Rothamsted Research

where knowledge grows


Penny Hirsch

Senior Research Scientist
Sustainable Agriculture Sciences Harpenden

Current Research Interests.

 My group investigates soil microbial ecology in agricultural systems focusing both on rhizosphere interactions and also considering wider soil functions that support plant health and productivity including nitrogen cycling. We use molecular approaches to link population size and diversity with relevant functions, increasingly by using metagenomic approaches. The Rothamsted long-term field experiments provide an invaluable resource for such studies and we have several international collaborations to expand the scope of this research, including metagenomic library construction, high throughput sequencing and the use of microarrays. Areas of interest extend from denitrification and nitrification in soil, to interactions between the root colonizing bacteria and fungi, especially those with potential to control plant parasitic nematodes. We also have an interest in the genetic structure of soil microbial populations, in particular the distribution of genetic elements within different constituent populations.

Recent findings:

  • When soil that was originally permanent grassland is deprived of plant inputs for > 50 years by frequent tilling, with a consequent reduction of soil carbon, soil fauna and microbial abundance, the genetic diversity of microbial communities remains at a similar level to that in the original grassland. We speculate that we are observing the underlying diversity of bacterial communities that survive on recalcitrant C, revealed when the more abundant phyla that rely on simple plant-derived carbohydrates are diminished.
  • Metagenomic seqeuqnce data from these soils indicates differences in community composition.
  • Denitrification rates may depend on soil moisture, carbon and nitrogen content but the genetic diversity of denitrifying bacteria is similar in arable soils under different long-term fertilizer inputs. However there are distinct differences when cultivation ceases and soils revert to grass or woodland.
  • The population structure of ammonia oxidizing bacteria differs in plots receiving different long-term N additions, and that a growth response to NH4 can be seen six weeks after fertilizer addition, although nitrification starts rapidly and is not directly proportional to population size.
  • There is no clear difference in rhizosphere populations of potatoes with an anti-fungal root-expressed transgene compared to parental lines and another potato cultivar, whereas there were distinct differences between plants +/- AM fungi.
  • Microscale sampling of bacteria on roots reveals that communities are less abundant at the apex compared to basal regions of the root, that there is less genetic diversity on the root compared to bulk soil, and that microcolony density is inversely correlated with root pH (joint research with Tony Miller)
  • The nematophagous fungus Pochonia chlamydosporia shows genetic diversity depending on geographic and host nematode origin, and biotypes show host preference associated with polymorphism in a serine protease implicated in infection of nematode eggs. However, saprotrophic competitiveness may not relate to parasitic activity in the rhizosphere of nematode infected plants.
  • Pochonia chlamydosporia genes associated with nematode egg infection, including the serine protease gene vcp1, show differential expression depending on nutrient availability, indicating that the carbon and nitrogen content of soil amendments may influence parasitic activity of the fungus.
+44 (0) 1582 763 133 ext: +44 1582 938669
Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ
Past Projects
Principal Investigator
  • BBSRC Quota Studentship: Evaluation of the nematicidal properties of the cysteine proteinases EP-B2 from barley and actinidin from kiwi fruits
Project Leader
  • Nutrient regulation of the saprotroph to parasite transition in Pochonia chlamydopsoria, a soil microbial inoculant for nematode control
  • Soil microbial community function and diversity
  • The diversity, biology and dynamics of microbial agents that regulate nematode populations in the rhizosphere
  • BBSRC Quota Studentship: Assessment of the impact of biofuel crops on the physical distribution of soil organic matter (SOM)
  • BBSRC Studentship: Investigating the link between the production of extracellular polymeric substances from soil microbial biomass & soil structure
  • Lawes Trust Studentship: Is immunity of the non-target insect Scathophaga stercoraria enhanced by use of vetinary pharmaceuticals?
  • LAT Studentship: Analysis of Escherichia Coli O157 colonisation of the plant environment
  • Lawes Trust Studentship: Rhizobia diversity: the effect of farm management, soil type and environment
  • Optimisation of nutrients in soil-plant systems: How can we control nitrogen cycling in soil?
  • LAT studentship:The microbiology of lean and obese soil
  • The importance of the wheat root microbiome for plant health and crop yields
  • *Food waste voucher-An investig
  • Multitrophic interactions in the rhizosphere and the management of nematode pests and diseases
  • BBSRC CASE Studentship: Characterisation and bio-prospecting of endophytic bacterial microbes in wheat
  • Optimisation of nutrients in soil-plant systems: Determining how phosphorus availability is regulated in soils
  • *BBSRC Embrapa -U/standing whea

Hirsch PR, Jhurreea D, Williams JK, Murray PJ, Scott T, Misselbrook, TH, Goulding KWT, Clark IM. (2016). Soil resilience and recovery: rapid community responses to management changes. Plant and Soil.  doi:10.1007/s11104-016-3068-x


Mehrabi Z, McMillan VE, Clark IM, Canning G, Hammond-Kosack KE, Preston G, Hirsch PR & Mauchline TH (2016). Pseudomonas spp. diversity is negatively associated with suppression of the wheat take-all pathogen. Scientific Reports 6:29905.  DOI: 10.1038/srep29905.   


Jones FP, Clark IM, King R, Shaw LJ, Woodward MJ, Hirsch PR (2016). Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes – a genome comparison. Scientific Reports 6: 25858. 


Robinson RJ, Fraaije BA, Clark IM, Jackson RW, Hirsch PR, Mauchline TH (2016). Wheat seed embryo excision enables the creation of axenic seedlings and Koch’s postulates testing of putative bacterial endophytes. Scientific Reports 6: 25581.


Pylro VS, Morais DK, Kalks KHM, Roesch LFW, Hirsch PR, Tótola MR et al (2016). Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases. J Microbiol Methods 126: 18-23. doi:10.1016/j.mimet.2016.04.012


Morais D, Pylro V, Clark IM, Hirsch PR, Tótola MR. (2016) Responses of microbial community from tropical pristine coastal soil to crude oil contamination. PeerJ 4:e1733


Mauchline TH, Chedom-Fotso D, Chandra G, Samuels T, Greenaway N, Backhaus A, McMillan V, Canning G, Powers SJ, Hammond-Kosack KE, Hirsch PR, Clark IM, Mehrabi Z, Roworth J, Burnell J, Malone JG. (2015) An analysis of Pseudomonas genomic diversity in take-all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota. Environmental Microbiology, 17, 4764–4778. doi: 10.1111/1462-2920.13038.


Robinson RJ, Fraaije BA, Clark IM, Jackson RW, Hirsch PR, Mauchline TH (2015) Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type, developmental stage and soil nutrient availability. Plant and Soil doi:10.1007/s11104-015-2495-4.


Hirsch PR, Mauchline TH (2015) The Importance of the microbial N cycle in soil for crop plant nutrition. Advances in Applied  Microbiology 93: 45-71. doi: 10.1016/bs.aambs.2015.09.001. 


Liang Y, Wu L, Clark IM, Xue K, Yang Y, Van Nostrand J, Deng Y, He Z, McGrath S, Storkey J, Hirsch PR, Sun B, Zhou J. (2015) Over 150 years long-term fertilization alters spatial scaling of microbial biodiversity. MBio (6(2):e00240-15. doi:10.1128/mBio.00240-15.


Zhalnina K, Dias R, Dörr de Quadros P, Davis-Richardson A, Camargo FAO, Clark IM, McGrath SP, Hirsch PR, Triplett EW (2015) Soil pH determines microbial diversity and composition in the Park Grass Experiment Microbial Ecology 69: 395-406 DOI 10.1007/s00248-014-0530-2.


Manzanilla-López RH, Devonshire J, Ward E, Hirsch PR (2014) A combined cryo-scanning electron microscopy/cryoplaning approach to study the infection of Meloidogyne incognita eggs by Pochonia chlamydosporia. Nematology, 16: 1059 – 1067. 10.1163/15685411-00002830


Redmile-Gordon MA, Brookes PC, Evershed RP, Goulding KWT, Hirsch PR (2014) Measuring the soil-microbial interface: Extraction of extracellular polymeric substances (EPS) from soil biofilms. Soil Biology and Biochemistry, 72, 163-171. doi: 10.1016/j.soilbio.2014.01.025


Mauchline TH, Hayat R, Roberts R, Powers SJ, Hirsch PR (2014) Assessment of core and accessory genetic variation in Rhizobium leguminosarum symbiovar trifolii strains from diverse locations and host plants using PCR-based methods. Letters in Applied Microbiology 59: 238–246, doi: 10.1111/lam.12270


Redmile-Gordon MA, Armenise E; Hirsch PR, Brookes PC (2014) Biodiesel Co-Product (BCP) Decreases Soil Nitrogen (N) Losses to Groundwater. Water Air and Soil Pollution 225: doi: 10.1007/s11270-013-1831-7


Davies N, Field D, Amaral-Zettler L, Clark MS, Deck J, Drummond A, Faith DP, Geller J, Gilbert J, Glöckner FO, Hirsch PR, Leong JA, Meyer C, Obst M, Planes S, Scholin C, Vogler AP, Gates RD, Toonen R, Berteaux-Lecellier V, Barbier M, Barker K, Bertilsson S, Bicak M, Bietz MJ, Bobe J, Bodrossy L, Borja A, Coddington J, Fuhrman J, Gerdts G, Gillespie R, Goodwin K, Hanson PC, Hero JM, Hoekman D, Jansson J, Jeanthon C, Kao R, Klindworth A, Knight R, Kottmann R, Koo MS, Kotoulas G, Lowe AJ, Marteinsson VT, Meyer F, Morrison N, Myrold DD, Pafilis E, Parker S, Parnell JJ, Polymenakou PN, Ratnasingham S, Roderick GK, Rodriguez-Ezpeleta N, Schonrogge K, Simon N, Valette-Silver NJ, Springer YP, Stone GN, Stones-Havas S, Sansone SA, Thibault KM, Wecker P, Wichels A, Wooley JC, Yahara T, Zingone A (2014) The founding charter of the Genomic Observatories Network. GigaScience. 3: 1-5, doi: 10.1186/2047-217X-3-2.


Florio A, Clark IM, Hirsch PR, Jhurreea D, Benedetti A. (2014) Effects of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on abundance and activity of ammonia oxidizers in soil. Biology and Fertility of Soils doi: 10.1007/s00374-014-0897-8.


Redmile-Gordon MA, Armenise E, White RP, Hirsch PR, Goulding KWT. (2013). A comparison of two colorimetric assays, based upon Lowry and Bradford techniques, to estimate total protein in soil extracts. Soil Biology and Biochemistry, 67, 166-173. doi: 10.1016/j.soilbio.2013.08.017.


Pylro VS, Roesch LFW, Morais DK, Clark IM, Hirsch PR, Totola MR (2014) Data analysis for 16S microbial profiling from different benchtop sequencing platforms. J Microbiol Methods 107: 30-37 doi: 10.1016/j.mimet.2014.08.018


Pylro VS, Roesch LF, Ortega JM, do Amaral AM, Tótola MR, Hirsch PR, Rosado AS, Góes-Neto A, da Costa da Silva AL, Rosa CA, Morais DK, Andreote FD, Duarte GF, de Melo IS, Seldin L, Lambais MR, Hungria M, Peixoto RS, Kruger RH, Tsai SM, Azevedo V. (2013). Brazilian Microbiome Project: Revealing the Unexplored Microbial Diversity—Challenges and Prospects. Microbial Ecology: doi:10.1007/s00248-013-0302-4.


Hirsch, P.R., Mauchline, T.H., and Clark, I.M. (2013). Culture-independent molecular approaches to microbial ecology in soil and the rhizosphere. In: Molecular Microbial Ecology of the Rhizosphere Volume 1 & 2. Ed F.J. de Bruijn. John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9781118297674.ch5


Hirsch, P.R., Miller, A.J., and Dennis, P.G. (2013). Do root exudates exert more influence on rhizosphere bacterial community structure than other rhizodeposits? In: Molecular Microbial Ecology of the Rhizosphere Volume 1 & 2. Ed F.J. de Bruijn. John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9781118297674.ch22, pp. 229-242.


Cardenas, L.M., Hatch, D.J., Scholefield, D., Jhurreea, D., Clark, I.M., Hirsch, P.R., Salazar, F., Rao-Ravella, S. & Alfaro, M. (2013) Potential mineralization and nitrification in volcanic grassland soils in Chile. Soil Science and Plant Nutrition DOI:10.1080/00380768.2013.789395


Zhalnina K., de Quadros P.D., Gano K.A., Davis-Richardson A., Fagen J.R., Brown C.T., Giongo A., Drew J.C., Sayavedra-Soto L.A., Arp D.J., Camargo F.A.O., Daroub S.H., Clark I.M., McGrath S.P., Hirsch P.R. & Triplett E.W. (2013) Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments. Frontiers in Microbiology 4:104. doi: 10.3389/fmicb.2013.00104.


Manzanilla-Lopez, R. H., Esteves, I., Finetti-Sialer, M. M., Hirsch, P. R., Ward, E., Devonshire, J. & Hidalgo-Diaz, L. (2013). Pochonia chlamydosporia: Advances and challenges to improve its performance as a biological control agent of sedentary endo-parasitic nematodes. Journal of Nematology, 45, 1-7.


Hirsch, P.R. & Mauchline, T.H. (2012). Who’s who in the plant root microbiome? Nature Biotechnology 30: 961-962.


Hirsch, P.R. & Mauchline, T.H. (2012). Plant-microorganism mutualism. In: Microbial Ecological Theory. Eds L.A. Ogilvie & P.R. Hirsch. Caister Academic Press, Norfolk, UK. p. 43-55.


L.A. Ogilvie & P.R. Hirsch. (2012). Microbial Ecological Theory. Caister Academic Press, Norfolk, UK. pp 112.


Delmont, T.O., Prestat, E., Keegan, K.P., Faubladier, M., Robe, P., Clark, I.M., Pelletier, E., Hirsch, P.R., Meyer, F., Gilbert, J.A., et al. (2012). Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME Journal 6: 1677-1687.


Ward, E., Kerry, B.R., Manzanilla-López, R.H., Mutua, G., Devonshire, J., Kimenju, J. & Hirsch, P.R. (2012) The Pochonia chlamydosporia serine protease gene vcp1 is subject to regulation by carbon, nitrogen and pH: implications for nematode biocontrol. PLoS ONE (7: e35657).


Clark, I.M., Buchkina, N., Jhurreea, D., Goulding, K.W.T. & Hirsch, P.R. (2012) Impacts of nitrogen application rates on the activity and diversity of denitrifying bacteria in the Broadbalk Wheat Experiment. Philosophical Transactions of the Royal Society 367: 1235–1244.


Mohan, S., Mauchline, T.H., Rowe, J., Hirsch, P.R. & Davies, K.G. (2012) Pasteuria endospores from Heterodera cajani (Nematoda: Heteroderidae) exhibit inverted attachment and altered germination in cross-infection studies with Globodera pallida (Nematoda: Heteroderidae). FEMS Microbiology Ecology 79: 675–684.


Mauchline, T.H., Knox, R., Mohan, S., Powers, S.J., Kerry, B.R., Davies, K.G. & Hirsch, P.R. (2011) Identification of new single nucleotide polymorphism-based markers for inter- and intraspecies discrimination of obligate bacterial parasites (Pasteuria spp.) of invertebrates. Applied and Environmental Microbiology 77: 6388–6394.


Macdonald, C.A., Clark, I.M., Hirsch, P.R., Zhao, F-J. &, McGrath, S. P. (2011) Development of a real-time PCR assay for detection and quantification of Rhizobium leguminosarum bacteria and discrimination between different biovars in zinc-contaminated soil. Applied and Environmental Microbiology 77: 4626-4633.


Rosso, L.C., Finetti-Sialer, M.M., Hirsch, P.R., Ciancio, A., Kerry, B.R. & Clark, I.M. (2011) Transcriptome analysis shows differential gene expression in the saprotrophic to parasitic transition of Pochonia chlamydosporia. Applied Microbiology & Biotechnology 90:1981-1994.


Macdonald, C.A., Clark, I.M., Singh, B.K.,  Zhao, F-J., Hirsch, P.R. & McGrath, S. P. (2011) Long-term impacts of zinc and copper enriched sewage sludge additions on bacterial, archaeal and fungal communities in arable and grassland soils. Soil Biology & Biochemistry 43: 932-941.


Delmont,T.O., Robe P., Cecillon S., Clark, I.M., Constancias, F., Simonet, P., Hirsch, P.R. & Vogel, T.M. (2011) Accessing the soil metagenome for studies of microbial diversity. Applied and Environmental Microbiology 77: 1315-1324.


Powlson D.S., Gregory P.J., Whalley W.R., Quinton J.N., Hopkins D.W., Whitmore A.P., Hirsch, P.R. & Goulding K.W.T. (2011) Soil management in relation to sustainable agriculture and ecosystem services. Food Policy 36: S72-S87.


Ogilvie, L.A. & Hirsch, P.R (2010) Exploring microbial diversity - methods and meaning. In: Species Diversity and Extinction, ed. G.H. Tepper. Nova Science Publishers, Inc., NY p. 215-238.


Macdonald, C.A., Yang, X., Clark, I.M., Zhao, F-J., Hirsch, P.R. & McGrath, S. P. (2010) Relative impact of soil, metal source and metal concentration on bacterial community structure and community tolerance. Soil Biology & Biochemistry 42: 1408-1417.


Dennis ,P.G., Miller, A.J. & Hirsch, P.R. (2010) Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiology Ecology 72: 313-327.


Mauchline, T.H., Mohan, S., Davies, K.G., Kerry B.R. & Hirsch, P.R. (2010) A method for release and multiple strand amplification of small quantities of DNA from endospores of the fastidious bacterium Pasteuria penetrans. Letters in Applied Microbiology 50: 515-521.


Hirsch, P.R., Mauchline, T.H. & Clark, I.M. (2010) Culture-independent molecular techniques for soil microbial ecology. Soil Biology & Biochemistry 42: 878-887.


Hirsch, P.R., Gilliam, L.M., Sohi, S.P., Williams, J.K., Clark, I.M. & Murray, P.J. (2009) Starving the soil of plant inputs for 50 years reduces abundance but not diversity of soil bacterial communities. Soil Biology & Biochemistry 41: 2021-2024.


Vogel, T.M., Simonet, P., Jansson, J.K., Hirsch, P.R., Tiedje, J.M., van Elsas, J.D., Bailey, M.J., Nalin, R. & Philippot, L. (2009) TerraGenome: a consortium for the sequencing of a soil metagenome Nature Reviews Microbiology 7: 252.


Atkins, S.D, Peteira, B., Clark, I.M., Kerry, B.R. & Hirsch, P.R. (2009) Use of real-time quantitative PCR to investigate root and gall colonisation by co-inoculated isolates of the nematophagous fungus Pochonia chlamydosporia. Annals of Applied Biology 155: 143-152.


Manzanilla-López, R.H., Atkins, S.D., Clark, I.M., Kerry, B.R. & Hirsch, P.R. (2009) Measuring abundance, diversity and parasitic ability in two populations of the nematophagous fungus Pochonia chlamydosporia var. chlamydosporia. Biocontrol Science and Tecnhology 19: 391-406.


Manzanilla-López, R.H., Clark, I.M., Atkins, S.D., Hirsch, P.R. & Kerry, B.R. (2009) Rapid and reliable DNA extraction and PCR fingerprinting methods to discriminate multiple biotypes of the nematophagous fungus Pochonia chlamydosporia isolated from plant rhizospheres. Letters in Applied Microbiology 48: 71-76.


Dennis, P.G., Hirsch, P.R., Smith, S.J., Taylor, R.G., Valsami-Jones, E. & Miller, A.J. (2009) Linking rhizoplane pH and bacterial density at the microhabitat scale. Journal of Microbiological Methods 76: 101-104.


Dennis, P.G., Miller, A.J., Clark, I.M., Taylor, R.G., Valsami-Jones, E. & Hirsch, P.R. (2008). A novel method for sampling bacteria on plant root and soil surfaces at the microhabitat scale. Journal of Microbiological Methods 75: 12-18.


Ogilvie, L.A., Hirsch, P.R. & Johnston, A.W.B. (2008). Bacterial diversity of the Broadbalk 'Classical' winter wheat experiment in relation to long-term fertilizer inputs. Microbial Ecology 56: 525-537.


Clark, I.M. & Hirsch, P.R. (2008). Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted Broadbalk experiment. Soil Biology Biochemistry 40: 1090-1102.


Cookson, W.R., Marschner, P., Clark, I.M., Milton, N., Smirk, N; Murphy, D.V., Osman, M., Stockdale, E.A., Hirsch, P.R. (2006) The influence of season, agricultural management, and soil properties on gross nitrogen transformations and bacterial community structure. Australian Journal of Soil Research 44: 453-465.


Chilima, B.Z., Clark, E.M, Floyd, S., Fine, P.E.M. & Hirsch, P.R. (2006) The distribution of environmental mycobacteria in Karonga District, northern Malawi.  Applied and Environmental Microbiology 72, 2343-2350.


Lilley, A.K., Bailey, M.J., Cartwright, C., Turner, S.L. & Hirsch, P.R. (2006). Life in earth: the impact of GM plants on soil ecology?  Trends in Biotechnology 24, 9-14


Peteira, B., Puertas, A., Hidalgo-Díaz, L., Hirsch, P., Kerry, B. & Atkins, S. (2005). Real-time PCR to monitor and assess the efficacy of two types of inoculums of the nematophagous fungus Pochonia chlamydosporia var. catenulata against root-knot nematode populations in the field. Biotecnología Aplicada 22, 261266.


Abaye, D.A., Lawlor, K., Hirsch, P.R. & Brookes, P.C. (2005).  Changes in the microbial community of an arable soil caused by long-term metal contamination. European Journal of Soil Science 56, 93-102.


Atkins, S.D., Clark, I.M., Pande, S., Hirsch, P.R. & Kerry, B.R. (2005). The use of real-time PCR and species-specific primers for the identification and monitoring of Paecilomyces lilacinus  FEMS Microbiology Ecology 51, 257-264.


Hirsch, P.R. (2004)  Release of transgenic bacterial inoculants - rhizobia as a case study. Plant & Soil 266, 1-10.


Hirsch, P.R. & Clark, I.M. (2004)  Impact of genetically modified bacterial inoculants on the soil microbial community.  In: GM Crops - Ecological Dimensions. Ed. H.F. van Emden & A.J. Gray, pub. AAB, Warwick HRI, Wellesbourne. 141-153.


Morton, O.M., Hirsch, P.R. & Kerry, B.R. (2004)  Infection of plant-parasitic nematodes by nematophagous fungi - a review of the application of molecular biology to understand infection processes and to improve biological control.  Nematology 6, 161-170.


Mauchline, T.H., Kerry, B.R. & Hirsch, P.R. (2004)  The biocontrol fungus Pochonia chlamydosporia shows nematode host preference at the infraspecific level.  Mycological Research 108,161-169.


Atkins S.D., Mauchline, T.H., Kerry, B.R. & Hirsch, P.R. (2004)  Development of a transformation system for the nematophagous fungus Pochonia chlamydosporia. Mycological Research 108, 654-661.


O'Flaherty, S. M., Hirsch, P.R. & Kerry, B. R. (2003)  The influence of the root-knot nematode Meloidogyne incognita , the nematicide aldicarb and the nematophagous fungus Pochonia chlamydosporia on heterotrophic bacteria in soil and the rhizosphere. European Journal of Soil Science 54, 759-766.


Atkins, S. D., Clark, I. M., Sosnowska, D., Hirsch, P. R. & Kerry, B. R. (2003)  Detection and quantification of Plectosphaerella cucumerina , a potential biological control agent of potato cyst nematodes, by using conventional PCR, real-time PCR, selective media, and baiting. Applied and Environmental Microbiology 69, 4788-4793.


Morton, C. O., Hirsch, P. R., Peberdy, J. P. & Kerry B. R. (2003). Cloning of and Genetic Variation in the Protease VCP1 from the nematophagous fungus Pochonia chlamydosporia. Mycological Research 107: 38-46.


Morton, C. O., Mauchline, T. H., Kerry B. R. & Hirsch P. R. (2003).  PCR-based DNA fingerprinting indicates host related genetic variation in the nematophagous fungus Pochonia chlamydosporia. Mycological Research 107: 198-205.


Atkins, S.D., Hildago-Diaz, L., Kalisz, H., Mauchline, T.H., Hirsch, P.R. & Kerry, B.R. (2003) Development of a new management strategy for the control of root-knot nematodes (Meloiogyne spp.) in organic vegetable production. Pest Management Science 59: 183-189.


Kerry, B. R., Atkins, S. D., Gray, P., Hidalgo-Diaz, L., Hirsch, P. R., Mauchline, T. H. & Morton, C. O. (2003). How does Pochonia chlamydosporia limit populations of root-knot nematodes?. Journal of Nematology 35, 346.


Clark, I. M., Mendum, T. A. & Hirsch, P. R. (2002). The influence of the symbiotic plasmid pRL1J1 on the distribution of GM rhizobia in soil and crop rhizospheres, and implications for gene flow. Antonie van Leeuwenhoek 81, 607-616.


Mauchline, T. H., Kerry, B. R. & Hirsch, P. R. (2002). Quantification in soil and the rhizosphere of the nematophagous fungus Verticillium chlamydosporium by competitive PCR and comparison with selective plating. Applied and Environmental Microbiology 68, 1846-1853.


Mendum, T.A. & Hirsch, P.R. (2002). Changes in the population structure of beta-group autotrophic ammonia oxidising bacteria in arable soils in response to agricultural practice. Soil Biology Biochemistry 34, 1479-1485.


Brandt L, Feino Cunha J, Weinreich Olsen A, Chilima B, Hirsch P, Appelberg R, Andersen P. (2002)  Failure of the Mycobacterium bovis BCG vaccine: some species of environmental mycobacteria block multiplication of BCG and induction of protective immunity to tuberculosis. Infection and Immunity 70: 672-8


Powlson, D.S., Hirsch, P.R. & Brookes, P.C (2001) The role of soil microorganisms in soil organic matter conservation in the tropics.  Nutrient Cycling in Agroecosystems 61: 41-51.


Hirsch, P.R., Atkins, S.D., Mauchline, T.H., Morton, C.O., Davies, K.G. & Kerry, B.R. (2001)  Methods for studying the nematophagous fungus Verticillium chlamydosporium in the root environment.  Plant & Soil 232: 21-30.


Mendum, T.A., Clark, I.M & Hirsch, P.R. (2001) Characterization of two novel Rhizobium leguminosarum bacteriophages from a field release site of genetically-modified rhizobia.  Antonie van Leeuwenhoek 79: 189-197.


O'Flaherty, S., McGrath, S. & Hirsch, P. (2001)  Comparison of phenotypic, functional and genetic diversity of bacterial communities in soils. In: Sustainable Management of Soil Organic Matter.  Eds. R.M. Rees, B.C. Ball, C.D. Campbell and C.A. Watson.  CAB International.


Hirsch, P. R. & Micanovic, D. (2001). Understanding and exploiting interactions between nitrogen-fixing bacteria and plants.  In: Genetics and breeding of small grains. Eds S. A. Quarrie, V. Janjic, A. Atanassov, D. Knezevic & S. Stojanovic.  ARI-Serbia, Belgrade.


Atkins, S. D., Peberdy, J., Kerry, B. R. & Hirsch, P. R. (2000). Development of a transformation system for the root-knot nematode biological control fungus Verticillium chlamydosporium. In: Biology of plant-microbe interactions. Vol. 2  Eds P. J. G. M. de Wit, T. Bisseling & W. J. Stiekema.  International Society for Molecular Plant-Microbe Interactions, St Paul.


Lawlor, K., Knight, B.P., Barbosa-Jefferson, V.L., Lane, P.W., Lilley, A.K., Paton, G.I., McGrath, S.P., O'Flaherty, S.M. & Hirsch, P.R. (2000) Comparison of methods to investigate microbial populations in soils under different agricultural management. FEMS Microbiology Ecology 33, 129-137.


Van Elsas, J.D., Fry, J., Hirsch, P. & Molin, S. (2000) Ecology of plasmid transfer and spread. In: The horizontal gene pool. Ed. C.M. Thomas. Harwood Academic Publishers, Amsterdam.


Mendum, T.A., Chilima, B.Z. & Hirsch, P.R. (2000) The PCR amplification of non-tuberculous mycobacterial 16S rRNA sequences from soil. FEMS Microbiological Letters. 185: 189-192.


Hirsch, P.R., Mauchline, T.H., Mendum, T.A & Kerry, B.R. (2000) Detection of the nematophagous Verticillium chlamydosporium in nematode-infested plant roots using PCR. Mycological Research 104: 435-439.


Hirsch, P.R., Mendum, T.A., Pühler, A. & Selbistchka, W. (2000) The field release and monitoring of GUS-marked hizobial strain CT0370. In: Tracking Genetically Engineered Microorganisms: Method Development from Microcosms to the Field. Eds. J.K. Jansson, J.D. van Elsas & M. Bailey. R.G. Landes Co., Austin, Texas, USA.


Mendum, T.A., Sockett, R.E. & Hirsch, P.R. (1999) Use of molecular and isotopic techniques to monitor the response of autotrophic ammonia-oxidizing populations of the subdivision of the class Proteobacteria in arable soils to nitrogen fertilizer.  Applied Environmental Microbiology 65: 4155-4162.


Lawlor, K., Chaudri, A.M., McGrath, S.P. & Hirsch, P.R. (1999) Gene transfer in bacteria from soils contaminated with heavy metals.  Letters in Applied Microbiology 28: 317-320.


Mendum, T.A., Sockett, R.E. & Hirsch, P.R. (1998) The detection of Gram-negative bacterial mRNA from soil by RT-PCR FEMS Microbiology Letters 164: 369-373.


Cullen, D.W., Nicholson, P.S., Mendum, T.A. & Hirsch, P.R. (1998) Monitoring genetically-modified rhizobia in field soils using the polymerase chain reaction. Journal of Applied Microbiology 84:1025-1034.


Cullen,D.W. & Hirsch, P.R. (1998) A simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biology and Biochemistry 30: 983-993.


Nicholson, P.S. & Hirsch, P.R. (1998) The effects of pesticides on the diversity of culturable soil bacteria.  Journal of Applied Microbiology 84: 551-558.


Rengel, Z., Ross, G. & Hirsch, P. (1998) Colonisation of wheat roots by soil bacteria depends on the plant genotype and micronutrient nutrition. Journal of Plant Nutrition 21: 99-113.


Phillips, D.A., Joseph, C.M. & Hirsch, P.R. (1997) Occurrence of flavonoids and nucleosides in agricultural soils. Applied and Environmental Microbiology 63: 4573-4577.


Rengel, Z., Gutteridge, R., Hirsch, P., & Hornby, D. (1996)  Plant genotype, micronutrient fertilization and take-all infection influence bacterial populations in the rhizosphere of wheat.  Plant & Soil 183: 269-277.


Arora, D.K., Hirsch, P.R. & Kerry, B.R. (1996)  PCR-based molecular discrimination of Verticillium chlamydosporium isolates.  Mycological Research 100, 801-809.


Hirsch, P.R. (1996)  Population dynamics of indigenous and genetically modified rhizobia in the field.  New Phytologist 133, 159-171.


Hirsch, P.R. (1996)  Potential manipulation of crop rhizosphere. In: Genetic Engineering of Crop Plants for Resistance to Pests and Diseases. Eds. W.S. Pierpoint and P.R. Shewry.  British Crop Protection Council.


Hirsch, P.R. (1995) Detection of microbial DNA sequences by colony hybridization. Molecular Microbial Ecology Manual 2.6.1, 1-12.


Selbitschka, W., Jording, D., Nieman, S., Schmidt, R., Puhler, A., Mendum, T. & Hirsch, P. (1995)  Construction and characterization of a Rhizobium leguminosarum biovar viciae strain designed to assess horizontal gene transfer in the environment.  FEMS Microbiology Letters 128, 255-263.


Hirsch, P.R. (1995) Monitoring genetically modified microorganisms following field release. In: Unanswered safety questions when employing GMOs, CCRO, The Netherlands.


Hirsch, P.R. & Spokes, J.D. (1994) Survival and dispersion of genetically modified rhizobia in the field and genetic interactions with native strains. FEMS Microbiology Ecology 15, 147-160.


Hirsch, P.R., Jones, M.J., Mcgrath, S.P. & Giller, K.E. (1993) Heavy metals from past applications of sewage sludge decrease the genetic diversity of Rhizobium leguminosarum biovar trifolii populations. Soil Biology Biochemistry 25, 1485-1490.


Nicholson, P.S., Jones, M.J. & Hirsch, P.R. (1992) Monitoring survival of genetically-modified Rhizobium in the field.  In The Release of Genetically Modified Microorganisms.  Eds D.E.S. Stewart-Tull & M. Sussman.  Plenum Press, New York.


Hirsch, P.R. & Skinner, F.A. (1992) The identification and classification of Rhizobium and Bradyrhizobium.  In Identification Methods in Applied and Environmental Microbiology.  Eds R.G. Board, D. Jones & F.A. Skinner.  Blackwell Scientific Publications, Oxford, pp. 45-65.


Hirsch, P.R. (1990) Factors limiting gene transfer in bacteria.  In Bacterial genetics in natural environments.  Eds J.C. Fry & M.J. Day, Chapman & Hall, London, 1990.


Hirsch, P.R., O'connell, M., Boistard, P., Puhler, A, & Priefer, U.B. (1990)  European Laboratory Without Walls (ELWW) in the field of The Rhizobium-Legume Symbiosis.  Paperback 7 pp, ed. A. Vassarotti, Brussels CEC 1990.


Hirsch, P.R. (1990) Past, present and future uses of Rhizobium inoculants. Journal of the Science of Food and Agriculture 50, 130-131.


Giller, K.E., Mcgrath, S.P. & Hirsch, P.R. (1989) Absence of  nitrogen fixation in clover grown on soil subject to long-term contamination with heavy metals is due to survival of only ineffective Rhizobium. Soil Biology & Biochemistry 21, 841-848.


Kahn, D., David, M., Domergue, O., Daveran, M-L., Ghai, J., Hirsch, P.R. & Batut, J. (1989) Rhizobium meliloti fixGHI sequence predicts involvement of a specific cation pump in symbiotic nitrogen fixation. Journal of Bacteriology 171, 929-939.


Mcgrath, S.P., Hirsch, P.R. & Giller, K.E. (1988) Effect of heavy metal contamination on the genetics of nitrogen-fixing populations of Rhizobium leguminosarum nodulating white clover.  In:  Environmental Contamination, Venice, (ed. A.A. Orio).  C.E.P. Edinburgh.


Giller, K.E., Mcgrath, S.P. & Hirsch, P.R. (1988) Suppression of N2-fixation in clover on soil contaminated with heavy metals.  In  Nitrogen Fixation: Hundred Years After (Ed. H. Bothe, F.J. de Bruijn & W.E. Newton). Gustav Fischer, Stuttgart, New York


Hirsch, P.R., Giller, K.E. & Mcgrath, S.P. (1988) Rhizobia isolated from root nodules of clover grown on soils with heavy metal contamination. In Nitrogen Fixation: Hundred Years After (Ed. H. Bothe, F.J. de Bruijn & W.E. Newton). Gustav Fischer, Stuttgart, New York


Hirsch, P.R. (1988) Assessing the environmental risks of releasing genetically manipulated organisms.  In: Science and Change in  Agriculture, (J. Hardcastle, Ed.), AFRC.


Hirsch, P.R. & Spokes, J.R. (1988) Rhizobium leguminosarum as a model for investigating gene transfer in soil.  In: Risk Assessment for Deliberate Releases, ed. Walter Klingmu"ller.  Heidelberg: Springer Verlag, pp. 10-17.


Wang, C.L. & Hirsch, P.R. (1988) Mutation, transfer and location of symbiotic genes of Rhizobium leguminosarum biovar phaseoli by insertion of Tn5-mob. Acta Genetica Sinica 15:25-33.


Hirsch, PR; Wang, CL; Beringer, JC. 1987. Instability in Rhizobium leguminosarum strains carrying 2 symbiotic plasmids. Heredity 59: 310-310, Part 2.


Hirsch, P.R., Wang, C.L. & Woodward, M.J. (1986) Construction of a Tn5 derivative determining resistance to gentamicin and spectinomycin using a fragment cloned from R1033.  Gene 48, 203-209.


Skøt, L., Hirsch, P.R. & Witty, J.F. (1986) Genetic factors in  Rhizobium affecting the symbiotic carbon costs of N2 fixation and host biomass production. Journal of Applied Bacteriology 61, 239-246.


Wang, C.L., Beringer, J.E. & Hirsch, P.R. (1986) Host plant effects on hybrids of Rhizobium leguminosarum biovars viceae and trifoliiJournal of General Microbiology 132, 2063-2070.


Hirsch, P.R. (1986) Gene cloning and its potential application to mycorrhizal fungi. Physiological and Genetical Aspects of Mycorrhizae. Proceedings of the 1st European Conference on Mycorrhizae, Dijon, France, July 1985. Edited by V. Gianinazzi Pearson & S. Gianinazzi. INRA, Paris.


Wang, C.L., Spokes, J.R., Woodward, M.J. & Hirsch, P.R. (1985) Transposon mutagenesis of Rhizobium using a derivative of Tn5 conferring gentamicin and spectinomycin resistance.  In: Nitrogen Fixation Research Progress.  Eds. Evans, H.J., Bottomley, P.J. & Newton, W.E.  Nijhoff/Junk, The Hague, The Netherlands.


Beringer, JE; Hirsch, PR; Witty, JF. (1985) Nitrogen fixation. Journal of the Science of Food and Agriculture 36: 651-651.


Hirsch, P.R. (1984) Improved crop plant productivity through genetic manipulation of mycorrhizal fungi? Chemistry and Industry 23, 833-838.


Hirsch, P.R. & Beringer, J.E. (1984) A physical map of pPH1JI and  pJB4JI. Plasmid 12, 139-141.


Beringer, J.E. & Hirsch, P.R. (1984) The role of plasmids in microbial ecology. In: Current Perspectives in Microbial Ecology. Eds. M.J.Klug & C.M. Reddy, American Society for Microbiology, Washington.


Hirsch, P.R. & Beggs, J.D. (1984) Agrobacterium tumefaciens T-DNA in the yeast Saccharomyces cerevisiae. Molecular and General Genetics  195, 209-214.


Beringer, J.E. & Hirsch, P.R. (1984) Genetic engineering and nitrogen fixation. Biotechnology and Genetic Engineering Reviews 1, 65-88.


Hoekema, A., Hirsch, P.R., Hooykaas, P.J.J. & Schilperoort, R.A. (1983) A binary plant vector strategy based on separation of vir- and T-region of the Agrobacterium tumefaciens Ti-plasmid. Nature 303, 179-180.


Hirsch, P.R., Van Montagu, M., Johnston, A.W.B., Brewin, N.J. & Schell, J. (1980) Physical identification of bacteriocinogenic, nodulation and other plasmids in strains of Rhizobium leguminosarum.  Journal of General Microbiology 120, 403-412.


Buchanan-Wollaston, A.V., Beringer, J.E., Brewin, N.J., Hirsch, P.R. & Johnston, A.W.B. (1980) Isolation of symbiotically defective mutants in Rhizobium leguminosarum by insertion of the transposon Tn5 into a transmissible plasmid. Molecular and General Genetics  178, 185-190.


Brewin, N.J., Beringer, J.E., Buchanan-Wollaston, A.V., Johnston, A.W.B. & Hirsch, P.R. (1980) Transfer of symbiotic genes with bacteriocinogenic plasmids in Rhizobium leguminosarum. Journal of  General Microbiology 116, 261-270.


Johnston, A.W.B., Beringer, J.E., Beynon, J.L., Brewin, N., Buchanan-Wollaston, A.V. & Hirsch, P.R. (1979) Plasmids and the Rhizobium-legume symbiosis. In: Plasmids of Medical, Environmental  and Commercial Importance. Eds. K.N. Timmis & A. Puhler, Elsevier Amsterdam.


Hirsch, P.R. (1979) Plasmid determined bacteriocin production by Rhizobium leguminosarum. Journal of General Microbiology 113, 219-228.


Johnston, A.W.B., Beynon, J.L., Buchanan-Wollaston, A.V., Setchell, S.M. Hirsch, P.R. & Beringer, J.E. (1978) High frequency transfer of nodulating ability between strains and species of Rhizobium. Nature  276, 635-636.



PhD in Microbial genetics (University of East Anglia)


BSc in Biological Sciences (University of East Anglia)

Measures of esteem


  • Yu-Jiun Hung,: University of Warwick, "The Environment in Tanzania as a Source of Mycobacterium tuberculosis Complex and Analysis of the Slow-Growing Mycobacteria"
  • The importance of the wheat root microbiome for plant health and crop yields Please enter a title: Invited talk at SGM Annual meeting, Birmingham UK April 2015
  • Metagenomics and metatranscriptomics enhance understanding of root endosymbionts: Invited talk at Rhizo4, Maastrict, the Netherlands June 2015
  • Heather Ruscoe: "Rhizosphere bacteria promote sustainable crop growth" - registered at the University of Lancaster


  • Kailin Hui: University of York; "Metabolism and host specificity in the Rhizobium leguminosarum species complex"
  • Caitlin Burns: University of Warwick; "Characterising the functional role of rhizosphere fungi in Miscanthus x giganteus bioenergy cropping systems"
  • Digging into the soil metagenome: Invited talk at Workshop "Mathematical, Statistical and Computational Aspects of the New Science of Metagenomics" Newton Institute, Cambridge
  • Sampling the soil metagenome and metatranscriptome: Invited talk at ComMet metagenomics workshop
  • Can we manage the nitrogen cycle to optimise plant nutrition?: Invited talk at SGM focussed meeting "Emerging challenges and opportunities in soil microbiology", Loughborough University


  • Andrzej Tkacz: University of East Anglia/John Innes Centre; "Plant genotype, immunity and soil composition control the rhizosphere microbiome"
  • GM biofertlizers â?? experimental releases of transgenic rhizobia: Invited talk, King's College, London - Workshop on Synthetic biology: containment and release of engineered micro-organisms
  • Professor: Visiting Professor at the University of Reading School of Archaeology, Geography and Environmental Science
  • invited expert: Invited as expert by the Bill and Melinda Gates Foundation to participate in the Rhizosphere Soil Microbiome Systems Biology Convening in Seattle


  • Madeleine Giles: University of Aberdeen/JHI Dundee; â??Where does denitrification occur in the rhizosphere?"
  • Frances Cheesman: "The microbiology of lean and obese soil" - registered at the University of Reading


  • Tom Delmont: Lâ??école centrale de Lyon, Lyon, France -â??Description des communautés microbiennes du sol par une approche metagénomiqueâ??
  • Miriam Herold: University of Aberdeen/JHI Dundee "Significance of fungal and bacterial denitrification in arable soil"
  • Journey to the Centre of the Earth: Exhibit at the Cheltenham Science Festival
  • Member, Helmholz Centre Review Panel: I was asked specifically to evaluate the Unit for Plant-Microbe Interactions, in addition to an overall review of the Helmholtz Centre in Munich
  • Soil Metagenomics at Rothamsted: Seminar at the James Hutton Institute, Dundee


  • FRSB: Elected Fellow of the Royal Society of Biology
  • Assessor for AERES: Member of team evaluating the Laboratoire des Symbioses Tropicales et Mediterraneennes (LSTM), Montpellier, France invited by the L'agence d'Evalution de la Recherche et de l'Enseignement Superieur / The Agency for evaluation of research and Higher Education.
  • Journey to the Centre of the Earth â?? the first 23 cm: Royal Society Summer Exhibition at the Southbank Centre, London.
  • Rebekah Robinson: "Characterisation and bio-prospecting of endophytic bacterial microbes in wheat" - registered at the University of Reading
  • Rachel Roberts: â??Rhizobium diversity and function in fertility-building leysâ?? - registered and based at the University of Reading
  • Emma Saxon: â??Understanding the roles of predatory Bdellovibrio bacteria as â??food security guardsâ?? - registered and based at the University of Nottingham
  • Soil biodiversity â?? the root of sustainability: CropWorld 2010, ExCel Centre, London


  • Marc Redmile-Gordon: â??The functional potential of microbial extracellular polymeric substances (EPS) in agricultural soilsâ?? - registered at the University of Bristol, based at Rothamsted
  • BAGECO 10, Uppsala, Sweden: BAGECO 10 (Bacterial Genetics & Ecology â?? co-existing on a changing planet) 15-18th June 2009 invited talk â??Sequencing the microbial metagenome of an iconic grassland soil, the Rothamsted Park Grass Experimentâ??.
  • MICROSOIL workshop, Dundee: Invited talk "Sampling bacteria at the microhabitat scale"
  • Glyn Barrett: "Analysis of Escherichia coli O157 colonisation of the plant environment" - registered and based at the University of Reading
  • Metagenomics workshop, EMBL-EBI, Hinxton, Cambridg: Invited speaker "TerraGenome: a consortium for the sequencing of a soil metagenome"
  • Scottish Root group meeting, Macaulay, Aberdeen: Invited speaker "What plants do for soil and what happens after theyâ??ve gone"


  • Advisor to RAE2008: Specialist Advisor to the Agriculture, Veterinary and Food Science sub-panel of RAE2008 â?? the recent Research Assessment Exercise of UK Universities (involved reading and commenting on a number of papers presented as research outputs from individual scientists being assessed by RAE2008)
  • Bill & Melinda Gates Foundation, Seattle, USA: Invited participant at the Biological Nitrogen Fixation Convening, contribution "Rhizobial symbioses - past, present and future"
  • Sam Gorny: "Evaluation of the nematicidal properties of the cysteine proteinases EP-B2 from barley and actinidin from kiwi fruits" - registered at the University of Nottingham


  • Darren McCabe: "Assessment of the impact of biofuel crops on the physical distribution of soil organic matter" - PhD awarded 2012 by the University of Reading,


  • Member of Assessment Team for CSL York: Member of the Plant Health & Biotechnology team assessing the scientific quality of work at CSL at York


  • Editorial Board Member: Soil Biology Biochemistry
  • Conference Organiser: Co-organiser of Applied Research Forum Workshop â??Manage your soils: grow your buisinessâ?? held at Rothamsted on 15-16 November (c. 100 participants); Chaired outbreak group & reported conclusions back to conference.


  • Conference Organiser: Member of steering group for BBSRC workshop "Interactions between the soil environment and the transmission of food-borne pathogens, Eynsham Hall, Oxfordshire


  • Conference Organiser: Co-organiser of the Rothamsted Millennium Conferenence 10-12 April 2001 & co-editor of subsequent "procedings" published in Plant & Soil"


  • Member of ACRE: Defra UK Advisory Committee on Releases to the Environment-I am retained as an expert advisor until a replacement can be appointed. I chaired the subgroup on Soil Ecology 2002-2006 which produced report & guidance documents published on Defra website


  • Member of HSE SCGM / ACGM / SACGM: The HSE Technical Sub-Committee on Genetic Manipulation, from 2001 the Advisory Committee on Genetic Manipulation, from 2004 the Scientific Advisory Commitee on Genetic Modification


  • European Expert: Invited participant on EU-sponsored mission to China to assess releases of GM bacteria


  • Member: Society for Applied Microbiology
  • Member of Editorial Board: Journal of Applied Microbiology, Letters in Applie


  • Chair of Trade Union Side: Chair of the TUS of the BBSRC Equal Opportunities Committee representing all union members in BBSRC. During this time the main trade union representing BBSRC staff was IPCS (now Prospect)


  • Member: Genetics Society
  • Member: Society for General Microbiology