCellulose 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...
Research Article | Ecological and Evolutionary ScienceExisting Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil ProkaryotesThere 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...
Research Article | Applied and Environmental ScienceSoil Viruses Are Underexplored Players in Ecosystem Carbon ProcessingThis 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,...
Research Article | Ecological and Evolutionary ScienceInvasive Plants Rapidly Reshape Soil Properties in a Grassland EcosystemIn 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...
Research Article | Ecological and Evolutionary ScienceBalance Trees Reveal Microbial Niche DifferentiationBy explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/gneiss.