Rothamsted Research

where knowledge grows

clarki

Ian Clark

Role(s):
Research Scientist
Agro Ecology
Harpenden
Phone:
+44 (0) 1582 763 133 ext: +44 1582 938819
Location:
Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ

Publications:

2016

Wan-Ying Xie., McGrath S.P., Jian-Qiang Su., Hirsch P.R., Clark I.M., Qirong Shen., Yong-Guan Zhu., Fang-Jie Zhao. (2016) Long-Term Impact of Field Applications of Sewage Sludge on Soil Antibiotic Resistome. Environ. Sci. Technol 50(23), pp 12602–12611 DOI: 10.1021/acs.est.6b02138

Mehrabi Z., McMillan V.E., Clark I.M., Canning G., Hammond-Kosack K.M., Preston G., Hirsch P.R., Mauchline T.H.  (2016) Erratum: Pseudomonas spp. diversity is negatively associated with suppression of the wheat take-all pathogen. Scientific Reports 6, Article number: 34681 (2016) doi:10.1038/srep34681

Hirsch P.R., Jhurreea D., Williams J.K., Murray P.J., Scott T., Misselbrook T.H., Goulding K.W.T., Clark I.M. (2016) Soil resilience and recovery: rapid community responses to management changes. Plant and Soil doi:10.1007/s11104-016-3068-x

Storkey J., Macdonald A.J., Bell J.R., Clark I.M., Gregory A.S., Hawkins N.J., Hirsch P.R., Todman L.C., Whitmore A.P. (2016) Chapter One – The Unique Contribution of Rothamsted to Ecological Research at Large Temporal Scales Advances in Ecological Research 55, Pages 3–42 Large-Scale Ecology: Model Systems to Global Perspectives doi.org/10.1016/bs.aecr.2016.08.002

Mehrabi Z., McMillan V.E., Clark I.M., Canning G., Hammond-Kosack K.M., Preston G., Hirsch P.R., Mauchline T.H. (2016) Pseudomonas spp. diversity is negatively associated with suppression of the wheat take-all pathogen. Scientific Reports 6 doi:10.1038/srep29905

Jones F.P., Clark I.M., King R., Shaw L.J., Woodward M.J., Hirsch P.R. (2106) Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes – a genome comparison Sci Rep. 6:25858 doi:10.1038/srep25858

Robinson R.J., Fraaije B.A., Clark I.M., Jackson R.W., Hirsch P.R., 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 doi:10.1038/srep25581

Morais D., Pylro V., Clark I.M., Hirsch PR., Tótola MR. (2016) Responses of microbial community from tropical pristine coastal soil to crude oil contamination. PeerJ. 18;4:e1733. doi: 10.7717/peerj.1733.

2015

Mauchline T.H., Chedom-Fotso D., Chandra G., Samuels T., Greenaway N., Backhaus A., McMillan V., Canning G., Powers S.J., Hammond-Kosack K.E., Hirsch P.R., Clark I.M., Mehrabi Z., Roworth J., Burnell J., 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. Environ Microbiol. 17(11):4764-78. doi: 10.1111/1462-2920.13038.

Robinson, R.J., Fraaije, B.A., Clark, I.M., Jackson, R.W., Hirsch, P.R. and Mauchline, T.H.(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

Liang Y., Wu L., Clark I.M., Xue K., Yang Y., Van Nostrand J.D., Deng Y., He Z., McGrath S., Storkey J., Hirsch P.R., Sun B., Zhou J. (2015)  Over 150 Years of Long-Term Fertilization Alters Spatial Scaling of Microbial Biodiversity. mBio 6(2). doi:10.1128/mBio.00240-15

Geisen S., Tveit AT., Clark I.M., Richter A., Svenning M.M., Bonkowski M., Urich T. (2015) Metatranscriptomic census of active protists in soils ISME J advance online publication, March 27, 2015 doi:10.1038/ismej.2015.30

Zhalnina K., Dias R., Dörr de Quadros P., Davis-Richardson A., Camargo FAO., Clark I.M., McGrath S.P., Hirsch P.R., Triplett E.W. (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.

2014

Pylro V.S., Roesch L.F.W., Morais D.K., Clark I.M., Hirsch P.R., Tótola M.R. (2014) Data analysis for 16S microbial profiling from different benchtop sequencing platforms, Journal of Microbiological Methods 107:30-37 doi.org/10.1016/j.mimet.2014.08.018 

Tahseen Q & Clark I.M. (2014) Attraction and preference of bacteriophagous and plant-parasitic nematodes towards different types of soil bacteria Journal of Natural History  48:1485-1502 doi:10.1080/00222933.2013.873088

Florio A., Clark I.M., Hirsch P.R., 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 50:1–13  doi: 10.1007/s00374-014-0897-8

2013

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

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 andBradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments. Frontiers in Microbiology4:104. doi: 10.3389/fmicb.2013.00104. 

2012

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. doi: 10.1098/rstb.2011.0314

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

Over 5yrs old

Delmont T.O., Robe P., Clark I.M., Simonet P. & Vogel T.M. (2011) Metagenomic comparison of direct and indirect soil DNA extraction approaches. J. of Microbiological Methods 86: 397-400

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.  

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 ofPochonia chlamydosporiaApplied Microbiology & Biotechnology 90:1981–1994. 

Macdonald C.A., Clark I.M., Hirsch P.R., Zhao F-J. & McGrath S. P. (2011) Development of a real-time PCRr assay for detection and quantification of Rhizobium leguminosarum bacteria and discrimination between different biovars in zinc-contaminated soil. Applied and Environmental Microbiology 77(13):4626-4633

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. 

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

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. 

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.

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.

Manzanilla-Lopez R.H., Atkins S.D., Clark I. M.,  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 chalamydospora isolated from plant rhizospheres. Letters in Applied Microbiology 48: 71-76.

Manzanilla-Lopez 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.chlamydosporiaBiocontrol Science and Technology 19 (4): 391-406.

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

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.

Cookson W.R., Osman M., Marschner P., Abaye D.A., Clark I.M., Murphy D.V., Stockdale E.A., Watson C.A. (2007) Controls on soil nitrogen cycling and microbial community composition across land use and incubation temperature  Soil Biology and Biochemistry 39, 744-756

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

Cookson W.R., Marschner P., Clark I.M., Milton N.,Smirk M.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.

Tahseen Q., Clark I.M., Atkins S.D., Hirsch P.R. & Kerry B.R. (2005).  Impact of the nematophagous fungus Pochonia chlamydosporia on nematode and microbial populations. Communications in Agricultural and Applied Biological Sciences 70 81-86.

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 lilacinusFEMS Microbiology Ecology 51 257-264.

Hirsch P.R. & Clark I.M. (2004). Impact of genetically modified bacterial inoculants on the soil microbial community. In GM Crops - Ecological Dimensions. Aspects of Applied Biology 74 141-153.

Atkins S.D., Sosnowska D., Evans V.J., Clark I.M., Hirsch P.R. & Kerry B.R. (2004). Investigation of three nematophagous fungi in two potato cyst nematode suppressive soils. IOBC/wprs Bulletin 27 1-8.

Atkins S.D., Hidalgo-Diaz, L., Clark I.M., Morton C.O., Montes de Oca N., Gray P.A. & Kerry B.R. (2003). Approaches for monitoring the release of   Pochonia chlamydosporia var. catenulata , a biocontrol agent of root-knot nematodes. Mycological Research 107, 206-212.

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.

Theodoulou F.L., Clark I.M., He X-L., Pallett K.E., Cole D.J. & Hallahan D.L.  (2003). Co-induction of glutathione-S-transferases and multidrug resistance associated protein by xenobiotics in wheat. Pest Management Science 59,   202-214.

Tahseen Q., Clark I.M. & Kerry B.R. (2003). Vorticella sp. infestations in nematodes: a report. Nematologia Mediterranea 31, 195-196

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.

Atkins S.D., Clark I.M., Sosnowska D. & 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 79-84.

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

Theodoulou F.L., Clark I.M., Pallett K.E. & 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). Plant Physiology 119, 1567.

Clark I.M., Forde B.G. & 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, 875-885.

Maughan J.A., Nugent J.H.A., Clark I.M., Westlake A.C.G. & Hallahan D.L. (1997). Molecular enzymology of plant cytochromes P450. Proceedings Brighton Crop Protection Conference - Weeds 597-604.

Burnie J.P., Clark I.M. (1995) Immunoblotting in the diagnosis of culture-negative endocarditis caused by Streptoccocci and Enterococci. J. of Clinical  Pathology. 48, 1130-1136.

Wilson A., Clark I.M., Heard S., Munro D,L., Kirkby J.S. (1993) Immunoblotting of Streptococcal antigens in guttate psoriasis.  Brit. J. Dermatology 128 151-  158.  

Clark I.M. and Burnie J.P. (1993). Isolation and sequence determination of an immunodominant antigen from Enterococcus faecalisSerodiagnosis and Immunotherapy of Infectious Diseases 5 85-92.

Hallahan D.L., Cheriton A.K., Hyde R., Clark I. & Forde, B. G. (1993). Plant cytochrome P-450 and agricultural biotechnology. Biochemical Society Transactions 21, 1068-1073.

Clark I.M., Burnie J.P. (1991)  Immunoblotting and culture positive endocarditis. J. of Clinical Pathology 44152-156.

Clark I.M., Burnie J.P., Coke A.P., Matthews R.C., Oppenheim B.A. (1990) Characterisation of the antibody response in Corynebacterium jeikeium septicaemia’s. Epidemol. Infect 105 229-236.

Clark I.M. & Burnie J.P. (1989) Diagnosing endocarditis with the cloned 112 kDa antigen of Enterococcus faecalis. J. Immunological Methods 123 217-225.

Matthews R., Burnie J.P., Fox.A., Baskerville A., Clark .I.M. (1989) The diagnostic and therapeutic potential of a monoclonal antibody to the 60 kD nuclear antigen of Candida albicans.  Serodiagnosis and Immunotherapy In Infectious Diseases 3 75-86.

Burnie J.P., Matthews R., Clark I.M. (1989) Immunoblot fingerprinting of Aspergillus fumigatus. (1989) J. of Immunological Methods 118 179-186.

Matthews R., Burnie J.P., Smith D., Clark I.M., Midgley J., Conolly M. & Gazzard B. (1988) Candida and AIDS: Evidence for protective antibody.  Lancet II 263-266.