A5052852254- Peatlands and Wetlands Ecology
- Botany and Plant Ecology Studies
- Coastal wetland ecosystem dynamics
- Microbial Community Ecology and Physiology
- Plant Pathogens and Fungal Diseases
- Plant-Microbe Interactions and Immunity
- Mycorrhizal Fungi and Plant Interactions
- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Metabolomics and Mass Spectrometry Studies
- Bryophyte Studies and Records
- Mercury impact and mitigation studies
- Legume Nitrogen Fixing Symbiosis
- Bioinformatics and Genomic Networks
- Plant Parasitism and Resistance
- Bioenergy crop production and management
- Plant and fungal interactions
- Mass Spectrometry Techniques and Applications
- Plant nutrient uptake and metabolism
- Photosynthetic Processes and Mechanisms
- Soil Carbon and Nitrogen Dynamics
- Probiotics and Fermented Foods
- Ecology and Vegetation Dynamics Studies
- Insect symbiosis and bacterial influences
- Yeasts and Rust Fungi Studies
Oak Ridge National Laboratory
2016-2025
University of Tennessee at Knoxville
2017-2020
Oak Ridge Associated Universities
2018
University of California, Merced
2014-2018
Duke University
2015-2016
Peatlands are crucial sinks for atmospheric carbon but critically threatened due to warming climates. Sphagnum (peat moss) species keystone members of peatland communities where they actively engineer hyperacidic conditions, which improves their competitive advantage and accelerates ecosystem-level sequestration. To dissect the molecular physiological sources this unique biology, we generated chromosome-scale genomes two species: S. divinum angustifolium. show no gene colinearity with any...
Historically neglected by microbial ecologists, soil viruses are now thought to be critical global biogeochemical cycles. However, our understanding of their distribution, activities and interactions with the microbiome remains limited. Here we present Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced metagenomes composed 616,935 uncultivated viral genomes 38,508 unique operational taxonomic units. Rarefaction curves Atlas indicate that most diversity...
Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops biofeedstocks. In some cases, the microbial community associated with plants has been shown alleviate stress increase under suboptimal growing conditions. A systematic understanding how changes these is required understand contribution microbiome water utilization, nutrient uptake, ultimately yield. Using a inoculation strategy, we studied belowground Populus...
Sphagnum-dominated peatlands comprise a globally important pool of soil carbon (C) and are vulnerable to climate change. While peat mosses the genus Sphagnum known harbor diverse microbial communities that mediate C nitrogen (N) cycling in peatlands, effects change on microbiome composition functioning largely unknown. We investigated impacts experimental whole-ecosystem warming moss microbiome, focusing N2 fixing microorganisms (diazotrophs). To characterize response warming, we performed...
Antimicrobial peptides (AMPs) are promising alternative antimicrobial agents. Currently, however, portable, user-friendly and efficient methods for predicting AMP sequences from genome-scale data not readily available. Here we present amPEPpy, an open-source, multi-threaded command-line application using a random forest classifier.amPEPpy is implemented in Python 3 freely available through GitHub (https://github.com/tlawrence3/amPEPpy).Supplementary at Bioinformatics online.
Abstract Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources decipher gene function and subsequently provide molecular targets improvement through editing. However, biological roles large proportions across the phylogeny are poorly annotated. Here we describe Joint Genome Institute (JGI) Plant Atlas, an updateable data resource consisting transcript...
Conifers predominantly occur on soils or in climates that are suboptimal for plant growth. This is generally attributed to symbioses with mycorrhizal fungi and conifer adaptations, but recent experiments suggest aboveground endophytic bacteria conifers fix nitrogen (N) affect host shoot tissue Because most cannot be grown the laboratory very little known about conifer-endophyte associations wild. Pinus flexilis (limber pine) Picea engelmannii (Engelmann spruce) growing a subalpine,...
Tropical forests generally occur on highly weathered soils that, in combination with the immobility of phosphorus (P), often result lacking orthophosphate, form P most easily metabolized by plants and microbes. In these soils, mineralization organic can be major source for orthophosphate. Both microbes encode phosphatases capable mineralizing a range compounds. However, activity enzymes depends several edaphic factors including availability, tree species, microbial communities. Thus,...
It is increasingly evident that the plant microbiome a strong determinant of health. While ability to manipulate in plants and ecosystems recovering from disturbance may be useful, our understanding regenerating communities currently limited. Using 16S ribosomal RNA (rRNA) gene internal transcribed spacer (ITS) region amplicon sequencing, we characterized leaf, stem, fine root, rhizome, rhizosphere < 1-yr-old aspen saplings associated bulk soil after recent high-intensity prescribed fire...
Sphagnum peatmosses are fundamental members of peatland ecosystems, where they contribute to the uptake and long-term storage atmospheric carbon. Warming threatens mosses is known alter composition their associated microbiome. Here, we use a microbiome transfer approach test if thermal origin influences host plant thermotolerance. We leveraged an experimental whole-ecosystem warming study collect field-grown Sphagnum, mechanically separate then onto germ-free laboratory for temperature...
ABSTRACT Temporal variation in community composition is central to our understanding of the assembly and functioning microbial communities, yet controls over temporal dynamics for microbiomes long-lived plants, such as trees, remain unclear. tree could arise primarily from seasonal (i.e., intra-annual) fluctuations or longer-term changes across years host plants age. To test these alternatives, we experimentally isolated plant microbiome using a common garden clonally propagated used...
Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant microbial traits can influence adaptation even 'extend' to community structure ecosystem level processes. Progress this area is limited model systems deep genetic genomic resources that often have negligible impact or interest. Thus, important linkages between adaptations their consequences at organismal scales are lacking. Here we introduce the Sphagnome Project,...
The endophytic bacterial microbiome, with an emerging role in plant nutrient acquisition and stress tolerance, is much less studied natural populations than agricultural crops. In a previous study, we found consistent associations between trees the pine family acetic acid bacteria (AAB) occurring at high relative abundance inside their needles. Our objective here was to determine if that pattern may be general conifers, or alternatively, more likely restricted pines conifers growing limited...
Interactions between Sphagnum (peat moss) and cyanobacteria play critical roles in terrestrial carbon nitrogen cycling processes. Knowledge of the metabolites exchanged, physiological processes involved, environmental conditions allowing formation symbiosis is important for a better understanding mechanisms underlying these interactions. In this study, we used cross-feeding approach with spatially resolved metabolite profiling metatranscriptomics to characterize Nostoc cyanobacteria. A pH...
Peat mosses (Sphagnum spp.) are keystone species in boreal peatlands, where they dominate net primary productivity and facilitate the accumulation of carbon thick peat deposits. Sphagnum harbor a diverse assemblage microbial partners, including N2 -fixing (diazotrophic) CH4 -oxidizing (methanotrophic) taxa that support ecosystem function by regulating transformations nitrogen. Here, we investigate response phytobiome (plant + constituent microbiome environment) to gradient experimental...
ABSTRACT Sphagnum moss is the dominant plant genus in northern peatlands responsible for long‐term carbon accumulation. hosts diverse microbial communities (microbiomes), and its phytobiome (plant host + constituent microbiome environment) plays a key role nutrient acquisition along with cycling. Climate change can modify ‐associated microbiome, resulting enhanced growth thermal acclimation as previously shown warming experiments. However, extent of benefits to influence host–microbe...
Abstract Cancer therapy-induced oral mucositis is a frequent major oncological problem, secondary to cytotoxicity of chemo-radiation treatment. Oral commonly occurs 7–10 days after initiation therapy; it dose-limiting side effect causing significant pain, eating difficulty, need for parenteral nutrition and rise infections. The pathobiology derives from complex interactions between the epithelial component, inflammation, microbiome. Our longitudinal study analysed dynamics microbiome...
We demonstrate the coupling of liquid extraction surface analysis (LESA) to structures for lossless ion manipulations in conjunction with serpentine ultralong path extending routing (SLIM SUPER) mobility-mass spectrometry (IM-MS) unambiguous annotation important isomeric glycoforms carbon-fixing communities.
One critical aspect of mass spectrometry imaging (MSI) is the need to confidently identify detected analytes. While orthogonal tandem MS (e.g., LC-MS2) experiments from sample extracts can assist in annotating ions, spatial information about these molecules lost. Accordingly, this could cause mislead conclusions, especially cases where isobaric species exhibit different distributions within a sample. In Technical Note, we employed multimodal approach, using matrix assisted laser...
Abstract Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long‐term whole‐ecosystem warming experiment at boreal peatland to answer how temperature CO 2 jointly influence communities of abundant, diverse, yet poorly understood, non‐fungi microbial Eukaryotes (protists). These microbes ecosystem function directly through photosynthesis respiration, indirectly, predation on decomposers (bacteria...
Pines in the subalpine environment at Niwot Ridge, CO, have been found to host communities of acetic acid bacteria (AAB) within their needles. The significance and ubiquity this pattern is not known, but recent evidence nitrogen (N)-fixing activity Pinus flexilis (limber pine) foliage calls for a better understanding processes that regulate endophytic forest tree canopies. Here, test if AAB dominate foliar bacterial microbiota other locations, we compared 16S rRNA community needles from P....
Abstract Bacterial endophytes may be fairly host‐specific; nonetheless, an important subset of taxa shared among numerous host species forming a community‐wide core microbiome. Moreover, other key factors, particularly the supply limiting macronutrients and disturbances, supersede importance identity. We tested following four non‐mutually exclusive hypotheses: (a) The Host Identity Hypothesis : vary substantially different host‐plant species. (b) Core Microbiome microbial will all (c). Soil...