Nkir, D., Aallam, Y., Idbella, M., Alegria-Terrazas, R., Benbrik, B., Ibnyasser, A., Haddine, M., Reid, T. E., Lund, G., b, T. H. M., c, J. H., Pawlett, M., Clark, I. M., Lyamlouli, K., Rchiad, Z. and Bargaz, A. 2025. Niche-conserved bacterial consortia enhanced maize agro-physiological performance and soil biological P-related traits under low-P conditions. Applied Soil Ecology. 213 (Sept), p. 106280. https://doi.org/10.1016/j.apsoil.2025.106280
Benbrik, B., Reid, T. E., Nkir, D., Chaouki, H., Aallam, Y., Clark, I. M., Mauchline, T. H., Harris, J., Pawlett, M., Barakat, A., Rchiad, Z. and Bargaz, A. 2025. Unlocking the agro-physiological potential of wheat rhizoplane fungi under low P conditions using a niche-conserved consortium approach. Journal of Experimental Botany. 76 (8), p. 2320–2337. https://doi.org/10.1093/jxb/eraf042
Bak, G., Lee, K. K., Clark, I. M., Mauchline, T. H., Kavamura, V. N., Jee, S., Lee, J., Kim, H. and Lee, Y. 2025. Changes in the potato rhizosphere microbiota richness and diversity occur in a growth stage-dependent manner - Author correction. Scientific Reports. 15, p. 5817. https://doi.org/10.1038/s41598-025-90259-x
Bak, G., Lee, K. K., Clark, I. M., Mauchline, T. H., Kavamura, V. N., Jee, S., Lee, J., Kim, H. and Lee, Y. 2025. Changes in the potato rhizosphere microbiota richness and diversity occur in a growth stage-dependent manner. Scientific Reports. 15, p. 2284. https://doi.org/10.1038/s41598-025-86944-6
Nkir, D., Aallam, Y., Ibnyasser, A., Haddine, M., Benbrik, B., Barakat, A., Reid, T. E., Lund, G., Mauchline, T. H., Clark, I. M., Bargaz, A. and Rchiad, Z. 2024. Geographic bioprospection of maize rhizoplane-associated bacteria for consortia construction and impact on plant growth and nutrient uptake under low P availability. Environmental and Experimental Botany. 226 (October), p. 105939. https://doi.org/10.1016/j.envexpbot.2024.105939
Chen, X., Feng, R., Du, Q., Mauchline, T. H., Clark, I. M., Lu, Y. and Liu, L. 2024. Identification and genomic analysis of a thermophilic bacterial strain that reduces ammonia loss from composting. Microbiology Spectrum. 0, pp. e00763-24. https://doi.org/10.1128/spectrum.00763-24
Reid, T., Kavamura, V. N., Torres-Ballesteros, A., Smith, M. E., Abadie, M., Pawlett, M., Clark, I. M., Harris, J. A. and Mauchline, T. H. 2024. Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat. The ISME Journal. 18 (1), p. wrae131. https://doi.org/10.1093/ismejo/wrae131
Oliveira, L. M. D., Kavamura, V. N., Clark, I. M., Mauchline, T. H. and Souza, J. T. D. 2024. Diversity and multifunctional potential for plant growth promotion in bacteria from soil and the rhizosphere. Soil Use and Management. 40 (2), p. e13082. https://doi.org/10.1111/sum.13082
Reid, T., Kavamura, V. N., Torres-Ballesteros, A., Smith, M., Abadie, M., Pawlett, M., Clark, I. M., Harris, J. A. and Mauchline, T. H. 2024. Data for: Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat. https://doi.org/10.23637/rothamsted.98zz7
Bak, G., Lee, K. K., Clark, I. M., Mauchline, T. H., Kavamura, V. N., Lund, G., Jee, S., Lee, J., Kim, H. and Lee, Y. 2024. The potato rhizosphere microbiota correlated to the yield of three different regions in Korea. Scientific Reports. 14, p. 4536. https://doi.org/10.1038/s41598-024-55263-7
Taketani, R. G., Ryan, M. J., Mauchline, T. H., Malone, J., Jones, S., Thompson, C., Bonnin, J. M., Stewart, H., Yau, P., Clark, I. M. and Holden, N. 2023. The UK Crop Microbiome Cryobank – Advancing Microbiome Research for Sustainable Agriculture.
Li, X., Storkey, J., Mead, A., Shield, I. F., Clark, I. M., Ostler, R., Roberts, B. and Dobermann, A. 2023. A new Rothamsted long-term field experiment for the twenty-first century: principles and practice. Agronomy for Sustainable Development. 43 (5), p. 60. https://doi.org/10.1007/s13593-023-00914-8
Ndour, P. M. S., Bargaz, A., Rchiad, Z., Pawlett, M., Clark, I. M., Mauchline, T. H., Harris, J. and Lyamlouli, K. 2023. Microbial Catabolic Activity: Methods, Pertinence, and Potential Interest for Improving Microbial Inoculant Efficiency. Microbial Ecology. 86, pp. 2211-2230. https://doi.org/10.1007/s00248-023-02250-6
Neal, A. L., Barrat, H., Bacq-Lebreuil, A., Qin, Y., Zhang, X., Takahashi, T., Rubio, V., Hughes, D. J., Clark, I. M., Cardenas, L. M., Gardiner, L., Krishna, R., Glendining, M. J., Ritz, K., Mooney, S. and Crawford, J. W. 2023. Arable soil nitrogen dynamics reflect organic inputs via the extended composite phenotype. Nature Food. 4, pp. 51-60. https://doi.org/10.1038/s43016-022-00671-z
Oszvald, M., Hassall, K. L., Hughes, D. J., Torres-Ballesteros, A., Clark, I. M., Riche, A. B. and Heuer, S. 2022. Genetic diversity in nitrogen fertilizer responses and N gas emission in modern wheat. Frontiers in Plant Science. 13, p. 816475. https://doi.org/10.3389/fpls.2022.816475
Barrat, H., Clark, I. M., Evans, J., Chadwick, D. R. and Cardenas, L. M. 2022. The impact of drought length and intensity on N cycling gene abundance, transcription and the size of an N2O hot moment from a temperate grassland soil. Soil Biology and Biochemistry. 168 (May), p. 108606. https://doi.org/10.1016/j.soilbio.2022.108606
Barrat, H., Charteris, A., Le Cocq, K., Abadie, M., Clark, I. M., Chadwick, D. R. and Cardenas, L. M. 2022. N2O hot moments were not driven by changes in nitrogen and carbon substrates or changes in N cycling functional genes. European Journal of Soil Science. 73 (1), p. e13190. https://doi.org/10.1111/ejss.13190
Ruscoe, H., Taketani, R., Clark, I. M., Lund, G., Hughes, D. J., Dodd, I., Hirsch, P. R. and Mauchline, T. H. 2021. Land management legacy affects abundance and function of the acdS gene in wheat root associated pseudomonads. Frontiers in Microbiology. 12, p. 611339. https://doi.org/10.3389/fmicb.2021.611339
Clark, I. M., Hughes, D. J., Fu, Q., Abadie, M. and Hirsch, P. R. 2021. Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils . Scientific Reports. 11, p. 15905. https://doi.org/10.1038/s41598-021-95100-9
Neal, A. L., Hughes, D. J., Clark, I. M., Jansson, J. K. and Hirsch, P. R. 2021. Microbiome Aggregated Traits and Assembly are More Sensitive to Soil Management than Diversity. mSystems. 6 (3), pp. e01056-20. https://doi.org/10.1128/mSystems.01056-20
Reid, T. E., Kavamura, V. N., Abadie, M., Torres-Ballesteros, A., Pawlett, M., Clark, I. M., Harris, J. and Mauchline, T. H. 2021. Inorganic Chemical Fertilizer Application to Wheat Reduces the Abundance of Putative Plant Growth-Promoting Rhizobacteria. Frontiers in Microbiology. 12 (article), p. 642587. https://doi.org/10.3389/fmicb.2021.642587
Castellano-Hinojosa, A., Le Cocq, K., Charteris, A., Abadie, M., Chadwick, D. R., Clark, I. M., Bedmar, E. J. and Cardenas, L. M. 2021. Relative contributions of bacteria and fungi to nitrous oxide emissions following nitrate application in soils representing different land uses. International Biodeterioration & Biodegradation. 159, p. 105199. https://doi.org/10.1016/j.ibiod.2021.105199
Bacq-Labreuil, A., Neal, A. L., Crawford, J. W., Mooney, S. J., Akkari, E., Zhang, X., Clark, I. M. and Ritz, K. 2020. Significant structural evolution of a long-term fallow soil in response to agricultural management practices requires at least 10 years after conversion. European Journal of Soil Science. https://doi.org/10.1111/ejss.13037
Clark, I. M., Fu, Q., Abadie, M., Dixon, E. R., Blaud, A. and Hirsch, P. R. 2020. Edaphic factors and plants influence denitrification in soils from a long-term arable experiment. Scientific Reports. 10 (Article), p. 16053. https://doi.org/10.1038/s41598-020-72679-z
Liang, Y., Ning, D., Lu, Z., Zhang, N., Hale, L., Wu, L., Clark, I. M., McGrath, S. P., Storkey, J., Hirsch, P. R., Sun ,B. and Zhou, J. 2020. Century long fertilization reduces stochasticity controlling grassland microbial community succession. Soil Biology and Biochemistry. 151 (Dec), p. 108023. https://doi.org/10.1016/j.soilbio.2020.108023
Neal, A. L., Bacq-Labreuil, A., Zhang, X., Clark, I. M., Coleman, K., Mooney, S. J., Ritz, K. and Crawford, J. W. 2020. Soil as an Extended Composite Phenotype of the Microbial Metagenome. Scientific Reports. 10, p. 10649. https://doi.org/10.1038/s41598-020-67631-0
Barrat, H., Evans, J., Chadwick, D. R., Clark, I. M., Le Cocq, K. and Cardenas, L. M. 2020. The impact of drought and rewetting on N2O emissions from soil in temperate and Mediterranean climates. European Journal of Soil Science. https://doi.org/10.1111/ejss.13015
Masters-Clark, E., Hirsch, P. R., Clark, I. M., Paradelo, M. and Mauchline, T. H. 2020. Development of a defined compost system for the study of plant-microbe interactions. Scientific Reports. 10, p. 7521. https://doi.org/10.1038/s41598-020-64249-0
Kavamura, V. N., Robinson, R. J., Hughes, D., Clark, I. M., Rossmann, M., De Melo, I.S., Hirsch, P. R., Mendes, R. and Mauchline, T. H. 2020. Wheat dwarfing influences selection of the rhizosphere microbiome. Scientific Reports. 10, p. 1452. https://doi.org/10.1038/s41598-020-58402-y
Fu, Q., Abadie, M., Blaud, A., Carswell, A. M., Misselbrook, T. H., Clark, I. M. and Hirsch, P. R. 2019. Effects of urease and nitrification inhibitors on soil N, nitrifier abundance and activity in a sandy loam soil . Biology And Fertility Of Soils. pp. 1-10. https://doi.org/10.1007/s00374-019-01411-5
Kavamura, V. N., Robinson, R. J., Hayat, R., Clark, I. M., Hughes, D. J., Rossmann, M., Hirsch, P. R., Mendes, R. and Mauchline, T. H. 2019. Land management and microbial seed load effect on rhizosphere and endosphere bacterial community assembly in wheat. Frontiers in Microbiology. 10 (2625). https://doi.org/10.3389/fmicb.2019.02625
Huang, R., McGrath, S. P., Hirsch, P. R., Clark, I. M., Storkey, J., Wu, L., Zhou, J. and Liang, Y. 2019. Plant–microbe networks in soil are weakened by century‐long use of inorganic fertilizers. Microbial Biotechnology. 12 (6), pp. 1464-1475. https://doi.org/10.1111/1751-7915.13487
Puissant, J., Briony, J., Goodall, T., Mang, D., Blaud, A., Gweon, H. S., Malik, A., Jones, D. L., Clark, I. M., Hirsch, P. R. and Griffiths, R. 2019. The pH optimum of soil exoenzymes adapt to long term changes in soil pH. Soil Biology and Biochemistry. 138, p. 107601. https://doi.org/10.1016/j.soilbio.2019.107601
Nessner-Kavamura-Noguchi, V., Hayat, R., Clark, I. M., Rossmann, M., Mendes, R., Hirsch, P. R. and Mauchline, T. H. 2018. Inorganic Nitrogen Application Affects Both Taxonomical and Predicted Functional Structure of Wheat Rhizosphere Bacterial Communities. Frontiers in Microbiology. 9, p. 1074. https://doi.org/10.3389/fmicb.2018.01074
Macdonald, A. J., Poulton, P. R., Clark, I. M., Scott, T., Glendining, M. J., Perryman, S. A. M., Storkey, J., Bell, J. R., Shield, I. F., Mcmillan, V. E. and Hawkins, J. M. B. Macdonald, A. J. (ed.) 2018. Rothamsted Long-term experiments : guide to the classical and other long-term experiments, datasets and sample archive. Rothamsted Research, Harpenden.
De Sosa, L. L., Glanville, C. C., Marshall, M. R., Williams, A. P., Abadie, M., Clark, I. M., Blaud, A. and Jones, D. L. 2018. Spatial zoning of microbial functions and plant-soil nitrogen dynamics across a riparian area in an extensively grazed livestock system. Soil Biology and Biochemistry. 120, pp. 153-164. https://doi.org/10.1016/j.soilbio.2018.02.004
Mauchline, T. H., Hayat, R., Clark, I. M. and Hirsch, P. R. 2018. Old meets new: most probable number validation of metagenomic and metatranscriptomic datasets in soil. Letters in Applied Microbiology. 66 (1), pp. 14-18. https://doi.org/10.1111/lam.12821
Fu, Q., Clark, I. M., Zhu, J., Hu, H. Q. and Hirsch, P. R. 2018. The short-term effects of nitrification inhibitors on the abundance and expression of ammonia and nitrite oxidizers in a long-term field experiment comparing land management. Biology And Fertility Of Soils. 54 (1), pp. 163-172. https://doi.org/10.1007/s00374-017-1249-2
Gao, W., Muñoz-Romero, V., Ren, T., Ashton, R. W., Morin, M., Clark, I. M., Powlson, D. S. and Whalley, W. R. 2017. Effect of microbial activity on penetrometer resistance and elastic modulus of soil at different temperatures. European Journal of Soil Science. 68 (4), pp. 412-419. https://doi.org/10.1111/ejss.12440
Neal, A. L., Blackwell, M. S. A., Akkari, E., Clark, I. M., Hirsch, P. R. and Guyomar, C. 2018. Phylogenetic distribution, biogeography and the effects of land management upon bacterial non-specific Acid phosphatase Gene diversity and abundance. Plant and Soil. 427, pp. 175-189. https://doi.org/10.1007/s11104-017-3301-2
Neal, A. L., Rossmann, M., Brearley, C., Akkari, E., Guyomar, C., Clark, I. M., Allen, E. and Hirsch, P. R. 2017. Land-use influences phosphatase gene microdiversity in soils. Environmental Microbiology. 19 (7), p. 2740–2753. https://doi.org/10.1111/1462-2920.13778
Hirsch, P. R., Jhurreea, D., Williams, J. K., Murray, P. J., Scott, T., Misselbrook, T. H., Goulding, K. W. T. and Clark, I. M. 2017. Soil resilience and recovery: rapid community responses to management changes. Plant and Soil. 412 (1-2), pp. 283-297. https://doi.org/10.1007/s11104-016-3068-x
Jones, F. P., Clark, I. M., King, R., Shaw, L. J., Woodward, M. J. and Hirsch, P. R. 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, p. 25858. https://doi.org/10.1038/srep25858
Robinson, R. J., Fraaije, B. A., Clark, I. M., Jackson, R. W., Hirsch, P. R. and Mauchline, T. H. 2016. Wheat seed embryo excision enables the creation of axenic seedlings and Koch's postulates testing of putative bacterial endophytes. Scientific Reports. 6, p. 25581. https://doi.org/10.1038/srep25581
Xie, W-Y., McGrath, S. P., Su, J. Q., Hirsch, P. R., Clark, I. M., Shen, Q., Zhu, Y-G. and Zhao, F-J. 2016. Long-Term Impact of Field Applications of Sewage Sludge on Soil Antibiotic Resistome. Environmental Science & Technology. 50 (23), pp. 12602-12611. https://doi.org/10.1021/acs.est.6b02138
Morais, D., Pylro, V., Clark, I. M., Hirsch, P. R. and Totola, M. R. 2016. Responses of microbial community from tropical pristine coastal soil to crude oil contamination. PeerJ. 4. https://doi.org/10.7717/peerj.1733
Robinson, R. J., Fraaije, B. A., Clark, I. M., Jackson, R. W., Hirsch, P. R. and Mauchline, T. H. 2016. Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type, developmental stage and soil nutrient availability. Plant and Soil. 405 (1-2), pp. 381-396. https://doi.org/10.1007/s11104-015-2495-4
Mehrabi, Z., Mcmillan, V. E., Clark, I. M., Canning, G., Hammond-Kosack, K. E., Preston, G., Hirsch, P. R. and Mauchline, T. H. 2016. Pseudomonas spp. diversity is negatively associated with suppression of the wheat take-all pathogen. Scientific Reports. 6. https://doi.org/10.1038/srep29905
Storkey, J., Macdonald, A. J., Bell, J. R., Clark, I. M., Gregory, A. S., Hawkins, N. J., Hirsch, P. R., Todman, L. C. and Whitmore, A. P. 2016. The unique contribution of Rothamsted to ecological research at large temporal scales. in: Dumbrell, A. J., Kordas, R. L. and Woodward, G. (ed.) Advances in Ecological Research 55: Large-Scale Ecology: Model Systems to Global Perspectives Academic Press, Oxford. pp. 3-42
Liang, Y., Wu, Liyou, Clark, I. M., Xue, K., Yang, Y., Van Nostrand, J. D., Deng, Y., He, Z., McGrath, S. P., Storkey, J., Hirsch, P. R., Sun, B. and Zhou, J. 2015. Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity. mBio. 6, pp. e00240-15. https://doi.org/10.1128/mBio.00240-15
Geisen, S., Tveit, A. T., Clark, I. M., Richter, A., Svenning, M. M., Bonkowski, M. and Urich, T. 2015. Metatranscriptomic census of active protists in soils. The ISME Journal. 9, pp. 2178-2190. https://doi.org/10.1038/ismej.2015.30
Zhalnina, K., Dias, R., De Quadros, P. D., Davis-Richardson, A., Camargo, F. A. O., Clark, I. M., McGrath, S. P., Hirsch, P. R. and Triplett, E. W. 2015. Soil pH determines microbial diversity and composition in the Park Grass Experiment. Microbial Ecology. 69, pp. 395-406. https://doi.org/10.1007/s00248-014-0530-2
Mauchline, T. H., Chedom-Fotso, D., Chandra, G., Samuels, T., Greenaway, N., Backhaus, A., Mcmillan, V. E., Canning, G., Powers, S. J., Hammond-Kosack, K. E., Hirsch, P. R., Clark, I. M., Mehrabi, Z., Roworth, J., Burnell, J. and Malone, J. G. 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 (11), pp. 4764-4778. https://doi.org/10.1111/1462-2920.13038
Macdonald, A. J., Powlson, D. S., Poulton, P. R., Watts, C. W., Clark, I. M., Storkey, J., Hawkins, N. J., Glendining, M. J., Goulding, K. W. T. and McGrath, S. P. 2015. The Rothamsted Long-term Experiments. Aspects of Applied Biology. 128.
Pylro, V. S., Roesch, L. F. W., Morais, D. K., Clark, I. M., Hirsch, P. R. and Totola, M. R. 2014. Data analysis for 16S microbial profiling from different benchtop sequencing platforms. Journal of Microbiological Methods. 107 (December), pp. 30-37. https://doi.org/10.1016/j.mimet.2014.08.018
Tahseen, Q. and Clark, I. M. 2014. Attraction and preference of bacteriophagous and plant-parasitic nematodes towards different types of soil bacteria. Journal Of Natural History. 48, pp. 1485-1502. https://doi.org/10.1080/00222933.2013.873088
Robinson, R. R., Fraaije, B. A., Clark, I. M., Jackson, R. W., Hirsch, P. R. and Mauchline, T. H. 2014. The impact of tissue type, growth stage and fertilizers on the community structure of cultured bacterial wheat endophytes in the Broadbalk experiment. American Phytopathological Society (APS).
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. and 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, p. 104. https://doi.org/10.3389/fmicb.2013.00104
Cardenas, L. M., Hatch, D. J., Scholefield, D., Jhurreea, D., Clark, I. M., Hirsch, P. R., Salazar, F., Rao-Ravella, S. and Alfaro, M. 2013. Potential mineralization and nitrification in volcanic grassland soils in Chile. Soil Science and Plant Nutrition. 59, pp. 380-391. https://doi.org/10.1080/00380768.2013.789395
Hirsch, P. R., Mauchline, T. H. and Clark, I. M. 2013. Culture-independent molecular approaches to microbial ecology in soil and rhizosphere. in: Debruijn, F. J. (ed.) Molecular microbial ecology of the rhizosphere, Volume 1 John Wiley & Sons Hoboken, N.J.. pp. 45-55
Clark, I. M., Buchkina, N., Jhurreea, D., Goulding, K. W. T. and 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 B-Biological Sciences. 367, pp. 1235-1244. https://doi.org/10.1098/rstb.2011.0314
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., Le Paslier, D., Simonet, P. and Vogel, T. M. 2012. Structure, fluctuation and magnitude of a natural grassland soil metagenome. The ISME Journal. 6, pp. 1677-1687. https://doi.org/10.1038/ismej.2011.197
Delmont, T. O., Robe, P., Clark, I. M., Simonet, P. and Vogel, T. M. 2011. Metagenomic comparison of direct and indirect soil DNA extraction approaches. Journal of Microbiological Methods. 86 (3), pp. 397-400. https://doi.org/10.1016/j.mimet.2011.06.013
Delmont, T. O., Robe, P., Cecillon, S., Clark, I. M., Constancias, F., Simonet, P., Hirsch, P. R. and Vogel, T. M. 2011. Accessing the soil metagenome for studies of microbial diversity. Applied and Environmental Microbiology. 77 (4), pp. 1315-1324. https://doi.org/10.1128/AEM.01526-10
Manzanilla-Lopez, R. H., Clark, I. M., Atkins, S. D., Hirsch, P. R. and Kerry, B. R. 2011. Exploring competitiveness and genetic variation in the nematophagous fungus Pochonia chlamydosporia var. chlamydosporia and its significance for biological control.
Rosso, L. C., Finetti-Sialer, M. M., Hirsch, P. R., Ciancio, A., Kerry, B. R. and Clark, I. M. 2011. Transcriptome analysis shows differential gene expression in the saprotrophic to parasitic transition of Pochonia chlamydosporia. Applied Microbiology and Biotechnology. 90, pp. 1981-1994. https://doi.org/10.1007/s00253-011-3282-7
Macdonald, C. A., Clark, I. M., Hirsch, P. R., Zhao, F-J. and 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, pp. 4626-4633. https://doi.org/10.1128/AEM.02232-10
Hirsch, P. R., Jhurreea, D., Scott, T., Misselbrook, T. H., Goulding, K. W. T. and Clark, I. M. 2011. Impacts of land use change on denitrifying bacteria and nitrous oxide emissions. Abstracts Theo Murphy Scientific Meeting: Nitrous Oxide, the Forgotten Greenhouse Gas, Chicheley, 23-24 May 2011 .
Macdonald, C. A., Clark, I. M., Zhao, F-J., Hirsch, P. R., Singh, B. K. and 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 and Biochemistry. 43, pp. 932-941. https://doi.org/10.1016/j.soilbio.2011.01.004
Hirsch, P. R., Mauchline, T. H. and Clark, I. M. 2010. Culture-independent molecular techniques for soil microbial ecology. Soil Biology and Biochemistry. 42 (6), pp. 878-887. https://doi.org/10.1016/j.soilbio.2010.02.019
Goulding, K. W. T., Murray, P. J., Sohi, S. P., Gilliam, L. M., Williams, J. K., Clark, I. M. and Hirsch, P. R. 2010. Soil without plants: the consequences for microorganisms and mesofauna. Gilkes, R. and Prakongkep, N. (ed.) Proceedings 19th World Congress of Soil Science, Brisbane, 1-6 August 2010 . Australian Society of Soil Science, Warragul. pp. 1622-1625
Wu, Liyou, Liang, Y., Clark, I. M., Wue, K., Deng, Y., He, Z., Van Nostrand, J., Macdonald, C., Hirsch, P. R., McGrath, S. P. and Zhou, J. 2010. Effects of long-term fertilization and liming on microbial functions and diversity in the grassland site at Rothamsted Research, UK. Abstracts 13th International Symposium on Microbial Ecology, Seattle, 22-27 August 2010 .
Macdonald, C. A., Yang, X., Clark, I. M., Zhao, F-J., Hirsch, P. R. and McGrath, S. P. 2010. Relative impact of soil, metal source and metal concentration on bacterial community structure and community tolerance. Soil Biology and Biochemistry. 42, pp. 1408-1417. https://doi.org/10.1016/j.soilbio.2010.05.002
Mccabe, D., Clark, I. M., Sohi, S., Shaw, E. and Hirsch, P. R. 2010. Targeting the active bacterial communities in soil pores. Abstracts 13th International Symposium on Microbial Ecology, Seattle, 22-27 August 2010 .
Liang, Y., Wu, Liyou, Clark, I. M., Xue, K., Deng, Y., He, Z., Hirsch, P. R., McGrath, S. P. and Zhou, J. 2010. Effects of long-term fertilization on spatial distribution patterns of microbial functional genes from the Rothamsted Experimental site. Abstracts 13th International Symposium on Microbial Ecology, Seattle, 22-27 August 2010 .
Giongo, A., Gano,K., Roesch, L., Casella, G., Daroub, S., Ramiez, K., Sayavedra-Soto, L., Arp, D., Clark, I. M., Hirsch, P. R., McGrath, S. P. and Triplett, E. 2010. Long-term agricultural experiments reveal N influence on ammonia oxidizers and the predominance of CA. nitrososphaera. Abstracts 13th International Symposium on Microbial Ecology, Seattle, 22-27 August 2010 .
Delmont, T., Cecillon, S., Clark, I. M., Simonet, P., Hirsch, P. R. and Vogel, T. 2010. Soil metagenomics: can we access the diversity? Abstracts 13th International Symposium on Microbial Ecology, Seattle, 22-27 August 2010 .
Cardenas, L. M., Bol, R., Bergstermann, A., Meijide, A., Hirsch, P. R., Jhurreea, D., Clark, I. M., Gilliam, L., Goulding, K. W. T., Well, R. and Scholefield, D. 2010. Role of antecedent soil moisture on microbial populations involved in gaseous N2O emissions - use of isotopomers to understand sources. Abstracts Stable Isotope Mass-Spectrometry User Group (SIMSUG) Meeting, Exeter, 28-30 April 2010 .
Murray, P. J., Hirsch, P. R., Gilliam, L. M., Sohi, S. P., Williams, J. K., Clark, I. M. and Brookes, P. C. 2009. Are long-term changes in soil organic matter reflected in the soil communities?
Brookes, P. C., Hirsch, P. R., Gilliam, L. M., Clark, I. M., Sohi, S. P., Williams, J. K. and Murray, P. J. 2009. Are long-term changes in soil organic matter reflected in the soil communities? Abstracts 2009 International Annual Meetings of ASA-CSSA-SSSA: Footprints in the Landscape: Sustainability through Plant and Soil Sciences, Pittsburgh, 1-5 November 2009 .
Murray, P. J., Hirsch, P. R., Gilliam, L. M., Sohi, S. P., Williams, J. K., Clark, I. M. and Brookes, P. C. 2009. Are long-term changes in soil organic matter reflected in the soil communities? Abstracts Forming Bridges in a Changing World: Society of Nematologists and Soil Ecology Society Conference, Burlington, 12-15 July 2009 .
Mccabe, D., Clark, I. M., Sohi, S. P., Shaw, L. and Hirsch, P. R. 2009. Through the keyhole: a key to open the bacterial lock; aka using BrdU to target pore space diversity. Abstracts Micro Soil: Integrating Biological, Physical and Chemical Techniques for the Study of Soil Micro-Habitats, Dundee, 16-17 September 2009 . pp. 24-25
Clark, I. M., Gilliam, L. M., Sohi, S. P., Williams, J., Murray, P. J. and Hirsch, P. R. 2009. Microbial diversity maintained in soils starved of plant inputs for 50 years. Abstracts BAGECO 10: Bacterial Genetics and Ecology - Coexisting on a Changing Planet, Uppsala, 15-19 June 2009 . pp. 119
Hirsch, P. R. and Clark, I. M. 2009. What plants do for soil and what happens after they've gone. Abstracts Plant Soil Interactions: Joint Meeting of the Scottish Root Group and the Scottish Discussion Group of the British Society of Soil Science, Aberdeen, 3 November 2009 .
Hirsch, P. R. and Clark, I. M. 2009. Sequencing the microbial metagenome of an iconic grassland soil, the Rothamsted Park Grass Experiment. Abstracts BAGECO 10: Bacterial Genetics and Ecology - Coexisting on a Changing Planet, Uppsala, 15-19 June 2009 . pp. 73
Hirsch, P. R., Gilliam, L. M., Sohi, S. P., Williams, J. K., Clark, I. M. and Murray, P. J. 2009. Starving the soil of plant inputs for 50 years reduces abundance but not diversity of soil bacterial communities. Soil Biology and Biochemistry. 41 (9), pp. 2021-2024. https://doi.org/10.1016/j.soilbio.2009.07.011
Atkins, S. D., Peteira, B., Clark, I. M., Kerry, B. R. and 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, pp. 143-152. https://doi.org/10.1111/j.1744-7348.2009.00333.x
Manzanilla-Lopez, R. H., Atkins, S. D., Clark, I. M., Kerry, B. R. and Hirsch, P. R. 2009. Measuring abundance, diversity and parasitic ability in two populations of the nematophagous fungus Pochonia chlamydosporia var. chlamydosporia. Biocontrol Science and Technology. 19, pp. 391-406. https://doi.org/10.1080/09583150902783793
Manzanilla-Lopez, R. H., Clark, I. M., Atkins, S., Hirsch, P. R. and Kerry, B. R. 2009. Exploring competitiveness and genetic variation in the nematophagous fungus Pochonia chlamydosporia var. chlamydosporia and its significance for biological control. Abstracts IOBC 5th Meeting on Multitrophic Interactions in Soil, Uppsala, 11-13 June 2009 . pp. 27
Manzanilla-Lopez, R. H., Clark, I. M., Atkins, S. D., Hirsch, P. R. and 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 (1), pp. 71-76. https://doi.org/10.1111/j.1472-765X.2008.02489.x
Macdonald, C., Yang, X., Clark, I. M., Hirsch, P. R. and McGrath, S. P. 2008. Long-term impacts of metal-rich sludge additions on soil microbial communities - effects of metal source and soil type. Abstracts 12th International Symposium on Microbial Ecology (ISME12): Microbial Diversity - Sustaining the Blue Planet, Cairns, 17-22 August 2008 .
Kerry, B. R., Clark, I. M., Esteves, I., Finetti, M., Hirsch, P. R., Gomez-Gil, L., Manzanilla-Lopez, R. H. and Rosso, L. C. 2008. Interactions on roots and the efficacy of Pochonia chlamydosporia as a biological control agent. Abstracts 6th Seminario Cientifico Internacional de Sanidad Vegetal, Habana, 22-26 September 2008 .
Clark, I. M. 2008. Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted Broadbalk experiment. Abstracts BSSS Autumn Meeting on Something Old, Something New: Integrating Molecular Biology with Other Techniques in Soil Science, Harpenden, 17 September 2008 .
Dennis, P. G., Miller, A. J., Clark, I. M., Taylor, R. G., Valsami-Jones, E. and 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, pp. 12-18. https://doi.org/10.1016/j.mimet.2008.04.013
Finetti-Sialer, M., Hirsch, P. R., Kerry, B. R. and Clark, I. M. 2008. Gene expression profiles in Pochonia chlamydosporia in conditions of saprotrophic-to-parasite transition. Abstracts 5th International Congress of Nematology, Brisbane, 13-18 July 2008 .
Clark, I. M. and Hirsch, P. R. 2008. Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted Broadbalk experiment. Soil Biology and Biochemistry. 40, pp. 1090-1102. https://doi.org/10.1016/j.soilbio.2007.11.021
Cookson, W. R., Osman, M., Marschner, P., Abaye, D. A., Clark, I. M., Murphy, D. V., Stockdale, E. A. and Watson, C. A. 2007. Controls on soil nitrogen cycling and microbial community composition across land use and incubation temperature. Soil Biology and Biochemistry. 39, pp. 744-756. https://doi.org/10.1016/j.soilbio.2006.09.022
Chilima, B. Z., Clark, I. M., Floyd, S., Fine, P. E. M. and Hirsch, P. R. 2006. Distribution of environmental mycobacteria in Karonga District, Northern Malawi. Applied and Environmental Microbiology. 72 (4), pp. 2343-2350. https://doi.org/10.1128/AEM.72.4.2343-2350.2006
Manzanilla-Lopez, R. H., Clark, I. M., Atkins, S., Hirsch, P. R. and Kerry, B. R. 2006. DNA fingerprinting methodology to monitor infectivity, competition and rhizosphere competence of Pochonia chlamydosporia isolates within bulk soil, rhizoshere and Meloidogyne incognita egg masses. Abstracts AAB Conference on Advances in Nematology, London, 12 December 2006 .
Manzanilla-Lopez, R. H., Clark, I. M., Hirsch, P. R. and Kerry, B. R. 2006. Assessing genetic diversity of Pochonia chlamydosporia populations using ERIC primers. Abstracts 38th ONTA Annual Meeting, San Jose, 26-30 June 2006 .
Clark, I. M., Cookson, W. R., Hampshire, D. and Hirsch, P. R. 2006. Monitoring active bacterial communities in soil. Abstracts 158th Meeting of the Society for General Microbiology, Warwick, 3-6 April 2006 . pp. 52
Cookson, W. R., Marschner, P., Clark, I. M., Milton, N., Smirk, M. N., Murphy, D. V., Osman, M., Stockdale, E. A. and 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, pp. 453-465. https://doi.org/10.1071/SR05042
Tahseen, Q., Clark, I. M., Atkins, S. D., Hirsch, P. R. and Kerry, B. R. 2005. Impact of the nematophagous fungus Pochonia chlamydosporia on nematode and microbial populations. Communications in Agricultural and Applied Biological Sciences. 70(1), pp. 81-86.
Atkins, S. D., Clark, I. M., Pande, S., Hirsch, P. R. and 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 (2), pp. 257-264. https://doi.org/10.1016/j.femsec.2004.09.002
Hirsch, P. R. and Clark, I. M. 2004. Impact of genetically modified bacterial inoculants on the soil microbial community. GM Crops - Ecological Dimensions. Aspects of Applied Biology 74 . pp. 141-153
Atkins, S. D., Sosnowska, D., Evans, V. J., Clark, I. M., Hirsch, P. R. and Kerry, B. R. 2004. Investigation of three nematophagous fungi in two potato cyst nematode suppressive soils.
Theodoulou, F. L., Clark, I. M., He, X-L., Pallett, K. E., Cole, D. J. and Hallahan, D. L. 2003. Co-induction of glutathione-S-transferases and multidrug resistance associated protein by xenobiotics in wheat. Pest Management Science. 59 (2), pp. 202-214. https://doi.org/10.1002/ps.576
Atkins, S. D., Clark, I. M., Sosnowska, D., Hirsch, P. R. and Kerry, B. R. 2003. Detection and quantification of Plectosphaerella cucumerina , a potential biological control agent of potato cyst nematodes, using real-time PCR. Abstracts 11th International Congress on Molecular Plant Microbe Interactions, St Petersburg, 18-27 July 2003 .
Atkins, S. D., Clark, I. M., Sosnowska, D., Hirsch, P. R. and 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, pp. 4788-4793.
Atkins, S. D., Hidalgo-Diaz, L., Clark, I. M., Morton, C. O., Montes De Oca, N., Gray, P. A. and Kerry, B. R. 2003. Approaches for monitoring the release of Pochonia chlamydosporia var. catenulata , a biocontrol agent of root-knot nematodes. Mycological Research. 107, pp. 206-212.
Atkins, S. D., Clark, I. M., Sosnowska, D. and Kerry, B. R. 2002. Initial testing of potential fungal biological control agents for potato cyst nematodes. Proceedings Brighton Crop Protection Conference - Pests and Diseases, 2002 . pp. 79-84
Hirsch, P. R. and Clark, I. M. 2002. Impact of GM bacterial inoculants on the soil microbial community. Abstracts International Conference on GMOs - Ecological Dimensions, Reading, 9-11 September 2002 .
Gilliam, L. M., Clark, I. M. and Hirsch, P. R. 2002. Genetic and functional diversity in the rhizosphere of oilseed rape, wheat and potatoes. Abstracts BAGECO-7: 7th Symposium on Bacterial Genetics and Ecology, Bergen, 15-19 June 2002 . pp. 86
Clark, I. M., Mendum, T. A. and 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, pp. 607-616.
Clark, I. M. and Hirsch, P. R. 2002. The role of the rhizobium symbiotic plasmid in survival in the soil and the rhizosphere. Abstracts BAGECO-7: 7th Symposium on Bacterial Genetics and Ecology, Bergen, 15-19 June 2002 .
Hirsch, P. R. and Clark, I. M. 2002. The fate of genetically modified rhizobial inoculants in the field. Abstracts 8th New Phytologist Symposium, Helsinki, 10-14 June 2002 .
Mendum, T. A., Clark, I. M. and Hirsch, P. R. 2001. Characterization of two novel Rhizobium leguminosarum bacteriophages from a field release site of genetically-modified rhizobia. Antonie van Leeuwenhoek. 79 (2), pp. 189-197. https://doi.org/10.1023/a:1010238412538
Hidalgo, L., Bourne, J. M., Rodriguez, M. G., Sanchez, L., Hernandez, M. A., Atkins, S. D., Clark, I. M. and Kerry, B. R. 2001. The development of Verticillium chlamydosporium as a biological control agent of root-knot nematodes in organic vegetable production in Havana. Abstracts 4th International Scientific Seminar of Plant Health/33rd Annual Meeting of the Organization of Nematologists of Tropical America (ONTA), Varadera, Cuba, 11-15 June 2001 . pp. 12
Clark, I. M., Mendum, T. A. and Hirsch, P. R. 2000. Inference of symbiotic plasmid involvement in the population dynamics of two GM rhizobia under different agricultural practices. Abstracts 2nd Symposium of the EU Concerted Action on Mobile Genetic Elements' Contribution to Bacterial Adaptability and Diversity (MECBAD), Prague, 17-19 September 2000 . pp. 27-28
Theodoulou, F. L., Clark, I. M., Mitchell, V. J., Moss, S. R. and Pallett, K. E. 1999. Role of ABC transporters in herbicide metabolism. Abstracts Society for Experimental Biology Plant Transport Group Meeting, Southampton, 8-10 September 1999 .
Theodoulou, F. L., Clark, I. M., Pallett, K. E. and Hallahan, D. L. 1999. Nucleotide sequence of Cla 30 (Accession No. Y17386), a xenobiotic- inducible member of the GST superfamily from Triticum aestivum L. (PGR99-049).
Mendum, T. A., Clark, I. M. and Hirsch, P. R. 1999. Interactions between rhizobia and bacteriophages isolated from soil. Abstracts BAGECO-6: 6th Symposium on Bacterial Genetics and Ecology, Florence, 20-24 June 1999 . pp. 17
Mendum, T. A., Clark, I. M. and Hirsch, P. R. 1999. The genetic implications of bacteriophages in Rhizobium leguminosarum. Abstracts 1st Symposium of the EU-concerted Action on Mobile Elements Contribution to Bacterial Adaptability (MECBAD), Le Mont Ste Odile, 23-27 April 1999 . pp. 23
Theodoulou, F. L., Clark, I. M., Pallett, K. E. and Hallahan, D. L. 1998. A herbicide safener-induced MRP homologue from wheat. Abstracts 11th International Workshop on Plant Membrane Biology, Cambridge, 9-14 August 1998 . pp. 77
Maughan, J. A., Nugent, J. H. A., Clark, I. M., Westlake, A. C. G. and Hallahan, D. L. 1997. Molecular enzymology of plant cytochromes P450. Proceedings Brighton Crop Protection Conference - Weeds, 1997 . pp. 597-604
Clark, I. M., Forde, B. G. and Hallahan, D. L. 1997. Spatially distinct expression of two new cytochrome P450s in leaves of Nepeta racemosa : identification of a trichome-specific isoform. Plant Molecular Biology. 33, pp. 875-885.
Clark, I. M., Crank, S. F., Forde, B. G. and Hallahan, D. L. 1995. Molecular analysis of cytochrome P450 cDNAs from Nepeta racemosa. Abstracts 3rd International Symposium on Cytochrome P450 Biodiversity, Woods Hole, 8-12 October 1995 .
Hallahan, D. L., Cheriton, A. K., Hyde, R., Clark, I. M. and Forde, B. G. 1993. Plant cytochrome P-450 and agricultural biotechnology. Biochemical Society Transactions. 21 (4), pp. 1068-1073. https://doi.org/10.1042/bst0211068