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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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    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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    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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    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)
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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)
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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)
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Home › Our Science › Science Programs & Platforms Leads › Genomics of Plant-Microbial Interactions Group

Genomics of Plant-Microbial Interactions Group

JGI_PlantlogoAdvances in microbiome research have led to a wealth of genetic information about how human and animal gut microbial communities become established and develop. Soil ecosystems are also richly populated by bacterial and fungal species either beneficial or detrimental to the growth of cohabitating plants. Plant growth-promoting microbes offer an opportunity to positively affect plant biomass production by allowing more efficient mineral usage, increasing disease defense, and directly stimulating growth. We are applying genetic screening methodologies to explore plant-microbial interactions, targeting genetic components that allow microbes to infect the interior and surface of plant root systems1. In coordination with other large-scale efforts at LBL2,3 these studies will help functionally annotate previously uncharacterized genomes using experimental evidence. In addition to screening, we have also applied 16S and metagenome sequencing strategies to explore the microbial landscape of drought-adapted plants (e.g. Agave)4,5. These studies have provided insight into common principles in plant colonization by soil bacteria, as well as laid a foundation for how those bacteria behave in severe environmental conditions. Overall, our work is aimed at providing a better understanding of plant/microbe communication and symbiosis, with the goal to ultimately allow us to engineer microbial strains with enhanced features important for the sustainable production of biofuel feedstocks.

Mutant strains of a root colonizing bacteria compete with a luciferase-producing strain when colonizing Arabidopsis roots

A genome-wide map of bacterial root colonization

Single-cell characterization of plant/microbial systems

Far from being monolithic entities, plants and their associated microbiomes are highly heterogeneous composites of cells, cell types, and microenvironments. Using cutting-edge single-cell characterization techniques (e.g. single-cell RNA-sequencing, spatial transcriptomics, and others), we are exploring plant and microbial behavior at single-cell precision. An initial characterization of Arabidopsis thaliana using single-cell transcriptomics revealed unique properties of root cell types6,7. We are extending these technologies to explore interactions between plants and arbuscular mycorrhizal fungi (AMF) in exquisite detail, with the goal of identifying key components that affect AM symbiosis under nutrient deficiency or drought. Apart from exploring plants or plant/microbial interaction, we are also working with community members to explore novel applications of single-cell technology for other environmental organisms8,9.

 

Research Team

axel-science-group
Axel Visel
Group Leader
More about Axel.
Benjamin Cole
Research Scientist
More about Benjamin.
Jonelle Basso
Research Scientist
Margot Bezrutczyk
Postdoctoral Researcher

Research Team Alumni

2_cr_Sabah Sai Prahabkar, 2017 UC Merced BLUR intern in Visel Lab
Keedrian
Olmstead

Alumnus, 
UCM Distinguished
Summer 
Graduate Fellow
Sabah Ul-Hasan
Alumnus, UCM Distinguished
Summer 
Graduate Fellow
Sai Prahabkar
Alumnus, UCM
Undergraduate Fellow

Candace Cole
Distinguished
Summer
Graduate Fellow

Brenda Yu
Alumnus, UCM Undergraduate Fellow

Lamprinos Frantzeskakis
Postdoctoral
Researcher

More About Axel

In addition to research on plant-microbial interactions, Dr. Visel is a member of the JGI Strategic Management team and leads a research program in Mammalian Functional Genomics in the Environmental Genomics and Systems Biology Division at Lawrence Berkeley National Laboratory.

Selected Plant/Microbial Publications

(for other publications, see Mammalian Functional Genomics or PubMed.)

  1. Cole, B.J., Feltcher, M.E., Waters, R.J., Wetmore, K.M., Mucyn, T.S., Ryan, E.M., Wang, G., Ul-Hasan, S., McDonald, M., Yoshikuni, Y., Malmstrom, R.R., Deutschbauer, A.M., Dangl, J.L., Visel, A., (2017). Genome-wide identification of bacterial plant colonization genes. PLOS Biol. 15, e2002860. https://doi.org/10.1371/journal.pbio.2002860
  2. Coleman‐Derr, D., Desgarennes, D., Fonseca‐Garcia, C., Gross, S., Clingenpeel, S., Woyke, T., North, G., Visel, A., Partida‐Martinez, L.P., Tringe, S.G. (2016). Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol. 209, 798–811. https://doi.org/10.1111/nph.13697
  3. Gross, S.M., Martin, J.A., Simpson, J., Abraham-Juarez, M.J., Wang, Z., Visel, A., (2013). De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. BMC Genomics 14, 563. https://doi.org/10.1186/1471-2164-14-563
  4. Mukherjee, S., Seshadri, R., Varghese, N.J., Eloe-Fadrosh, E.A., Meier-Kolthoff, J.P., Göker, M., Coates, R.C., Hadjithomas, M., Pavlopoulos, G.A., Paez-Espino, D., Yoshikuni, Y., Visel, A., Whitman, W.B., Garrity, G.M., Eisen, J.A., Hugenholtz, P., Pati, A., Ivanova, N.N., Woyke, T., Klenk, H.-P., Kyrpides, N.C., (2017). 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nat. Biotechnol. 35, 676–683. https://doi.org/10.1038/nbt.3886
  5. Price, M.N., Wetmore, K.M., Waters, R.J., Callaghan, M., Ray, J., Liu, H., Kuehl, J.V., Melnyk, R.A., Lamson, J.S., Suh, Y., Carlson, H.K., Esquivel, Z., Sadeeshkumar, H., Chakraborty, R., Zane, G.M., Rubin, B.E., Wall, J.D., Visel, A., Bristow, J., Blow, M.J., Arkin, A.P., Deutschbauer, A.M., (2018). Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 557, 503–509. https://doi.org/10.1038/s41586-018-0124-0
  6. C. N. Shulse, B. J. Cole, D. Ciobanu, J. Lin, Y. Yoshinaga, M. Gouran, G. M. Turco, Y. Zhu, R. C. O’Malley, S. M. Brady, D. E. Dickel, High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types. Cell Rep. 27, 2241-2247.e4 (2019)
  7. Shahan, R, Hsu, CW, Nolan, TM, Cole, BJ, Taylor, IW, Vlot, AHC, Benfey, PN, Ohler, U. A single cell Arabidopsis root atlas reveals developmental trajectories in wild type and cell identity mutants. bioRxiv 2020.06.29.178863; doi: https://doi.org/10.1101/2020.06.29.178863 (2020)
  8. Cole BJ, Basso JTR, Visel A. Power in isolation: insights from single cells. Nat Rev Microbiol. 18(7):364. doi: 10.1038/s41579-020-0381-4. (2020)
  9. Cole, B., Bergmann, D., Blaby-Haas, CE., Blaby, IK., Bouchard, KE., Brady, SM., Ciobanu, D., Coleman-Derr, D., Leiboff, S., Mortimer, JC., Nobori, T., Rhee, SY., Schmutz, J., Simmons, BA., Singh, AK., Sinha, N., Vogel, JP., O’Malley, RC., Visel A., Dickel, DE. Plant single-cell solutions for energy and the environment. Comm. Biol. 4:962 (2021)
  10. Ngan CY, Wong CH, Choi C, Yoshinaga Y, Louie K, Jia J, Chen C, Bowen B, Cheng H, Leonelli L, Kuo R, Baran R, García-Cerdán JG, Pratap A, Wang M, Lim J, Tice H, Daum C, Xu J, Northen T, Visel A, Bristow J, Niyogi KK, Wei CL (2015). Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae. Nature Plants 1: 15107, doi:10.1038/nplants.2015.107
  11. Ivanova NN, Schwientek P, Tripp HJ, Rinke C, Pati A, Huntemann M, Visel A, Woyke T, Kyrpides NC, Rubin EM (2014).  Stop codon reassignments in the wild.  Science 344:909-13.
  12. Lewis SM, Gross S, Visel A, Kelly M, Morrow W (2014).  Fuzzy GIS-based multi-criteria evaluation for US Agave production as a bioenergy feedstock.  GCB Bioenergy advance online, doi: 10.1111/gcbb.12116
  13. Shi W, Moon CD, Leahy SC, Kang D, Froula J, Kittelmann S, Fan C, Deutsch S, Gagic D, Seedorf H, Kelly WJ, Atua R, Sang C, Soni P, Li D, Pinares-Patiño CS, McEwan JC, Janssen PH, Chen F, Visel A, Wang Z, Attwood GT, Rubin EM (2014). Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome.  Genome Research advance online, pii: gr.168245.113.
  14. Gross SM, Martin JA, Simpson J, Abraham-Juarez MJ, Wang Z, Visel A (2013). De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. BMC Genomics 14, 563.
  15. Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM (2011). Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331, 463-7.
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