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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    A More Intuitive Phytozome Interface
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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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Our Science
Home › Our Science › Science Programs & Platforms Leads › Microbial Systems Group

Microbial Systems Group

Group within the Metagenomics Program.

Research in the Tringe group focuses on sequence-based approaches to studying microbial community assembly, function and dynamics.  Members of the group aid in communicating and interpreting sequencing results to collaborators in addition to performing collaborative and independent research in microbial community genomics.  Major foci of these research efforts are the roles of microbial communities in wetland carbon cycling and the interactions of plants with their associated microbiomes.

Microbiology of produced water recycling

Hydrocarbon extraction through methods such as hydraulic fracturing produces large volumes of chemically contaminated produced water that must be managed and disposed of appropriately.  There is interest in exploiting produced water for crop irrigation, especially in drought-prone areas, but treatment is necessary to remove the diverse chemical components, many of which are potentially toxic to plants, animals and humans. Biological treatment methods are effective at removing many contaminants found in produced water, but the microbial communities inhabiting the treatment reactors have been minimally characterized and thus exhibit variable performance that is challenging to optimize.

We aim to characterize the microbial communities found in bioreactors treating produced water and assign key activities to specific organisms, using metagenome sequencing, genome binning and metabolic reconstruction. Additionally, we would also cultivate and study individual members of these communities based on their predicted metabolisms, in order to construct stable defined consortia for produced water treatment.

Wetland greenhouse gas cycling

Wetlands occupy less than 10% of the Earth’s land surface but harbor up to a third of soil organic carbon.  Wetland preservation and restoration has the potential to sequester significant amounts of terrestrial carbon, but they can also produce the potent greenhouse gas methane, meaning different types of wetlands may serve as either greenhouse gas sources or sinks.  This uncertainty leads to considerable variability in predictions from climate models, both in the overall carbon budget and in how wetlands are expected to respond to climate change.

More accurate prediction of wetland carbon dynamics requires better understanding of the belowground microbial communities that are key to recycling or storing biomass carbon and producing greenhouse gases.  To gain insight into these systems we are applying microbial community genomics to wetland microbial communities in coastal wetlands across the San Francisco Bay / Delta region, including in-depth metagenome and metatranscriptome sequencing of natural and restored wetlands. (Watch the video here.) These studies are revealing organisms and genes involved in promoting or repressing greenhouse gas emissions, enabling a mechanistic understanding of belowground carbon cycling. Ultimately these findings are expected to aid in planning wetland restoration projects to maximize carbon storage. Download a copy of the JGI wetlands handout.

Plant-microbe interactions

The interactions of plants with microbial communities found in the endosphere and rhizosphere (within plant tissues and adjacent to the roots) have been shown to be critical to plant growth, health and disease resistance and manipulation of these organisms could potentially improve yields of both bioenergy and food crops.  Yet how these communities form and to what extent plants exert active control over the organisms involved is largely unknown, and genomic investigation of endophytic and rhizosphere microbes has been largely confined to culture-based methods due to both the challenges associated with soil metagenomics described above, and the close association with plant cells which harbor large and complex genomes.  In close collaboration with Jeff Dangl at the University of North Carolina, we are addressing these obstacles with high-throughput 16S profiling of rhizosphere and endophyte communities combined with single cell genomics, metagenomics and metatranscriptomics to characterize key plant-associated microbes, using Arabidopsis thaliana as a plant model system.  These investigations have revealed reproducible rhizosphere and endophyte community assemblage and plant genotype-specific associations with rhizosphere organisms. Ultimately, this work will allow us to identify genes, proteins and molecules involved in plant-microbe and microbe-microbe interactions in the plant root environment.

Group Members

lr_susannah_tringe_wetlands Jinglie Zhou Shwetha Acharya Kyle Hartman
Susannah Green Tringe, PI Jinglie Zhou, Postdoc Shwetha Acharya, Postdoc Kyle Hartman, Postdoc
More about Susannah. Jinglie received his Ph.D. degree in biological science from Auburn University. His research interests include metagenomic analysis, viral genome analysis, carbon cycling in wetlands and arbuscular mycorrhizal fungi associating with sorghum roots. He also has a background in bioinformatics, machine learning, data engineering and statistics. Shwetha holds a Ph.D. in Urban Engineering from The University of Tokyo and specializes in water and wastewater microbiology. She is investigating microbial communities involved in biological treatment of produced water.
Kyle completed his Ph.D. at the University of Zürich and Agroscope, a Swiss federal research institute. His current research uses DNA sequence-based methods to investigate how nutrient and water stress influence host-microbe and microbe-microbe interactions in sorghum-associated microbial communities.

 

Mo Kaze Xiaohui Li
Mo Kaze, Affiliate Xiaohui Li, Affiliate
Mo Kaze is finishing up her PhD at the University of California, Merced in Quantitative Systems Biology. Her DOE SCGSR Fellowship project at JGI examines carbon flux and microbial community structure in engineered interfaces between aquatic and terrestrial systems. Xiaohui is a visiting scholar from Ningbo University, China. He is interested in mechanisms of interaction between plants and microorganisms. At JGI, he is investigating the rhizosphere microbiome of sorghum in order to clarify their roles in plant abiotic stress.

Group Alumni

  • Dawn Chiniquy is a Project Scientist in the Deutschbauer lab at Lawrence Berkeley National Laboratory
  • Devin Coleman-Derr is Principal Investigator at the Plant Gene Expression Center (devin.coleman-derr@ars.usda.gov)
  • Filipa Godoy-Vitorino is currently Assistant Professor at the Inter American University of Puerto Rico (filipagodoyvitorino@gmail.com)
  • Wyatt Hartman is a Soil Microbiome Data Scientist at Trace Genomics.
  • Susanna Theroux is an Ecologist at the Southern California Coastal Water Research Project.
  • Julien Tremblay is Bioinformatician at National Research Council Canada (jtremblay514@gmail.com)
  • Qingpeng Zhang is a Staff Data Scientist at Illumina.

Publications

  1. Sieber, CMK., AJ  Probst, A Sharrar, BC Thomas, M Hess, SG Tringe, JF Banfield.  Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nature Microbiology, 3: 836-843, 2018. doi: 10.1038/s41564-018-0171-1. (Co-corresponding author)
  2. Hartman, WH, R Ye, WR Horwath, SG Tringe. A genomic perspective on stoichiometric regulation of soil carbon cycling. ISME Journal 11: 2652-2665, 2017. doi:10.1038/ismej.2017.115
  3. Singer, E, D Coleman-Derr, B Bowman, B Bushnell, E Gies, JF Cheng, A Copeland, S Hallam, SG Tringe, T Woyke (2016) High-resolution phylogenetic microbial community profiling. ISME Journal. doi: 10.1038/ismej.2015.249.
  4. Tremblay, J, K Singh, A Fern, ES Kirton, S He, J Lee, T Woyke, F Chen, JL Dangl, SG Tringe (2015) Primer and platform effects on 16S rRNA tag sequencing. Frontiers in Microbiology 6: 771. doi: 10.3389/fmicb.2015.00771.
  5. Nobu, MK, T Narihiro, C Rinke, Y Kamagata, SG Tringe, T Woyke, WT Liu (2015) Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME Journal 9: 1710-1722. doi: 10.1038/ismej.2014.256.
  6. He, S, SA Malfatti, JW McFarland, FE Anderson, A Pati, M Huntemann, J Tremblay, T Glavina del Rio, M Waldrop, L Windham-Myers, SG Tringe (2015) Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions. Mbio 6: e00066-15. doi: 10.1128/mBio.00066-15.

    ORCiD link – https://orcid.org/0000-0001-6479-8427

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