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 large-scale genetic screening methodologies to explore plant-microbial interactions, with a particular interest in genetic components allowing microbes to infect the interior and surface of plant root systems. This work will afford us a better understanding of plant/microbe communication and symbiosis, and ultimately allow us to engineer microbial strains with enhanced features important for the sustainable production of biofuel feedstocks. We are also interested in understanding cis-regulatory control of spatial gene expression in plants, and are building a functional genomics pipeline to identify novel promoter and enhancer elements driving tissue-specific gene expression. This work will allow us to target engineering strategies to tissues most likely to benefit from modification.
Summer Graduate Fellow
Summer Graduate Fellow
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
- 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
- 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.
- 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
- 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.
- 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.
- 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.