Genomics of Plant-Microbial Interactions Group

Advances 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 LBL^2,3 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 types^6,7. 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 organisms^8,9.

 

Research Team

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

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.