Recent Poole Group publications

  • Ledermann, R., Schulte, C. C. M. & Poole, P. S. (2021) How bacteria adapt to the nodule environment. J. Bact.
  • Pardo-Diaz, J., Bozhilova, L. V.,  Beguerisse-Díaz, M., Poole, P. S., Deane, C. M. & Reinert G. (2021) Robust gene coexpression networks using signed distance correlation. Bioinformatics.
  • Knights, H. E., Jorrín, B., Haskett, T. L. & Poole, P. S. (2021) Deciphering bacterial mechanisms of root colonization. Environmental Microbiology Reports
  • Raittz, R. T., Reginatto De Pierri, C., Maluk, M., Bueno Batista, M., Carmona, M., Junghare, M., Faoro, H., Cruz, L. M., Battistoni, F., d’Souza, E., Pedrosa F. dO, Chen W.-M., Poole, P. S., Dixon, R. A. & James,  E. K.. (2021) Comparative Genomics Provides Insights into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera. Genes, 12:71.
  • Rutten, P. J., Steel, H., Hood, G. A., Ramachandran, V. K., McMurty, L., Geddes, B. A., Papachristodoulou, A. & Poole, P. S. (2021) Multiple sensors provide spatiotemporal oxygen regulation of gene expression in a Rhizobium-legume symbiosis. PLoS Genetics,
  • Haskett, T., Tkacz, A. & Poole, P. S. (2020) Engineering Bacteria for Sustainable Agriculture.ISME J.
  • Wheatley, R. M., Ford, B. L., Li, L., Aroney, S. T. N., Knights, H. E., Ledermann, R., East, A. K., Ramachandran, V. K. & Poole P. S. (2020) Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis. Proceedings of the National Academy of Sciences USA,
  • Tkacz, A. & Poole P. S. (2020) The dark and dirty secrets of plant growth. Plants, People, Planet
  • Rubia, M.I., Ramachandran, V.K., Arrese-Igor, C., Larrainzar, E. & Poole, P. S. (2020) A novel biosensor to monitor proline in pea root exudates and nodules under osmotic stress and recovery. Plant Soil.
  • Sánchez-Cañizares, C., Prell, J., Pini, F., Rutten, P., Kraxner, K., Wynands, B., Karunakaran, R. & Poole, P. S. (2020) Global control of bacterial nitrogen and carbon metabolism by a PTSNtr-regulated switch. Proceedings of the National Academy of Sciences USA, 12;117:10234-10245.
  • Mendoza-Suárez, M. A., Geddes, B. A., Sánchez-Cañizares, C., Ramírez-González, R. H., Kirchhelle, C., Jorrin, B. & Poole, P. S. (2020) Optimizing Rhizobium-legume symbioses by simultaneous measurement of rhizobial competitiveness and N2 fixation in nodules. Proceedings of the National Academy of Sciences USA, 5;117:9822-9831.
  • Tkacz, A., Pini, F., Turner, T. R., Bestion, E.,  Simmonds J., Howell P., Greenland, A., Cheema, J., Emms, D. M., Uauy, C. & Poole, P. S. (2020) Agricultural Selection of Wheat Has Been Shaped by Plant-Microbe Interactions. Front. Microbiol.,
  • Tkacz, A., Bestion, E.,  Bo, Z., Hortala, M. & Poole, P. S. (2020) Influence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom Comparison. mBio
  • Ryu, M-H., Zhang, J., Toth, T., Khokhani, D., Geddes, B.A., Mus, F., Garcia-Costas, A., Peters, J.W., Poole, P.S., Ané J.-M. & Voigt, C.A. (2019) Control of nitrogen fixation in bacteria that associate with cereals. Nature Microbiology, 
  • Rutten, P.J. & Poole, P.S. (2019) Oxygen regulatory mechanisms of nitrogen fixation in rhizobia. Advances in Microbial Physiology, 75:325-389.
  • Geddes, B.A., Paramasivan, P., Joffrin, A., Thompson, A.L., Christensen, K., Jorrin, B., Brett, P., Conway, S.J., Oldroyd, G.E.D. & Poole, P.S. (2019) Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria. Nature Communications, 
  • Green, R.T., East, A.K., Karunakaran, R., Downie, J.A. & Poole, P.S. (2019) Transcriptomic analysis of Rhizobium leguminosarum bacteroids in determinate and indeterminate nodules. Microbial Genetics. doi: 10.1099/mgen.0.000254.
  • Geddes, B.A., Mendoza Suárez, M.A. & Poole, P.S. (2019) A Bacterial Expression Vector Archive (BEVA) for Flexible Modular Assembly of Golden Gate-Compatible Vectors. Frontiers in Micobiology
  • Tkacz, A., Hortola, M. & Poole, P.S. (2018) Absolute quantitation of microbiota abundance in environmental samples. Microbiome. 6:110
  • Haskett, T. L., Terpolilli, J.J., Ramachandran, V.K.,  Verdonk, C.J., Poole, P.S., O’Hara, G.W. & Ramsay, J.P. (2018) Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements. PLoS Genet 14(3): e1007292.
  • Wheatley, R.M. & Poole, P.S. (2018) Mechanisms of bacterial attachment to roots. FEMS Microbiology Reviews. 42:448-461.
  • Poole, P.S., Ramachandran, V.K. & Terpolilli, J. (2018) Rhizobia: from saprophytes to endosymbionts. Nature Reviews Microbiology. 16:291-303.
  • Sanchez-Cañizares, C., Jorrín, B., Poole P. & Tkacz, A. (2017) Understanding the holobiont: the interdependence of plants and their microbiome. Current Opinion in Microbiology. 38:188-196.
  • Xu, J., Webb, I., Poole, P. & Huang, W.E. (2017) Label-Free Discrimination of Rhizobial Bacteroids and Mutants by Single-Cell Raman Microspectroscopy. Analytical Chemistry. 89(12):6336-6340.
  • Hood, G., Ramachandran, V.K., East, A.K., Downie, J.A. & Poole, P.S. (2017) Manganese transport is essential for N2 -fixation by Rhizobium leguminosarum in bacteroids from galegoid but not phaseoloid nodules. Environmental Microbiology. doi: 10.1111/1462-2920.13773
  • Pini, F., East, A.K., Appia-Ayme, C., Tomek, J.,  Karunakaran, R., Mendoza-Suárez, M., Edwards, A., Terpolilli, J., Roworth, J., Downie, J.A. & Poole, P.S. (2017) Lux bacterial biosensors for in vivo spatiotemporal mapping of root secretion. Plant Physiology 174: 1289-1306.
  • Westhoek, A, Field E., Rehling, F., Mulley, G., Webb, I., Poole, P.S. & Turnbull, L.A. (2017) Policing the legume-Rhizobium symbiosis: a critical test of partner choice. Scientific Reports 7: 1419 doi:10.1038/s41598-017-01634-2.
  • Poole, P.S. (2017) Shining a light on the dark world of plant root-microbe interactions. Proceedings of the National Academy of Sciences USA 114: 4281-4283.
  • Cheng, G., Karunakaran, R., East, A.K., Munoz-Azcarte, O. & Poole, P.S. (2017) Glutathione affects the transport activity of Rhizobium leguminosarum 3841 and is essential for efficient nodulation. FEMS Microbiology Letters 364 (8): fnx045.
  • Wheatley, R.M., Ramachandran, V.K., Geddes, B.A., Perry, B.J., Yost, C.K. & Poole, P.S. (2017) Role of O2 in the Growth of Rhizobium leguminosarum bv, viciae 3841 on Glucose and Succinate. J. Bacteriol. 199 (1) doi:10.1128/JB.00572-16.
  • Terpolilli, J.J, Masakapalli, S.K., Karunakaran, R., Webb, I.U., Green, R., Watmough, N.J., Kruger, N.J., Ratcliffe, R.G. & Poole, P.S. (2016) Lipogenesis and Redox Balance in Nitrogen-Fixing Pea Bacteroids. J. Bacteriol. 198(20):2864-75. doi: 10.1128/JB.00451-16.
  • Mus, F., Crook, M., Garcia, K., Garcia-Costas, A., Geddes, B., Diamanto Kouri, E., Paramasivan, P., Ryu, M-H., Oldroyd, G., Poole, P., Udvardi, M., Voigt, C., Ané, J-M. & Peters, J. (2106) Symbiotic Nitrogen Fixation and Challenges to Extending it to Non-Legumes. Appl. Environ. Microbiol. doi:10.1128/AEM.01055-16.
  • Cheng, G., Karunakaran, R., East, A.K. & Poole, P.S. (2016) Multiplicity of Sulfate and Molybdate Transporters and Their Role in Nitrogen Fixation in Rhizobium leguminosarum bv. viciae Rlv3841. Mol. Plant Microbe Interact. 29:143-52.
  • Prell, J., Poole, P., Untiet, V. & Karunakaran, R. (2015) The PTS-Ntr System Globally Regulates ATP-Dependent Transporters in Rhizobium leguminosarum. In Biologiacal Nitrogen Fixation Vol 1, Ed. F. J. de Bruijn, John Wiley & Sons Inc.pp 349-355.
  • Hood, G., Karunakaran, R., Downie, J.A. & Poole, P. (2015)  MgtE From Rhizobium leguminosarum Is a Mg2+ Channel Essential for Growth at Low pH and N2 Fixation on Specific Plants. Mol. Plant Microbe Interact. 28:1281-1287.
  • Tkacz, A. & Poole, P. (2015) Role of root microbiota in plant productivity. J. Exp. Bot. 66 (8): 2167-2175. This article appears in: Special Issue: Roots to Global Food Security
  • Tkacz, A., Cheema, J., Chandra, G., Grant, A. & Poole, P. S. (2015) Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. The ISME Journal doi:10.1038/ismej.2015.41
  • Geddes, B.A., Ryu, M-H., Mus, F., Garcia Costas, A., Peters, J.W., Voigt, C.A. &  Poole, P. (2015) Use of plant colonizing bacteria as chassis for transfer of N2-fixation to cereals. Current Opinion in Biotechnology 32: 216-222.
  • Garcia-Fraile, P., Seaman, J.C., Karunakaran, R., Edwards, A., Poole, P.S. & Downie, J.A. (2015Arabinose and protocatechuate catabolism genes are important for growth of Rhizobium leguminosarum biovar viciae in the pea rhizosphere. Plant and Soil 390: 251-264.
  • Frederix, M., Edwards, A., Swiderska, A., Stanger, A., Karunakaran, R., Williams, A., Abbruscato, P., Sanchez-Contreras, M., Poole, P.S. & Downie, J.A. (2014) Mutation of praR in Rhizobium leguminosarum enhances root biofilms, improving nodulation competitiveness by increased expression of attachment proteins. Molecular Microbiology 93: 464-78.
  • Tett, A.J., Karunakaran, R. & Poole, P.S. (2014) Characterisation of SalRAB a salicylic acid inducible positively regulated efflux system of Rhizobium leguminosarum bv viciae 3841. PLoS One 9(8):e103647.
  • Terpolilli, J., Rui, T., Yates, R., Howieson, J., Poole, P., Munk, C., Tapia, R., Han, C., Markowitz, V., Tatiparthi, R., Mavrommatis, K., Ivanova, N., Pati, A., Goodwin, L., Woyke, T., Kyrpides, N. & Reeve, W. (2013) Genome sequence of Rhizobium leguminosarum bv trifolii strain WSM1689, the microsymbiont of the one flowered clover Trifolium uniflorum. Standards in Genomic Science 31;9(3): 527-39.
  • Turner, T.R., Karunakaran, R., Walshaw, J., Heavens, D., Alston, M., Swarbreck,D., Osbourn, A., Grant, A. & Poole, P.S. (2013) Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. The ISME Journal 7: 2248-2258.
  • Karunakaran, R., East, A.K. & Poole, P.S. (2013) Malonate catabolism does not drive nitrogen fixation in legume nodules. Applied and Environmental Microbiology 79 (14): 4496-4498.
  • Untiet, V., Karunakaran, R., Maria Krämer, M., Poole, P., Priefer, U. & Prell, J. (2013) ABC transport is inactivated by the PTSNtr under potassium limitation in Rhizobium leguminosarum 3841. PLoS One 8(5):e64682.
  • Turner, T.R, James, E.K. & Poole, P.S. (2013) The plant microbiome. Genome Biology 14: 209-218.
  • Udvardi, M. & Poole, P.S. (2013). Transport and Metabolism in Legume Root Nodules. Annual Review of Plant Biology 64: 781-805.
  • Zhang, Y., Aono, T., Poole, P. & Finan, T.M. (2012) NAD(P)+-malic enzyme mutants of Sinorhizobium sp. strain NGR234, but not Azorhizobium caulinodans ORS571, maintain symbiotic N2 fixation capabilities. Applied and Environmental Microbiology 78: 2803-2812.
  • Tett, A.J., Rudder, S.J., Bourdes, A., Karunakaran, R. & Poole, P.S. (2012) Regulatable vectors for environmental gene expression in Alphaproteobacteria. Applied and Environmental Microbiology 78: 7137-7140.
  • Bourdès, A., Rudder, S., East, A.K. & Poole, P.S. (2012) Mining the Sinorhizobium meliloti transportome to identify FRET biosensors for sugars, dicarboxylates and aromatic compounds. PLoS One 7 (9) e43578.
  • Tett, A., Turner, T. & Poole, P.S. (2012). Genomics and the Rhizosphere. Encyclopaedia of Life Sciences inivited review DOI:10.1002/9780470015902.a0023728
  • Terpolilli, J., Hood, G. & Poole, P.S. (2012). What determines the efficiency of N2-fixing Rhizobium-legume symbioses? Advances in Microbial Physiology 60: 326-389.
  • Prell, J., Mulley, G., Haufe, F., White, J.P., Williams, A., Karunakaran, R., Downie, J.A. & Poole P.S. (2012) The PTSNtr system globally regulates ATP-dependent transporters in Rhizobium leguminosarum. Molecular Microbiology 84:117-129.
  • Ramachandran, V., East, A.K., Karunakaran, R., Downie, J.A. & Poole, P.S. (2011) Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Genome Biology 12:R106.
  • Oldroyd, G.E.D., Murray, J.D., Poole, P.S. & Downie, J.A. (2011). The rules of engagement in the legume-rhizobial symbiosis. Annual Review of Genetics 45: 119-144.
  • Mulley, G., White, J.P., Karunakaran, R., Prell, J., Bourdès, A., Bunnewell, S., Hill, L., Chandra, G. & Poole, P. S. (2011) Mutation of GOGAT prevents pea bacteroid formation and N2 fixation by globally down-regulating transport of organic nitrogen sources. Molecular Microbiology 80: 149-167.
  • Prell, J., Bourdès, A., Kumar, S., Lodwig, E., Hosie, A., Kinghorn, S., White, J. & Poole, P.S. (2010) Role of symbiotic auxotrophy in the Rhizobium-legume symbioses. PLoS One 5(11):e13933.
  • Karunakaran, R., Haag, A.F., East, A.K., Ramachandran, V.K., Prell, J., James, E.K., Scocchi, M., Ferguson, G.P. & Poole, P.S. (2010) BacA is essential for bacteroid development in nodules of galegoid, but not phaseoloid, legumes. Journal of Bacteriology 192: 2920-2928.
  • Prell, J., White, J.P., Bourdès, A., Bunnewell, S., Bongaerts, R.J. & P. S. Poole (2009) Legumes regulate Rhizobium bacteroid development and persistence by the supply of branched-chain amino acids. Proceedings of the National Academy of Sciences USA 106, 12477-12482.
  • Karunakaran, R., Ramachandran, V.K., Seaman, J.C., East, A.K., Moushine, B., Mauchline, T.H., Prell, J., Skeffington, A. & Poole, P.S. (2009) Transcriptomic analysis of Rhizobium leguminosarum biovar viciae in symbiosis with host plants Pisum sativum and Vicia cracca. Journal of Bacteriology 191, 4002-4014.
  • Mulley, G. Lopez-Gomez, M., Zhang, Y., Terpolilli, J., Prell, J., Finan, T. & Poole, P.S (2010) Pyruvate is synthesized by two pathways in pea bacteroids with different efficiencies for nitrogen fixation. Journal of Bacteriology 192: 4944-4953.
  • Prell, J.P., Bourdès, A., Karunakaran, R., Lopez-Gomes, M. & Poole, P. (2009) Pathway of GABA metabolism in Rhizobium leguminosarum 3841 and its role in symbiosis. Journal of Bacteriology 191, 2177-2186.
  • East, A.K., Mauchline, T.H. & Poole, P.S. (2008) Biosensors for ligand detection. Advances in Applied Microbiology 64,137-166.
  • White, J.P., Prell, J., Ramachandran, V.K. & Poole P.S. (2009) Characterization of a GABA transport system of Rhizobium leguminosarum bv viciae 3841. Journal of Bacteriology 191, 1547-1555.
  • Fox, M.A., Karunkaran, R., Leonard, M.E., Moushine, B., Williams, A., East, A.K., Downie, J.A. & Poole, P.S. (2008) Characterisation of the quaternary amine transporters of Rhizobium leguminosarum bv. viciae 3841. FEMS Microbiology Letters 287, 212-220.
  • Barr, M, East A.K., Leonard, M., Mauchline, T. & Poole, P.S. (2008) In vivo expression technology (IVET) selection of genes of Rhizobium leguminosarum biovar viciae A34 expressed in the rhizosphere. FEMS Microbiology Letters 282, 219-227.
  • White, J., Prell, J., James, E.K. and Poole, P. (2007) Nutrient sharing between symbionts. Plant Physiology 144, 604-614.
  • Mauchline, T.H., Fowler, J.E., East, A.K., Sartor, A.L., Zaheer, R., Hosie, A.H.F., Poole, P.S. & Finan, T. M. (2006) Mapping the Sinorhizobium meliloti 1021 solute binding protein-dependent transportome. Proceedings of the National Academy of Sciences USA 103, 17933-17938.
  • Karunakaran, R., Ebert, K., Harvey, S., Leonard, M.E., Ramachandran, V. & Poole, P.S. (2006) Thiamine is synthesized by a salvage pathway in Rhizobium leguminosarum bv viciae strain 3841. Journal of Bacteriology 188, 6661-6668.
  • Young, J.P.W et al. (2006) The genome of Rhizobium leguminosarum has recognisable core and accessory components. Genome Biology 7, R34.
  • Prell, J. & Poole, P.S. (2006) Metabolic changes in rhizobia. Trends in Microbiology 141: 161-168.
  • Fox, M.A., White, J.P., Hosie, A.H F., Lodwig, E.M. & Poole, P.S. (2006). Osmotic upshift transiently inhibits uptake via ABC transporters in Gram-negative bacteria. Journal of Bacteriology 188, 5304-5307.
  • Kumar, S., Bourdès, A. & Poole, P.S. (2005) De novo alanine synthesis by bacteroids of Mesorhizobium loti is not required for nitrogen transfer in the determinate nodules of Lotus corniculatus. Journal of Bacteriology. 187: 5493-5495.
  • Karunakaran, R., Mauchline, T.H., Hosie, A.H, Poole, P.S. (2005) A family of promoter probe vectors incorporating autofluorescent and chromogenic reporter proteins for studying gene expression in Gram-negative bacteria. Microbiology 151: 3249-3256.
  • Lodwig, E.M., Leonard, M., Marroqui, S.M., Wheeler,T.R., Findlay, K., Downie, J.A. & Poole, P.S. (2005) Role of polyhydroxybutyrate and glycogen as carbon storage compounds in pea and bean bacteroids. Molecular Plant Microbe Interaction 18: 67-74.
  • Lodwig, E.M., Kumar, S., Allaway, D., Bourdès, A., Prell, J., Priefer, U. & Poole, P.S. (2004) Regulation of L-alanine dehydrogenase in Rhizobium leguminosarum bv. viciae and its role in pea nodules. Journal of Bacteriology 186: 842-849.
  • Lodwig, E.M., Hosie, A.H.F., Bourdes, A., Findlay, K., Karunakaran, R., Downie, J.A.& Poole, P.S. (2003) Amino-acid cycling drives nitrogen fixation in the legume-Rhizobium symbiosis. Nature 422: 722-726.
  • Lodwig, E.M. & Poole, P.S. (2003) Metabolism in legume nodules. CRC Reviews in Plant Sciences 22: 37-78.

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