Publications – Lab of Ann Hirsch

Martínez-Hidalgo P, Humm EA, Baochen S, Pellegrini M, de la Roca G, Still D, Veliz E, Kosty M, Maymon M, Bru P, Huntemann M, Clum A, Foster B, Foster B, Roux S, Palaniappan K, Varghese N, Mukherjee S, Reddy TBK, Daum C, Copeland A, Ivanova NN, Kyrpides NC, Shapiro N, Eloe-Fadrosh EA, Hirsch AM. Medicago root nodule microbiomes: Insights into a complex ecosystem with potential candidates for plant growth promotion. Plant and Soil. In review.

Youseif SH, Abd El-Megeed FH, Humm EA, Maymon M, Mohamed H, Saleh SA, Hirsch A. 2021. Comparative analysis of the cultured and total bacterial community in the wheat rhizosphere microbiome using culture-dependent and culture-independent approaches. Microbiology Spectrum. https://doi.org/10.1128/Spectrum.00678-21.

Kouas S, Khan N, Hirsch AM. 2021. The hologenome hypothesis and its application to plant-microbe interactions on an evolutionary scale. In: Microbes: The Foundation Stone of the Biosphere. C.J. Hurst (ed.), Springer Nature. Chapter 21, pp. 425-440. DOI: 10.1007/978-3-030-63512-1_21.

Elissiry LJ, Sun J, Hirsch AM, Liu C. 2021. Silica sol-gene microbead encapsulation as a novel delivery method for symbiotic microbes. ChemRxiv. https://doi.org/10.26434/chemrxiv.13277495.

Kosty M, Pule-Meulenberg F, Humm EA, Maymon M, Mohammadi S, Cary J, Yang P, Reddi K, Huntemann M, Clum A, Foster B, Foster B, Roux S, Palaniappan K, Varghese N, Mukherjee S, Reddy TBK, Daum C, Alex Copeland A, Ivanova NN, Kyrpides NC, Shapiro N, Eloe-Fadrosh EA, Hirsch AM. 2020. Isolation of potential plant growth-promoting bacteria (PGPB) from nodules of legumes grown in arid Botswana soils. BioRxiv. Publ. 9.2.2020. https://doi.org/10.1101/2020.09.02.257907.

Khan N, Martínez-Hidalgo P, Humm EA, Maymon M, Kaplan D, Hirsch AM. 2020. Inoculation with a microbe isolated from the Negev Desert enhances corn growth. Front. Microbiol. Vol. 11. https://doi.org/10.3389/fmicb.2020.01149.

Primo ED, Cossovich S, Nievas F, Bogino P, Humm EA, Hirsch AM , Giordano W. 2019. Exopolysaccharide production in Ensifer meliloti laboratory and native strains and their effects on alfalfa inoculation. Arch. Microbiol. https://doi.org/10.1007/s00203-019-01756-3.

Amaya-Gómez, C.V., Hirsch, A.M., and Soto, M.J. 2015. Biofilm formation assessment in Sinorhizobium meliloti reveals interlinked control with surface motility. BMC Microbiology, 15:58 doi:10.1186/s12866-015-0390-z

Sanders, E.R., and Hirsch, A.M. 2014. 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. doi: 10.3389/fpls.2014.00157. eCollection 2014.

Angus, A.A., Agapakis, C.M., Fong, S., Yerrapragada, S., Estrada-de los Santos, P., Yang, P., et al. (2014). Plant-associated symbiotic Burkholderia species lack hallmark strategies required in mammalian pathogenesis. PLoS ONE, 9(1), e83779. doi:10.1371/journal.pone.0083779

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., Valdés, M. (2013). Complete genomesequence of Micromonospora Strain L5, a potential plant-growth-regulating actinomycete, originally isolated from Casuarina equisetifolia root nodules. Genome Announc, 1(5). pii: e00759-13. doi: 10.1128/genomeA.00759-13

Martínez-Aguilar, L., Salazar-Salazar, C., Méndez, R.D., Caballero-Mellado, J., Hirsch, A.M., Vásquez-Murrieta, M.S., Estrada-de los Santos, P. (2013). Burkholderia caballeronis sp. nov., a nitrogen fixing species isolated from tomato (Lycopersicon esculentum) with the ability to effectively nodulate Phaseolus vulgaris. Antonie Van Leeuwenhoek, 104(6):1063-71. doi: 10.1007/s10482-013-0028-9

Kaplan, D., Maymon, M., Agapakis, C.M., Lee, A., Wang, A., Prigge, B.A., Volkogon, M., Hirsch, A.M. (2013). A survey of the microbial community in the rhizosphere of two dominant shrubs of the Negev Desert highlands, Zygophyllum dumosum (Zygophyllaceae) and Atriplex halimus (Amaranthaceae), using cultivation-dependent and cultivation-independent methods. Am J Bot, 00(9):1713-25. doi: 10.3732/ajb.1200615

Estrada-de los Santos, P., Vinuesa, P., Martínez-Aguilar, L., Hirsch, A.M., Caballero-Mellado, J. (2013). Phylogenetic analysis of burkholderia species by multilocus sequence analysis. Curr Microbiol, 67(1):51-60. doi: 10.1007/s00284-013-0330-9

Robledo, M., Rivera, L., Jiménez-Zurdo, J.I., Rivas, R., Dazzo, F., Velázquez, E., Martínez-Molina, E., Hirsch, A.M., Mateos, P.F. (2012). Role of Rhizobium endoglucanase CelC2 in cellulose biosynthesis and biofilm formation on plant roots and abiotic surfaces. Microb Cell Fact, 11:125. doi: 10.1186/1475-2859-11-125

Shigeyama, T., Tominaga, A., Arima, S., Sakai, T., Inada, S., Jikumaru, Y., Kamiya, Y., Uchiumi, T., Abe, M., Hashiguchi, M., Akashi, R., Hirsch, A.M., Suzuki, A. (2012). Additional cause for reduced JA-Ile in the root of a Lotus japonicus phyB mutant. Plant Signal Behav. 7(7):746-8. doi: 10.4161/psb.20407

Suzuki, A., Suriyagoda, L., Shigeyama, T., Tominaga, A., Sasaki, M., Hiratsuka, Y., Yoshinaga, A., Arima, S., Agarie, S., Sakai, T., Inada, S., Jikumaru, Y., Kamiya, Y., Uchiumi, T., Abe, M., Hashiguchi, M., Akashi, R., Sato, S., Kaneko, T., Tabata, S., Hirsch, A.M. (2011). Lotus japonicus nodulation is photomorphogenetically controlled by sensing the red/far red (R/FR) ratio through jasmonic acid (JA) signaling. Proc Natl Acad Sci U S A, 108(40):16837-42. doi: 10.1073/pnas.1105892108

Gyaneshwar, P., Hirsch, A.M., Moulin, L., Chen, W.M., Elliott, G.N., Bontemps, C., Estrada-de Los Santos, P., Gross, E., Dos Reis, F.B., Sprent, J.I., Young, J.P., James, E.K. (2011). Legume-nodulating betaproteobacteria: diversity, host range, and future prospects. Mol Plant Microbe Interact, 24(11):1276-88. doi: 10.1094/MPMI-06-11-0172

Hirsch, A.M., Lee, A., Deng, W., Tucker, S.C. (2010) An open-flower mutant of Melilotus alba: Potential for floral-dip transformation of a papilionoid legume with a short life cycle? Am J Bot, 97(3):395-404. doi: 10.3732/ajb.0900152

Angus, A.A., Hirsch, A.M. (2010) Insights into the history of the legume-betaproteobacterial symbiosis. Mol Ecol. 19(1):28-30. doi: 10.1111/j.1365-294X.2009.04459.x

Tominaga, A., Nagata, M., Futsuki, K., Abe, H., Uchiumi, T., Abe, M., Kucho, K., Hashiguchi, M., Akashi, R., Hirsch, A.M., Arima, S., Suzuki, A. (2009). Enhanced nodulation and nitrogen fixation in the abscisic acid low-sensitive mutant enhanced nitrogen fixation1 of Lotus japonicus. Plant Physiol, 151(4):1965-76. doi: 10.1104/pp.109.142638

De Hoff, P.L., Brill, L.M. and Hirsch, A.M. (2009). Plant lectins: the ties that bind in root symbiosis and plant defense. Mol. Gen. Genom. 282:1-15. DOI 10.1007/s00438-009-0460-8

Hirsch, A.M., Lum, M.R. and Fujishige, N.A. (2009). Microbial encounters of a symbiotic kind — attaching to roots and other surfaces. In: Emons, A.M.C. and T. Ketelaar (eds.). Root Hairs. Plant Cell Monographs. Vol. 12. Pp. 295-314. DOI 10.1007/7089_2008

Hirsch, A.M. and Fujishige, N.A. (2008). Commensalism. In: Population Dynamics, Vol. 1, Encyclopedia of Ecology, 5 Vols. Eds. S.E. Jorgensen and B. D. Fath. Elsevier, Oxford. pp. 679-683.

Lee, A., Giordano, W., and Hirsch, A.M. (2008). Cytokinin induces expansin gene expression in Melilotus alba Desr. wild-type and the non-nodulating, non-mycorrhizal (Nod-Myc-) mutant Masym3. Plant Signal. Behavior. 3:218-223.

Fujishige, N.A., Lum, M.R., De Hoff, P.L., Whitelegge, J.P., Faull, K.F., and Hirsch, A.M. (2008). Rhizobium common nod genes are required for biofilm formation. Mol. Microbiol. 67:504-515.

Suzuki, A., Hara, H., Kinoue, T., Abe,, M., Uchiumi, T., Kucho, K., Higashi, S., Hirsch, A.M., and Arima, S. (2008). Split-root study of autoregulation of nodulation in the model legume Lotus japonicus. J. Plant Res. 121:245-249.

Woo, H.-H., Jeong, B.R., Hirsch, A.M., and Hawes, M.C. (2007). Altered expression of closely related UDP-glycosyltransferases from pea and Arabidopsis results in altered root development and function. Physiol. Plant. 130:250-260.

Woo, H.-H., Jeong, B.R., Hirsch, A.M., and Hawes, M.C. (2007). Characterization of Arabidopsis gene families related to pea UDP-glycosyltransferase and Scutellaria glucuronidase. Genomics 90:143-153.

Lee, A., Lum, M.R. and Hirsch, A.M. (2007). ENOD40 gene expression and cytokinin responses in the non-nodulating non-mycorrhizal (Nod-Myc-) mutant, Masym3, of Melilotus alba Desr. Plant Signal. Behav. 2:33-42.

Lum, M.R., Baycher, A., Prigge, B.A., Hardy, M., Heber, D., and Hirsch, A.M. (2007). Identification of green tea (Camellia sinensis L.) and tea oil (Camellia oleifera Abel.) by molecular biological and anatomical methods. In: Authentication of Food and Wine, S. E. Ebeler, G. R. Takeoka, P. Winterhalter, eds. Oxford University Press. pp. 290-304.

Lee, A. and Hirsch, A.M. (2006). Signals and responses: choreographing the complex interaction between legumes and alpha- and beta-rhizobia. Plant Signal. Behavior. 1:161-168.

Rinaudi, L., Fujishige, N.A., Hirsch, A.M. 2006, Banchio, E., Zorreguieta, and Giordano, W. (2006). Effects of nutritional and environmental conditions on Sinorhizobium meliloti biofilm formation. Res. Microbiol. 157:867-875.

Fujishige, N.A., Kapadia, N.N., De Hoff, P.L., and Hirsch, A.M. (2006). Investigations of Rhizobium biofilm formation. FEMS Microbiol. Ecol. 56:195-205.

Fujishige, N.A., Kapadia, N.N. and Hirsch, A.M. (2006). A feeling for the microorganism: structure on a small scale. Biofilms on plant roots. Bot. J. Linn. Soc. 150:79-88.

Luckow, M., Hughes, C., Schrire, B., Pedley, L., Fagg, C., Fortunato, R., Hurter, J., Rico, L., Bruneau, A., Caccavari, M., Crisp, M., Delgado S., A., Doyle, J.J., Harris, S., Herendeen, P.S. Hernandez, H.M., Hirsch, A.M., Jobson, R., Klitgaard, B.B., Simpson, B.B., Smith, G.F., Sousa S., M., Timberlake, J., Wills, C.K., Winter, P., and Wojciechowski, M.F. (2005). Acacia: the case against moving the type to Australia. Taxon. 54:513-519.

Lum, M., Potter, E., Dang, T., Heber, D., Hardy, M., and Hirsch, A.M. (2005). Identification of botanicals and potential contaminants through RFLP and sequencing. Planta Med. 71:841-846.

Valdés, M., Pérez, N.-O., Estrada-de los Santos, P., Caballero-Mellado, J., Normand , P., and Hirsch, A.M. (2005) Non- Frankia actinomycetes isolated from surface-sterilized roots of Casuarina equisetifolia possess nifH sequences. Appl. Environ. Microbiol. 71: 460-466.

Hirsch, A.M., Lum, M.R., Giordano, W.F., Fujishige, N.A., and Woo, H.-H. (2004). Changes elicited by Rhizobium inoculation in expression of genes influenced by phytohormone levels. In: Biology of Molecular Plant-Microbe Interaction, Vol. 4 , eds: B. Lugtenberg, I. Tikhonovich, N. Provorov, IS-MPMI, St. Paul, Minnesota, USA, pp. 383-388.

Hirsch, A.M. (2004). Plant-microbe symbioses: a continuum from commensalism to parasitism. Symbiosis. 37:345-363.

Wen, F., Woo, H.H., Hirsch, A.M., and Hawes, M.C. 2004. Lethality of inducible, meristem localized ectopic expression of ß-glucuronidase in plants. Plant Mol. Biol. Rep. 22:7-14.

Wildman, S.G., Hirsch, A.M., Kirchanski, S.J., and Spencer, D. (2004). Chloroplasts in living cells and the string-of-grana concept of chloroplast structure revisited. Photosyn. Res.80:345-352.

Giordano, W. and Hirsch, A.M. (2004). The expression of MaEXP1, a Melilotus alba expansin gene is up-regulated during the sweetclover- Sinorhizobium meliloti interaction. Mol. Plant-Microbe Inter.17:613-622.

Woo, H.-H., Hirsch, A.M., and Hawes, M.C. (2004). Altered susceptibility to infection by Sinorhizobium meliloti and Nectria haematococcain alfalfa roots with altered cell cycle. Plant Cell Rep. 12:967-973.

Lum, M.R. and Hirsch, A.M. (2004). Overcoming fixed nitrogen deficiency by nodulation. In : R.M. Goodman (ed.). Encyclopedia of Crop and Plant Sciences. Marcel Dekker, Inc., NY. pp. 448-451.

Brill, L.M., Fujishige, N.A., Hackworth, C.A. and Hirsch A.M. (2004). Expression of MsLEC1 -transgenes in alfalfa plants causes symbiotic abnormalities. Mol. Plant-Microbe Inter. 17:16-26.

Woo, H.- H., Faull, K.F., Hirsch, A.M., and Hawes, M.C. (2003). Altered life cycle in Arabidopsis thalianaplants expressing PsUGT1, a UDP-glucuronosyltransferase encoding gene from Pisum sativum. Plant Physiol.133:538-548.

Lum, M.R, and Hirsch, A.M. (2003). Roots and their symbiotic microbes: strategies to obtain nitrogen and phosphorous in a nutrient-limiting environment. J. Plant Growth Regul. 21:368-382.

Karlowski, W.M. and Hirsch, A.M. (2003). The overexpression of an alfalfa RING-H2 gene induces pleiotropic effects on plant growth and development. Plant Mol. Biol. 52: 121-133.

De Hoff, P. and Hirsch, A.M. (2003). Nitrogen comes down to earth. Report from the 5 th European Nitrogen Fixation Conference. Mol. Plant-Microbe Inter. 16:371-375.

Hirsch, A.M., Bauer, W.D., Bird, D.M., Cullimore, J., Tyler, B., and Yoder, J.I. (2003). Molecular signals and receptors – controlling rhizosphere interactions between plants and other organisms. Ecology. 84: 858-868.

Giordano, W., Lum, M.R., and Hirsch, A.M. (2002). Effects of a Nod-factor overproducing strain of Sinorhizobium meliloti on the expression of the ENOD40 gene in Melilotus alba. Can. J. Bot. 80: 907-915.

Leroy, A., Potter, E., Woo, H.-H., Heber, D., and Hirsch, A.M. (2002). PCR-based identification of degraded DNA and monitoring of flavonoids isolated from alfalfa and red clover commercial preparations used as botanicals in dietary supplements. J. Agr. Food Chem. 50: 5063-5069.

Hirsch, A.M., Krupp, R.S.N., Lin, Y., Wang, S.S., Yang, W., and Tucker, S.C. (2002). Inflorescence and flower development in wild-type and sid mutant Melilotus alba, white sweetclover. Can. J. Bot. 80: 732-740.

Lum, M., Li, Y., LaRue, T.A., Schwartz, R.D., Kapulnik, Y. and Hirsch, A.M. (2002). Investigation of four non-nodulating mutants of white sweetclover (Melilotus alba annua Desr.) mutants and their response to arbuscular-mycorrhizal fungi. Int. Comp. Biol. 42: 113-121.

Woo, H.-H., Kuleck, G., Hirsch, A.M., and Hawes, M.C. (2002). Flavonoids: signal molecules in plant development. Adv. Exp. Med. Biol. 505:51-60.

Youseif SH, Abd El-Megeed FH, Humm EA, Maymon M, Mohamed H, Saleh SA, Hirsch AM. 2021.Comparative analysis of the cultured and total bacterial community in the wheat rhizosphere microbiome using culture-dependent and culture-independent approaches. Microbiology Spectrum. https://doi.org/10.1128/Spectrum.00678-21.