Publications by authors named "Christopher Schadt"

Mitigating climate change in soil ecosystems involves complex plant and microbial processes regulating carbon pools and flows. Here, we advocate for the use of soil microbiome interventions to help increase soil carbon stocks and curb greenhouse gas emissions from managed soils. Direct interventions include the introduction of microbial strains, consortia, phage, and soil transplants, whereas indirect interventions include managing soil conditions or additives to modulate community composition or its activities.

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sp. strain Populi is an actinobacterium isolated from the rhizosphere of a black cottonwood tree, . We completely sequenced its 5.

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sp. strain Populi is a bacterium from the phylum Verrucomicrobiota, isolated from the rhizosphere of a black cottonwood tree, , from the Cascade mountains in Washington. Its 6.

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Article Synopsis
  • - Borgs are large extrachromosomal elements associated with "Candidatus Methanoperedens" archaea, and researchers used nanopore sequencing to validate and reconstruct genomes, revealing 13 complete and four near-complete genomes that share 40 key genes.
  • - These conserved genes helped identify new Borgs in peatland soil and map their evolutionary relationships, showing two main clades; importantly, Borg genes related to electron transfer and cell surface proteins are more highly expressed than those of the host.
  • - The study also reconstructed the first complete genome of a Methanoperedens thought to host Borgs, revealing unique methylation patterns that may help distinguish their genomes, and suggests that Borgs could exist independently from
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The sources and sinks of nitrous oxide, as control emissions to the atmosphere, are generally poorly constrained for most environmental systems. Initial depth-resolved analysis of nitrous oxide flux from observation wells and the proximal surface within a nitrate contaminated aquifer system revealed high subsurface production but little escape from the surface. To better understand the environmental controls of production and emission at this site, we used a combination of isotopic, geochemical, and molecular analyses to show that chemodenitrification and bacterial denitrification are major sources of nitrous oxide in this subsurface, where low DO, low pH, and high nitrate are correlated with significant nitrous oxide production.

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Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P.

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Article Synopsis
  • Temporal variation in microbial community composition is crucial for understanding how these communities of long-lived plants like trees assemble and function, yet the factors influencing these changes remain largely unclear.
  • Research was conducted to investigate these variations by isolating the microbial composition in a controlled environment over different seasons and years, revealing that community composition varied significantly with both seasonal and long-term factors, accounting for up to 21% of the observed changes.
  • The study highlights the importance of considering both seasonal fluctuations and longer-term changes as they interact to shape unique patterns in tree microbiomes over time, emphasizing the need for more research on how these dynamics impact plant health and responses to environmental changes.
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Microbial community changes in response to climate change drivers have the potential to alter the trajectory of important ecosystem functions. In this paper, we show that while microbial communities in peatland systems responded to manipulations of temperature and CO concentrations, these changes were not associated with similar responses in peat decomposition rates over 3 years. It is unclear however from our current studies whether this functional resiliency over 3 years will continue over the longer time scales relevant to peatland ecosystem functions.

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Objective: Brief dynamic interpersonal therapy (DIT) is an evidence-based psychodynamic intervention for depression offered by the U.K. National Health Service and previously studied in the context of a U.

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Article Synopsis
  • Peatlands play a crucial role in global carbon and nitrogen cycles, holding 15 to 30% of the world's soil carbon stock, but their varying chemistry complicates global carbon inventories.
  • A study analyzed 436 peat cores from 24 countries, finding significant differences in carbon, nitrogen, and organic matter content between different peatland categories, mainly influenced by pH levels.
  • The results indicate predictable differences in carbon and organic matter concentrations across peatland types, which can help enhance future assessments of global peatland carbon and nitrogen stocks.
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Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of . Here, we investigated the metabolome of Populus trichocarpa and Populus deltoides leaves and roots and the microbiome of the leaf and root endospheres, phylloplane, and rhizosphere to understand the systematic impacts of abundance and infection on species in a common garden field setting.

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Understanding the contribution of soil microbial communities to ecosystem processes is critical for predicting terrestrial ecosystem feedbacks under changing climate. Our current understanding lacks a consistent strategy to formulate the linkage between microbial systems and ecosystem processes due to the presumption of functional redundancy in soil microbes. Here we present a global soil microbial metagenomic analysis to generalize patterns of microbial taxonomic compositions and functional potentials across climate and geochemical gradient.

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Article Synopsis
  • Peatlands play a dual role by storing carbon and releasing methane, but the specific microorganisms involved in carbon cycling are not fully understood due to varying environmental conditions.
  • A study was conducted analyzing the methanogenic archaea in 17 peatlands across eastern North America, focusing on how metal contamination influences community structure by using advanced sequencing techniques.
  • The findings revealed that higher levels of trace metals, especially nickel and copper, significantly shaped the composition of methanogenic communities, indicating that trace metal levels in peatlands are key predictors of which microbial groups thrive there.
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Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus' genotype and its phenotype.

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Background: Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales.

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Within the forest community, competition and facilitation between adjacent-growing conspecific and heterospecific plants are mediated by interactions involving common mycorrhizal networks. The ability of plants to alter their neighbor's microbiome is well documented, but the molecular biology of plant-fungal interactions during competition and facilitation has not been previously examined. We used a common soil-plant bioassay experiment to study molecular plant-microbial interactions among rhizosphere communities associated with (native host) and (non-native host).

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Aims: Slow decomposition and isolation from groundwater mean that ombrotrophic peatlands store a large amount of soil carbon (C) but have low availability of nitrogen (N) and phosphorus (P). To better understand the role these limiting nutrients play in determining the C balance of peatland ecosystems, we compile comprehensive N and P budgets for a forested bog in northern Minnesota, USA.

Methods: N and P within plants, soils, and water are quantified based on field measurements.

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In this study, a suite of complementary environmental geochemical analyses, including NMR and gas chromatography-mass spectrometry (GC-MS) analyses of central metabolites, Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) of secondary metabolites, and lipidomics, was used to investigate the influence of organic matter (OM) quality on the heterotrophic microbial mechanisms controlling peatland CO, CH, and CO:CH porewater production ratios in response to climate warming. Our investigations leverage the Spruce and Peatland Responses under Changing Environments (SPRUCE) experiment, where air and peat warming were combined in a whole-ecosystem warming treatment. We hypothesized that warming would enhance the production of plant-derived metabolites, resulting in increased labile OM inputs to the surface peat, thereby enhancing microbial activity and greenhouse gas production.

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The integral role of microbial communities in plant growth and health is now widely recognized, and, increasingly, the constituents of the microbiome are being defined. While phylogenetic surveys have revealed the taxa present in a microbiome and show that this composition can depend on, and respond to, environmental perturbations, the challenge shifts to determining why particular microbes are selected and how they collectively function in concert with their host. In this study, we targeted the isolation of representative bacterial strains from environmental samples of roots using a direct plating approach and compared them to amplicon-based sequencing analysis of root samples.

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Soil microbiomes are rapidly becoming known as an important driver of plant phenotypic variation and may mediate plant responses to environmental factors. However, integrating spatial scales relevant to climate change with plant intraspecific genetic variation and soil microbial ecology is difficult, making studies of broad inference rare. Here we hypothesize and show: 1) the degree to which tree genotypes condition their soil microbiomes varies by population across the geographic distribution of a widespread riparian tree, Populus angustifolia; 2) geographic dissimilarity in soil microbiomes among populations is influenced by both abiotic and biotic environmental variation; and 3) soil microbiomes that vary in response to abiotic and biotic factors can change plant foliar phenology.

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Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes.

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Article Synopsis
  • The study explores how the plant microbiome affects the health of young aspen saplings, particularly after experiencing a high-intensity prescribed fire.
  • Researchers used advanced sequencing techniques to analyze the microbiomes of various plant tissues and surrounding soil, discovering that fire alters both soil and plant microbiomes.
  • The findings indicate that while soil microbiomes are influenced by fire-related soil chemistry, plant microbiomes do not correlate with the chemical composition of the tissues, suggesting a complex relationship that warrants further investigation for enhancing plant resilience and ecosystem recovery.
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