NorthenLab: Exometabolomics linking genomes with environments to understand how webs of microbes sustain biomes

New papers highlight metabolomics contributions to JGI research

The JGI metabolomics group and Northen Lab members (including Katherine Louie, Benjamin Bowen, Andrea Kuftin, and Trent Northen) have contributed to multiple recent papers. Some of the highlights include the following:

Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism [1]

Sphagnum (or peat moss) forms symbiotic relationships with cyanobacteria, and these interactions affect carbon and nitrogen cycling. To study this relationship, LCMS was used to analyze exometabolomic results of metabolic cross-feeding experiments. 

Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan [2]

Thermoflexus hugenholtzii is the only cultured bacteria from Thermoflexales, an order of bacteria that occupy geothermal systems. To further understand it, various -omics approaches were explored, including targeted exometabolomics. Supernatants from Thermoflexus media were used to determine substrates and products of the bacteria’s growth. 

Metabolomic Patterns of Septoria Canker Resistant and Susceptible Populus trichocarpa Genotypes 24 Hours Postinoculation [3]

Sphaerulina musiva is a fungal pathogen that causes stem canker and leaf spot disease in Populus (cottonwood) trees. The colonization of Sphaerulina was examined through metabolic analysis of small molecules found in resistant and susceptible polar plants after inoculation. 

Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE [4]

Phenazines are an important compound family that have a variety of effects, from antibacterial to anticancer properties. Biosynthetic gene clusters that produce phenazine derivatives (PCA and PDC) were integrated into 23 bacterial species using CRAGE. Production of derivatives was measured using LCMS. 

Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes [5]

Xylariales are an order of endophytic fungi with a broad range of hosts, including land plants and lichens. Secondary metabolite gene clusters across 96 Xylariales genomes were examined, and metabolomic analysis was conducted on products of the fungi. 

References:

  1. Carrell, A. A., Veličković, D., Lawrence, T. J., Bowen, B. P., Louie, K. B., Carper, D. L., Chu, R. K., Mitchell, H. D., Orr, G., Markillie, L. M., Jawdy, S. S., Grimwood, J., Shaw, A. J., Schmutz, J., Northen, T. R., Anderton, C. R., Pelletier, D. A., & Weston, D. J. (2021). Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism. The ISME Journal, 16(4), 1074–1085. https://doi.org/10.1038/s41396-021-01136-0
  2. Thomas, S. C., Payne, D., Tamadonfar, K. O., Seymour, C. O., Jiao, J. Y., Murugapiran, S. K., Lai, D., Lau, R., Bowen, B. P., Silva, L. P., Louie, K. B., Huntemann, M., Clum, A., Spunde, A., Pillay, M., Palaniappan, K., Varghese, N., Mikhailova, N., Chen, I. M., . . . Hedlund, B. P. (2021). Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021.632731
  3. Lenz, R. R., Louie, K. B., Søndreli, K. L., Galanie, S. S., Chen, J. G., Muchero, W., Bowen, B. P., Northen, T. R., & LeBoldus, J. M. (2021). Metabolomic Patterns of Septoria Canker Resistant and Susceptible Populus trichocarpa Genotypes 24 Hours Postinoculation. Phytopathology®, 111(11), 2052–2066. https://doi.org/10.1094/phyto-02-21-0053-r
  4. Ke, J., Zhao, Z., Coates, C. R., Hadjithomas, M., Kuftin, A., Louie, K., Weller, D., Thomashow, L., Mouncey, N. J., Northen, T. R., & Yoshikuni, Y. (2022). Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE. Metabolic Engineering, 69, 188–197. https://doi.org/10.1016/j.ymben.2021.11.012
  5. Franco, M. E. E., Wisecaver, J. H., Arnold, A. E., Ju, Y., Slot, J. C., Ahrendt, S., Moore, L. P., Eastman, K. E., Scott, K., Konkel, Z., Mondo, S. J., Kuo, A., Hayes, R. D., Haridas, S., Andreopoulos, B., Riley, R., LaButti, K., Pangilinan, J., Lipzen, A., Louie, K., Northen, T., . . . U’Ren, J. M. (2021). Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes. New Phytologist, 233(3), 1317–1330. https://doi.org/10.1111/nph.17873