Later, we began to investigate what-are-known as "non-traditional" nitrogen fixers, the newly discovered beta-rhizobia, as well as the plants associated with them. Because many of these bacteria exhibit metabolic activities, such as cellulose degradation as well as nodulation and nitrogen fixation (in the case of the beta-rhizobia), they have the potential, not only to be used for enhancing nitrogen nutrition in crop plants, especially as increased energy costs result in greater fertilizer expenditures, but also in the production of biofuels. To this end, I coordinated the sequencing and annotation of four Burkholderia genomes, including a species that nodulates agronomically important legumes growing in arid and acidic soils. In addition, two Micromonospora (actinobacteria) genomes were sequenced and these data are published. Micromonospora is an important Plant Growth Promoting Bacterial (PGPB) species. My lab has also determined that symbiotic Burkholderia spp. are unlikely pathogens based on bioinformatics analyses and by employing HeLa cell and Caenorhabditis elegans assays to determine non-pathogenicity. We recently published on the different arrangement of nodulation and nitrogen fixation genes in the plant-associated Burkholderia versus the well-studied alpha rhizobial species.
Because my research has always focused on the ?hidden half? of the plant, i.e. the root, and especially on the beneficial interactions that take place between plant roots and microbes in the rhizosphere microbiome, I made the transition early on to working on plant microbiomes. In so doing, we began to investigate a broader range of plant-growth promoting bacteria (PGPB), which are associated with roots, especially those isolated from arid environments. Our rationale is that as the climate changes, agricultural productivity will decline because crop-growing regions will become drier and less fertile. Novel drought-adapted, nitrogen-fixing bacteria are likely to provide genetic traits that increase both nutrient availability and environmental tolerance to salinity and drought brought about by reduced rainfall, higher soil acidity, and increased temperatures. In addition, many PGPB are effective at inhibiting plant pathogens, either directly by killing the pathogens or indirectly by making plants healthier so they can overcome pathogen infection. Moreover, a combination of nitrogen-fixing bacteria and one or more PGPB, such as Micromonospora or Bacillus spp., enhance plant growth and yield beyond single inoculation. The development of microbial consortia for plant inocula is the next direction of research that the Hirsch lab is pursuing. The microbes that inhabit nitrogen-fixing nodules grown in field conditions are the best way to determine which bacteria are compatible with another and could be used to establish consortia. My lab is also pursuing metagenomic and cultivation-dependent analysis of dryland soils as a means to find novel bacteria for inoculum development. We have licensed our discoveries from the Negev Desert (Israel) research, and we have a pending agreement with an agricultural company that is developing novel inocula to replace chemical amendments for certain crops. Studies in other deserts and dry environments are also in place.
De Meyer SE, Briscoe L, Martinez-Hidalgo P, Agapakis CM, Estrada de-los Santos P, Seshadri R, Reeve W, Weinstock G, O'Hara G, Howieson J, Hirsch AM., "Symbiotic Burkholderia species show diverse arrangements of nif/fix and nod genes, and lack typical high affinity cytochrome cbb3 oxidase genes", Mol. Plant-Microbe Interact 29: 609-619 (2016). [link]
Nagata M, Yamamoto N, Miyamoto T, Shimomura A, Arima S, Hirsch AM, Suzuki A. 2016. Enhanced hyphal growth of arbuscular mycorrhizae by root exudates derived from high R/FR treated Lotus japonicus., "Enhanced hyphal growth of arbuscular mycorrhizae by root exudates derived from high R/FR treated Lotus japonicus", Plant Signal. Behav 11: 1-3 (2016). [link]
Shimomura A, Naka A, Miyazaki N, Moriuchi S, Arima S, Sato S, Hirakawa H, Tabata S, Hayashi M, Maymon M, Hirsch AM, Suzuki A., "Blue light perception by both roots and rhizobia inhibits nodule formation in Lotus japonicus", Molecular Plant-Microbe Interactions 29: 786-796 (2016). [link]
Sanders ER, Moberg-Parker J, Hirsch AM, Lee PY, Shapiro C, Toma S, Levis-Fitzgerald M., "Transforming laboratory education in the life sciences", Microbe 11: 69-74 (2016).
Nagata, M., Yamamoto, N., Shigeyama, T. Terasawa, Y., Anai, T., Sakai, T., Inada, S., Arima, S., Hashiguchi M., Akashi, R., Hirsch, A.M., Suzuki, A, "Red/far red light controls mycorrhizal colonization via jasmonic acid and strigolactone secretion", Plant Cell Physiol 56: 2100-2109 (2015). [link]
Maymon M, Martínez-Hidalgo P, Tran SS, Ice T, Craemer K, Anbarchian T, Sung T, Chou M, Hwang L, Fujishige NA, Ventosa J, Villella W, Sikorski J, Faull KF, Sanders ER. Hirsch AM., "Mining the phytomicrobiome to understand how bacterial coinoculations enhance plant growth", Frontiers in Plant Science 6: 1-14 (2015). [link]
Amaya-Gomez, C.V., Hirsch, A.M., and Soto, M.J., ", "Biofilm formation assessment in Sinorhizobium meliloti reveals interlinked control with surface motility", BMC Microbiology 15: 1-147 (2015). [link]
Estrada-de los Santos P, Rojas-Rojas FU, Tapia-García EY, Vásquez-Murrieta MS, Hirsch AM., "To split or not to split: an opinion on dividing the genus Burkholderia", Ann. Microbiol 66: 1303-1314 (2015). [link]
Tariq M, Lum MR, Chong AW, Amirapu AB, Hameed S, Hirsch AM., "A reliable method for the selection and confirmation of transconjugants of plant growth-promoting bacteria especially plant-associated Burkholderia spp", J. Microbiol. Methods 117: 49-53 (2015). [link]
Coutinho Moraes, D.F., Still D., Lum, M.R., Hirsch, A.M., "DNA-based authentication of botanicals and plant-derived dietary supplements: where have we been and where are we going?", Planta Medica 81: 687-695 (2015). [link]
Nagata, M., Hirsch, A.M., and Suzuki, A., "Lotus japonicum nodulates when it sees red. Chapter 44", In: Biological Nitrogen Fixation 2: 441-445 (2015).
Walker, R., Agapakis, C.M., Watkin, E., and Hirsch, A.M., "Symbiotic nitrogen fixation in legumes: perspectives on the diversity and evolution of nodulation by Rhizobium and Burkholderia species. Chapter 89", In: Biological Nitrogen Fixation, Volume 2 2: 913-923 (2015).
Angus, A.A., Agapakis, C.M., Fong, S., Yerrapragada, S., Estrada-de los Santos, P., Yang, P., Song, N., Kano, S., Caballero-Mellado, J., de Faria, S.M., Dakora, F.D., Weinstock, G., and Hirsch, A.M., "Plant-associated symbiotic Burkholderia species lack hallmark strategies required in mammalian pathogenesis", PLoS ONE 9 (1): 1-12 (2014). [link]
Sanders, E.R., and Hirsch, A.M., "Immersing undergraduate students into research on the metagenomics of the plant rhizosphere: a pedagogical strategy to engage civic-mindedness and retain undergraduates in STEM", Front. Plant Sci 5 (57): 1-4 (2014).
Hirsch, A.M., Alvarado, J., Bruce, D., Chertkov, O., De Hoff, P.L., Detter, J.C., Fujishige, N.A., Goodwin, L.A., Han, J., Han, S., Ivanova, N., Land, M.L., Lum, M.R., Milani-Nejad, N., Nolan, M., Pati, A., Pitluck, S., Tran, S.S., Woyke, T. and Valdés, M., "Complete genome sequence of Micromonospora strain L5, a potential plant-growth-regulating actinomycete, originally isolated from Casuarina equisetifolia root nodules", Genome Announc 1: 1-2 (2013). [link]