Susannah Tringe
Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Department Member
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
79 files of metagenomic DNA sequence data, README file, OTU tables (community matrices), and metadata file for relating sequence files to original samples. NOTE: sequence data is available at http://lib-vm-rdmi.uoregon.edu/data/21993/
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Background Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely... more
Background Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities. Results We performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry. Conclusion This catalog lays the foundation for expanding knowledge...
Research Interests:
Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant... more
Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water...
Research Interests:
Research Interests:
Author(s): Mcgowan, Marcia | Abstract: The JGI Project Management Office (PMO) was formed in 2006 to better handle the tracking, organization and flow of projects through the JGI sequencing pipeline. Each project manager specializes in... more
Author(s): Mcgowan, Marcia | Abstract: The JGI Project Management Office (PMO) was formed in 2006 to better handle the tracking, organization and flow of projects through the JGI sequencing pipeline. Each project manager specializes in specific project types and is responsible for communication and coordination.
Research Interests:
Research Interests:
A major challenge facing the biofuels industry is the identification of high-yield plant feedstocks that can be cultivated with minimal resource inputs without competing for land and water supplies with existing food crops. Recent... more
A major challenge facing the biofuels industry is the identification of high-yield plant feedstocks that can be cultivated with minimal resource inputs without competing for land and water supplies with existing food crops. Recent research has demonstrated that the Agave plant, cultivated in Mexico and Southwestern United States for the production of fiber and alcohol, meets these criteria1. Agaves grow on non-arable rocky soils in regions characterized by prolonged drought and extreme temperatures, due in part to physiological adaptions that prevent excess water-loss in arid environments2. Plant-microbial symbioses can play a role in helping plants adapt to heat and drought stress, increasing the accessibility of soil nutrients, or compete with plant pathogens3. Whether agaves have similar beneficial microbe interactions in their native environment is unknown. We aim to provide a comprehensive characterization of the Agave microbiome, with the goal of identifying specific community...
Research Interests: Computer Science, Biology, Mexico, Biofuels, Agave, and 4 moreMicrobiome, Arid, MEXICO, and opuntia robusta
BackgroundDrought is a major abiotic stress that limits agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere and may lead to enrichment of... more
BackgroundDrought is a major abiotic stress that limits agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere and may lead to enrichment of specific groups of microbes, such as Actinobacteria. How these changes ultimately affect plant health is not well understood. In parallel, model systems have been used to tease apart the specific interactions between plants and single, or small groups of microbes. However, translating this work into crop species and achieving increased crop yields within noisy field settings remains a challenge. Thus, the next scientific leap forward in microbiome research must cross the great lab-to-field divide. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key beneficial and detrimental, root associated microbes that robustly affect drought stressed plant phenotypes.ResultsFi...
Research Interests: Biology, Actinobacteria, Sorghum, Arabidopsis, Rhizosphere, and 3 moreMicrobiome, Crop, and Arthrobacter
Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management... more
Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management contexts. However, despite the widespread availability of crop-associated microbiome data, variation in field sampling and laboratory processing methodologies, as well as metadata collection and reporting, significantly constrains the potential for integrative and comparative analyses. Here we discuss the need for agriculture-specific metadata standards for microbiome research, and propose a list of “required” and “desirable” metadata categories and ontologies essential to be included in a future minimum information metadata standards checklist for describing agricultural microbiome studies. We begin by briefly reviewing existing metadata standards relevant to agricultural microbiome research, and describe ongoing efforts to enhance the potential for integr...
Research Interests:
Research Interests:
Research Interests:
Research Interests: Microbiology, Biology, Ecology, Medicine, Land Use Change, and 15 moreBiological Sciences, Environmental Sciences, Forest, Denitrification, Bacteria, Forests, Amazon, Microorganisms, Ecosystem, Amazon rainforest, Microbiota, Conservation of Natural Resources, Ecological Network, Medical and Health Sciences, and Biogeochemical Cycle
Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown.... more
Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfur...
Research Interests:
The hoatzin (Opisthocomus hoazin) is a South American herbivorous bird, that has an enlarged crop analogous to the rumen, where foregut microbes degrade the otherwise indigestible plant materials, providing energy to the host. The crop... more
The hoatzin (Opisthocomus hoazin) is a South American herbivorous bird, that has an enlarged crop analogous to the rumen, where foregut microbes degrade the otherwise indigestible plant materials, providing energy to the host. The crop harbors an impressive array of microorganisms with potentially novel cellulolytic enzymes. Thie study describes the composition ofthe particle-associated microbiota in the hoatzin crop, combining a survey of 16S rRNA genes in 7 adult birds and metagenome sequencing of two animals. The pyrotag survey demonstrates that Prevotellaceae, are the most abundant and ubiquitous taxa, suggesting that the degradation of hemicellulose is an important activity in the crop. Nonetheless, preliminary results from the metagnome of the particle-associated microbiota of two adult birds show that the crop microbiome contains a high number of genes encoding cellulases (such as GH5) more abundant than those of the termite gut, as well as genes encoding hemicellulases. These preliminary results show that the carbohydate-active enzyme genes in the cropmetagenome could be a source of biochemical catalysts able to deconstruct plant biomass.
Research Interests:
High-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical... more
High-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions. Acidilobus spp. (order Desulfurococcales ) comprise one of the dominant phylotypes in hypoxic geothermal sulfur sediment and Fe(III)-oxide environments along with members of the Thermoproteales and Sulfolobales . Consequently, the primary goals of the current study were to analyze and compare replicate de novo sequence assemblies of Acidilobus -like populations from four different mildly acidic (pH 3.3 to 6.1) high-temperature (72°C to 82°C) environments and to identify metabolic pathways and/or protein-encoding genes that provide a detailed foundation of the potential functional role of these populations in situ. De novo assemblies of the highly similar Acidilobus -like populations (>99% 16S rRNA gene identity) represent near-complet...
Research Interests:
ABSTRACT A significant amount of carbon (C) is processed and stored in prairie soils: grasslands cover 6.1-7.4% of the earth's land surface and hold 7.3-11.4% of global soil C. Global change models predict that the future... more
ABSTRACT A significant amount of carbon (C) is processed and stored in prairie soils: grasslands cover 6.1-7.4% of the earth's land surface and hold 7.3-11.4% of global soil C. Global change models predict that the future precipitation regime across the North American Great Plains will entail less frequent but larger rainfall events. The response of prairie soil microbial C processing and allocation to this scenario of higher hydrologic variability is not known, but will be a key determiner of the future capacity for prairie soil C sequestration. We are approaching this problem by assessing soil microbial function (respiration, C utilization efficiency, extracellular enzyme activity) and molecular indicators of dominant C allocation pathways (soil transcriptome, proteome and metabolome) under ambient and experimentally modified precipitation regimes. The rainfall manipulation plots (RaMPs) at the Konza Prairie Long-Term Ecological Research (LTER) site in eastern Kansas, USA is a replicated field manipulation of the magnitude and frequency of natural precipitation that was established in 1998. We collected soil before, during and after a rainfall event in both ambient and modified precipitation treatments and measured the microbial response. Microbial respiration doubled in both treatments during the water addition, and cellobiohydrolase enzyme potential activity (a catalyst of cellulose hydrolysis) increased slightly, but no significant effect of altered precipitation treatment has emerged. The fungal and bacterial ribosomal gene composition was also similar between precipitation treatments. Although pools of genes and extracellular enzymes may be relatively static during short-term dynamic conditions, transcript and intracellular protein abundances may be more indicative of the active microbial metabolic response to rapid shifts in soil moisture. Thus, analysis of transcript and protein composition is underway. In addition, we have implemented a series of lab experiments to optimize and link transcript and protein recovery and analysis procedures using the model soil bacterium Arthrobacter chlorophenicolus strain A6 (ArtchA6). Konza prairie soil was inoculated with ArchA6 and incubated for 72 h with no supplemental C, with acetate or with 4-chlorophenol (a xenobiotic compound that ArtchA6 can utilize as its sole C source), then RNA and protein were extracted from the soil. Quantitatively representative recovery of ArtchA6 genes, rRNA, mRNA and protein was successful. The ratio of ArtchA6 isocitrate lyase (icl, indicative of 2-C metabolism) to succinyl CoA synthetase (suCAB, indicative of total respiratory activity) transcript was highest in soils amended with acetate. Proteomic signatures were distinct in soils with different supplemental C sources. This experiment confirms our capability of recovering transcript and protein from the study soil and of identifying the functional molecules representative of distinct C metabolism pathways.
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests: Genetics, Microbiology, Comparative Genomics, Biology, Activated Sludge, and 15 moreBiodiversity, Metagenomics, Medicine, Biological Sciences, Phosphorus, Phylogeny, Environmental Sciences, Denitrification, Genome, Sewage, Bioreactors, Candidatus Accumulibacter Phosphatis, Enhanced Biological Phosphorus Removal, Synteny, and isme
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests: Evolutionary Biology, Genetics, Microbiology, Technology, Polymorphism, and 15 moreBiology, Metagenomics, Medicine, Biological Sciences, Phylogeny, Environmental Sciences, Population, Bacteria, Genome, Biological evolution, Single Nucleotide Polymorphism, Genetic variation, Bacterial, Gene frequency, and Single nucleotide
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled unprecedented insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this powerful approach to... more
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled unprecedented insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this powerful approach to over 10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, human- and animal-host associated microbiomes, engineered environments, and natural and agricultural soils to capture extant microbial metabolic and functional potential. We present a comprehensive catalogue of 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units (OTUs), spanning 135 phyla, which expand the known phylogenetic diversity of Bacteria and Archaea by 44%. We also demonstrate the utility of this collection for secondary metabolite biosynthetic potential and predicting host-virus linkage, which can provide a view into the global distribution of lysogenic viruses. This resource...
Research Interests: Narrative and Microbiome
Research Interests:
An amendment to this paper has been published and can be accessed via a link at the top of the paper.