Tim Daniell
Currently a Honorary Associate of the Ecological Sciences programme at the James Hutton Institute and an honorary lecturer at Dundee University teaching Microbial Ecology, I have held postdoctoral positions at York, Lancaster and Durham Universities after completing a PhD at Warwick University and degree at Nottingham University.
Current research interests
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Arbuscular mycorrhizal ecology
For many years I have been involved in mycorrhizal ecology focussing on the dynamics of arbuscular mycorrhizal (AM) fungi. I have been heavily involved in the development of the application of molecular methods to improve understanding of community dynamics of this key fungal group resulting in the publication of a number of high impact papers. Work has focussed on the impact of arable farming on AM fungi with published work highlighting the depauperate nature of the group under conventional farming. Additionally work in grasslands discovered both host preference and links to bacterial communities and recent work in a boreal system, through collaboration with the University of Tartu including Maarja Öpik, uncovered an unexpected high richness in AM fungi, linked community structure to functional differences and identified a link between community structure and plant functional group. Current projects include: work primarily by Jane Davidson further exploring community dynamics in arable systems, a PhD student, Alex van den Bos, co supervised by Alison Bennett and Dave Johnson (University of Aberdeen) exploring the effect of tillage on AM fungi community structure and function and work with Alison Bennett and Sandra Caul exploring the role of plant breeding in reducing crop response to AM fungi. -
Microbial nitrogen cycling
Since appointment at the Institute I have been involved in the area of microbial nitrogen cycling in soil. This work area has recently been expanded mainly through an active collaboration with Liz Baggs at Aberdeen). This collaboration has taken the form of joint studentships funded either through NERC CASE or the Institute/University joint scheme. Miriam Herold undertook a project examining the relative role of fungal and bacterial denitrification in arable systems mainly utilising a long term pH gradient at SAC Craibstone. Maddy Giles is exploring the role of rhizodeposition in driving denitrification using artificial root systems. Marcin Skiba, who is also jointly supervised by Tim George, is undertaking a project examining the mechanisms lying behind variation in biological nitrification inhibition (BNI) observed between barley cultivars. Other work in this area, undertaken primarily by Susan Mitchell, is exploring the differences in nitrous oxide emission observed between different barley lines that may provide breeding targets to aid reduced arable farming environmental impacts. -
Free-living nematode dynamics
Nematodes provide an opportunity to understand the soil food web since they are a keystone group with representation at most trophic levels within the soil food web. For this reason free living nematodes have often been suggested as an ideal group for the estimation of soil health although issues associated with sample processing due to time consuming traditional identification have often limited application. A student at the Institute, Suzanne Donn, funded by the BBSRC and supervised jointly with Roy Neilson and Bryan Griffiths (currently at SAC Edinburgh) developed and tested a molecular method based on terminal restriction length polymorphism (T-RFLP). This method allows a massive increase in the numbers of samples that can be analysed which will allow the application of nematode community dynamics to be considered as an indicator of soil health for monitoring purposes. The methodology has been tested in other systems as part of joint student projects undertaken by Xiaoyun Chen, in Ireland also supervised by Bryan Griffiths, Roy Neilson and Vincent O’Flaherty (UNI Galway), and Stefanie Vink on the Machair of the Western Isles (supervised jointly with Roy Neilson and David Robinson, University of Aberdeen). Recently we have undertaken a project, employing Lea Wiesel, exploring spatial structure in a sand dune system to further test and develop the methodology. -
EnPrint
The intransigent nature of soil ecology driven largely by the lack of culturability and high diversity of the associated microbial community has driven a reliance on molecular methodology. These tools have been developed to be robust in relation to co-extracted inhibitors and provide the high throughput of samples required to allow the testing of ecological hypotheses. These tools have other applications that are being exploited through the spin out company EnPrint. Recent developments include a project co-funded by the Technology Strategy Board and Scottish Water to quantify and identify Cryptosporidium species in regulatory water samples.
Bibliography
- Zhou, S.Y.D.; Zhu, D.; Giles, M.; Yang, X-R.; Daniell, T.; Neilson, R.; Zhu, Y-G. (2019) Phyllosphere of staple crops under pig manure fertilization, a reservoir of antibiotic resistance genes., Environmental Pollution, 252, 227-235.
- Zheng, F.; Zhu, D.; Giles, M.E.; Daniell, T.; Neilson, R.; Zhu, Y-G.; Yang, X.R. (2019) Mineral and organic fertilization alters the microbiome of a soil nematode Dorylaimus stagnalis and its resistome., Science of the Total Environment, 680, 70-78.
- Berdeni, D.; Cotton, T.E.A.; Daniell, T.J.; Bidartondo, M.I.; Cameron, D.D.; Evans, K.L. (2018) The effects of arbuscular mycorrhizal fungal colonisation on nutrient status, growth, productivity, and canker resistance of apple (Malus pumila)., Frontiers in Microbiology, 9, Article No. 1461.
- Langarica-Fuentes, A.; Manrubia, M.; Giles, M.E.; Mitchell, S.; Daniell, T.J. (2018) Effect of model root exudate on denitrifier community dynamics and activity at different water-filled pore space levels in a fertilised soil., Soil Biology and Biochemistry, 120, 70-79.
- Herold, M.B.; Giles, M.E.; Alexander, C.J.; Baggs, E.M.; Daniell, T.J. (2018) Variable response of nirK and nirS containing denitrifier communities to long term pH manipulation and cultivation., FEMS Microbiological Letters, 364. Article No. fny035.
- Giles, M.E.; Daniell, T.J.; Baggs, E.M. (2017) Compound driven differences in N2 and N2O emission from soil; the role of substrate use efficiency and the microbial community., Soil Biology and Biochemistry, 106, 90-98.
- Hopkins, D.W.; Wheatley, R.E.; Coakley, C.M.; Daniell, T.J.; Mitchell, S.M.; Newton, A.C.; Neilson, R. (2017) Soil carbon and nitrogen and barley yield responses to repeated additions of compost and slurry., Journal of Agricultural Science, 155, 141-155.
- Shuzhong, G.; Jenkins, A.; Gao, S.J.; Lu, Y.L.; Li, H.; Li, Y.Y.; Ferrier, R.C.; Bailey, M.; Wang, Y.W.; Zhang, Y.; Qi, X.B.; Yu, L.L.; Ding, L.Q.; Daniell, T.; Williams, R.; Hannaford, J.; Acreman, M.; Kirk, S.; Liu, H.X.; Liu, Z.T.; Luo, L.G.; Yan, D.H.; Liu, X.J.; Yu, F.; Wang, D.; Zhang, B.; Ding, A.Z.; Xie, X.R.; Liu, J.; Ma, C.; Jobson, A. (2017) Ensuring water resource security in China; the need for advances in evidence-based policy to support sustainable management., Environmental Science and Policy, 75, 65-69.
- Avó, A.P.; Daniell, T.J.; Neilson, R.; Oliveira, S.; Branco, J.; Adão, H. (2017) DNA barcoding and morphological identification of benthic nematodes assemblages of estuarine intertidal sediments: advances in molecular tools for biodiversity assessment., Frontiers in Marine Science, 4, Article No.66.
- Paterson, E.; Sim, A.; Davidson, J.; Daniell, T.J. (2016) Arbuscular mycorrhizal hyphae promote priming of native soil organic matter mineralisation., Plant and Soil, 408, 243-254.
- Stone, D.; Costa, D.; Daniell, T.J.; Mitchell, S.M.; Topp, C.F.E.; Griffiths, B.S. (2016) Using nematode communities to test a European scale soil biological monitoring programme for policy development., Applied Soil Ecology, 97, 78-85.
- Marshall, J.; Rossez, Y.; Mainda, G.; Gally, D.L.; Daniell, T.J.; Holden, N.J. (2016) Alternate thermoregulation and functional binding of Escherichia coli type 1 fimbriae in environmental and animal isolates., FEMS Microbiology Letters, 363, Article No. fnw251.
- Sjogersten, S.; Caul, S.; Daniell, T.J.; Jurd, A.P.S.; O'Sullivan, O.S.; Stapleton, C.S.; Titman, J.J. (2016) Organic matter chemistry controls greenhouse gas emissions from permafrost peatlands., Soil Biology and Biochemistry, 98, 42-53.
- Squire, G.; Cammarero, D.; Daniell, T.; Newton, A.C.; White, P.J. (2016) Agriculture and forestry climate change report card technical paper. 3. Arable Crops., Living With Environmental Change (LWEC) Network with additional support from the Scottish Government.
- Chen, X.; Daniell, T.J.; Neilson, R.; O'Flaherty, V.; Griffiths, B.S. (2015) Microbial and microfaunal communities in phosphorus limited, grazed grassland change composition but maintain homeostatic nutrient stoichiometry (vol 75, pg 94, 2014)., Soil Biology and Biochemistry, 85, 21.
- Griffiths, B.S.; Hallett, P.D.; Daniell, T.J.; Hawes, C.; Squire, G.S.; Mitchell, S.M.; Caul, S.; Valentine, T.A.; Binnie, K.; Adeloye, A.J.; Rustum, R.; Nevison, I. (2015) Probing soil physical and biological resilience data from a broad sampling of arable farms in Scotland., Soil Use and Management, 31, 491-503.
- Gulden, R.H.; Tenuta, M.; Mitchell, S.; Langarica Fuentes, A.; Daniell, T.J. (2015) Preceding crop and weed management history affect denitrification and denitrifier community structure throughout the development of durum wheat., Agriculture, Ecosystems and Environment, 212, 49-63.
- Wiesel, L.; Daniell, T.J.; King, D.; Neilson, R. (2015) Determination of the optimal soil sample size to accurately characterise nematode communities in soil., Soil Biology and Biochemistry, 80, 89-91.
- Brooker, R.W.; Bennett, A.E.; Cong, W.F.; Daniell, T.J.; George, T.S.; Hallett, P.D.; Hawes, C.; Iannetta, P.P.M.; Jones, H.G.; Karley, A.J.; Li, L.; McKenzie, B.M.; Pakeman, R.J.; Paterson, E.; Schob, C.; Shen, J.; Squire, G.; Watson, C.A.; Zhang, C.; Zhang, J.; White, P.J. (2015) Improving intercropping: a synthesis of research in agronomy, plant physiology and ecology., New Phytologist, 206, 107-117.
- Chen, X.; Daniell, T.J.; Neilson, R.; O'Flaherty, V.; Griffiths, B.S. (2014) Microbial and microfaunal communities in phosphorus limited, grazed grassland change composition but maintain homeostatic nutrient stoichiometry., Soil Biology and Biochemistry, 75, 94-101.
- George, T.S.; French, A.S.; Brown, L.K.; Karley, A.J.; White, P.J.; Ramsay, L.; Daniell, T.J. (2014) Genotypic variation in the ability of landraces and commercial cereal varieties to avoid manganese deficiency in soils with limited manganese availability: is there a role for root-exuded phytases?, Physiologia Plantarum, 151, 243-256.
- Holden, N.J.; Wright, F.; MacKenzie, K.; Marshall, J.; Mitchell, S.; Mahajan, A.; Wheatley, R.; Daniell, T.J. (2014) Prevalence and diversity of Escherichia coli isolated from a barley trial supplemented with bulky organic soil amendments: green compost and bovine slurry., Letters in Applied Microbiology, 58, 205-212.
- Bender, F.S.; Plantenga, F.; Neftel, A.; Jocher, M.; Oberholzer, H-R.; Kohl, L.; Giles, M.; Daniell, T.; Van der Heijden, M.G.A. (2014) Symbiotic relationships between soil fungi and plants reduce N2O emissions from soil., ISME Journal, 8, 1336-1345.
- Sun, B.; Roberts, D.M.; Dennis, P.G.; Caul, S.; Daniell, T.J.; Hallett, P.D.; Hopkins, D.W. (2014) Microbial properties and nitrogen contents of arable soils under different tillage regimes., Soil Use and Management, 30, 152-159.
- Vink, S.N.; Neilson, R.; Robinson, D.; Daniell, T. (2014) Temporal and land use effects on soil bacterial community structure of the machair, an EU Habitats Directive Annex I low-input agricultural system., Applied Soil Ecology, 73, 116-123.
- Hough, R.L.; Bengough, A.G.; Chapman, S.J.; Daniell, T.; Matthews, R.; Squire, G.; Towers, W.; White, P.J. (2014) Heat in the soil form (NIA-NGGT0017)., Interim Report for National Grid.
- Bennett, A.E.; Daniell, T.J.; Opik, M.; Davison, J.; Moora, M.; Zobel, M.; Selosse, M-A.; Evans, D. (2013) Arbuscular mycorrhizal fungal networks vary throughout the growing season and between successional stages., PLoS ONE, 8, Article No. e83241.
- Rivington, M.; Dinnie, E.; Craig, T.; Heslop, S.; Slee, B.; Matthews, R.; Nijnik, M.; Morris, S.; Stewart, D.; Martin-Ortega, J.; Dawson, L.A.; Daniell, T. (2013) Climate: public understanding and policy implications., The James Hutton Institute response to the UK Parliament House of Commons Select Committee Inquiry, April 2013.
- Bennett, A.E.; Daniell, T.J.; White, P.J. (2013) Benefits of breeding crops for yield response to soil organisms., In: de Bruijn, F.J. (ed.). Molecular Microbial Ecology of the Rhizosphere. Wiley-Blackwell, Hoboken, New Jersey. Volume 1, pp17-28.
- Griffiths, B.S.; Daniell, T.J.; Donn, S.; Neilson, R. (2012) Bioindication potential of using molecular characterisation of the nematode community: response to soil tillage., European Journal of Soil Biology, 49, 92-97.
- Giles, M.E.; Morley, N.; Baggs, E.M.; Daniell, T.J. (2012) Soil nitrate reducing processes - drivers, mechanisms for spatial variation, and significance for nitrous oxide production., Frontiers in Microbiology, 3, 407.
- Daniell, T.J.; Davidson, J.; Alexander, C.J.; Caul, S.; Roberts, D. (2012) Improved real-time PCR estimation of gene copy number in soil extracts using an artificial reference., Journal of Microbiological Methods, 91, 38-44.
- Dennis, P.G.; Rushton, S.P.; Laudicina, V.A.; Daniell, T.J.; Ord, V.; Newsham, K.K.; O'Donnell, A.G.; Hopkins, D.W. (2012) Soil fungal community composition does not alter along a latitudinal gradient through the maritime and sub-Antarctic., Fungal Ecology, 5, 403-408.
- Herold, M.B.; Baggs, E.M.; Daniell, T.J. (2012) Fungal and bacterial denitrification are differently affected by long-term pH amendment and cultivation of arable soil., Soil Biology and Biochemistry, 54, 25-35.
- Clark, E.L.; Daniell, T.J.; Wishart, J.; Hubbard, S.F.; Karley, A.J. (2012) How conserved are the bacterial communities associated with aphids? A detailed assessment of the cabbage aphid (Brevicoryne brassicae) using 16S rDNA., Environmental Entomology, 41, 1386-1397.
- Donn, S.; Neilson, R.; Griffiths, B.S.; Daniell, T.J. (2012) A novel molecular approach for rapid assessment of soil nematode assemblages û variation, validation and potential applications., Methods in Ecology and Evolution, 3, 12-23.
- Roberts, D.M.; Schofield, P.; Donn, S.; Daniell, T.J. (2012) Directed terminal restriction analysis tool (DRAT): an aid to enzyme selection for directed terminal restriction fragment length polymorphisms., Methods in Ecology and Evolution, 3, 24-28.
- Neilson, R.; Wiesel, L.; Daniell, T.J. (2012) Validation of a high-throughput nematode molecular tool as a bio-indicator of soil health and quality., Final Report for Genomia, 1-18.
- Davison, J.; Opik, M.; Daniell, T.J.; Moora, M.; Zobel, M. (2011) Arbuscular mycorrhizal fungal communities in plant roots are not random assemblages., FEMS Microbiology Ecology, 78, 103-115.
- Sun, B.; Hallett, P.D.; Caul, S.; Daniell, T.J.; Hopkins, D.W. (2011) Distribution of soil carbon and microbial biomass in arable soils under different tillage regimes., Plant and Soil, 338, 17-25.
- Zhou, S.Y.D.; Zhu, D.; Giles, M.; Yang, X-R.; Daniell, T.; Neilson, R.; Zhu, Y-G. (2019) Phyllosphere of staple crops under pig manure fertilization, a reservoir of antibiotic resistance genes., Environmental Pollution, 252, 227-235.
- Zheng, F.; Zhu, D.; Giles, M.E.; Daniell, T.; Neilson, R.; Zhu, Y-G.; Yang, X.R. (2019) Mineral and organic fertilization alters the microbiome of a soil nematode Dorylaimus stagnalis and its resistome., Science of the Total Environment, 680, 70-78.
- Berdeni, D.; Cotton, T.E.A.; Daniell, T.J.; Bidartondo, M.I.; Cameron, D.D.; Evans, K.L. (2018) The effects of arbuscular mycorrhizal fungal colonisation on nutrient status, growth, productivity, and canker resistance of apple (Malus pumila)., Frontiers in Microbiology, 9, Article No. 1461.
- Langarica-Fuentes, A.; Manrubia, M.; Giles, M.E.; Mitchell, S.; Daniell, T.J. (2018) Effect of model root exudate on denitrifier community dynamics and activity at different water-filled pore space levels in a fertilised soil., Soil Biology and Biochemistry, 120, 70-79.
- Herold, M.B.; Giles, M.E.; Alexander, C.J.; Baggs, E.M.; Daniell, T.J. (2018) Variable response of nirK and nirS containing denitrifier communities to long term pH manipulation and cultivation., FEMS Microbiological Letters, 364. Article No. fny035.
- Giles, M.E.; Daniell, T.J.; Baggs, E.M. (2017) Compound driven differences in N2 and N2O emission from soil; the role of substrate use efficiency and the microbial community., Soil Biology and Biochemistry, 106, 90-98.
- Hopkins, D.W.; Wheatley, R.E.; Coakley, C.M.; Daniell, T.J.; Mitchell, S.M.; Newton, A.C.; Neilson, R. (2017) Soil carbon and nitrogen and barley yield responses to repeated additions of compost and slurry., Journal of Agricultural Science, 155, 141-155.
- Shuzhong, G.; Jenkins, A.; Gao, S.J.; Lu, Y.L.; Li, H.; Li, Y.Y.; Ferrier, R.C.; Bailey, M.; Wang, Y.W.; Zhang, Y.; Qi, X.B.; Yu, L.L.; Ding, L.Q.; Daniell, T.; Williams, R.; Hannaford, J.; Acreman, M.; Kirk, S.; Liu, H.X.; Liu, Z.T.; Luo, L.G.; Yan, D.H.; Liu, X.J.; Yu, F.; Wang, D.; Zhang, B.; Ding, A.Z.; Xie, X.R.; Liu, J.; Ma, C.; Jobson, A. (2017) Ensuring water resource security in China; the need for advances in evidence-based policy to support sustainable management., Environmental Science and Policy, 75, 65-69.
- Avó, A.P.; Daniell, T.J.; Neilson, R.; Oliveira, S.; Branco, J.; Adão, H. (2017) DNA barcoding and morphological identification of benthic nematodes assemblages of estuarine intertidal sediments: advances in molecular tools for biodiversity assessment., Frontiers in Marine Science, 4, Article No.66.
- Paterson, E.; Sim, A.; Davidson, J.; Daniell, T.J. (2016) Arbuscular mycorrhizal hyphae promote priming of native soil organic matter mineralisation., Plant and Soil, 408, 243-254.
- Stone, D.; Costa, D.; Daniell, T.J.; Mitchell, S.M.; Topp, C.F.E.; Griffiths, B.S. (2016) Using nematode communities to test a European scale soil biological monitoring programme for policy development., Applied Soil Ecology, 97, 78-85.
- Marshall, J.; Rossez, Y.; Mainda, G.; Gally, D.L.; Daniell, T.J.; Holden, N.J. (2016) Alternate thermoregulation and functional binding of Escherichia coli type 1 fimbriae in environmental and animal isolates., FEMS Microbiology Letters, 363, Article No. fnw251.
- Sjogersten, S.; Caul, S.; Daniell, T.J.; Jurd, A.P.S.; O'Sullivan, O.S.; Stapleton, C.S.; Titman, J.J. (2016) Organic matter chemistry controls greenhouse gas emissions from permafrost peatlands., Soil Biology and Biochemistry, 98, 42-53.
- Chen, X.; Daniell, T.J.; Neilson, R.; O'Flaherty, V.; Griffiths, B.S. (2015) Microbial and microfaunal communities in phosphorus limited, grazed grassland change composition but maintain homeostatic nutrient stoichiometry (vol 75, pg 94, 2014)., Soil Biology and Biochemistry, 85, 21.
- Griffiths, B.S.; Hallett, P.D.; Daniell, T.J.; Hawes, C.; Squire, G.S.; Mitchell, S.M.; Caul, S.; Valentine, T.A.; Binnie, K.; Adeloye, A.J.; Rustum, R.; Nevison, I. (2015) Probing soil physical and biological resilience data from a broad sampling of arable farms in Scotland., Soil Use and Management, 31, 491-503.
- Gulden, R.H.; Tenuta, M.; Mitchell, S.; Langarica Fuentes, A.; Daniell, T.J. (2015) Preceding crop and weed management history affect denitrification and denitrifier community structure throughout the development of durum wheat., Agriculture, Ecosystems and Environment, 212, 49-63.
- Wiesel, L.; Daniell, T.J.; King, D.; Neilson, R. (2015) Determination of the optimal soil sample size to accurately characterise nematode communities in soil., Soil Biology and Biochemistry, 80, 89-91.
- Brooker, R.W.; Bennett, A.E.; Cong, W.F.; Daniell, T.J.; George, T.S.; Hallett, P.D.; Hawes, C.; Iannetta, P.P.M.; Jones, H.G.; Karley, A.J.; Li, L.; McKenzie, B.M.; Pakeman, R.J.; Paterson, E.; Schob, C.; Shen, J.; Squire, G.; Watson, C.A.; Zhang, C.; Zhang, J.; White, P.J. (2015) Improving intercropping: a synthesis of research in agronomy, plant physiology and ecology., New Phytologist, 206, 107-117.
- Chen, X.; Daniell, T.J.; Neilson, R.; O'Flaherty, V.; Griffiths, B.S. (2014) Microbial and microfaunal communities in phosphorus limited, grazed grassland change composition but maintain homeostatic nutrient stoichiometry., Soil Biology and Biochemistry, 75, 94-101.
- George, T.S.; French, A.S.; Brown, L.K.; Karley, A.J.; White, P.J.; Ramsay, L.; Daniell, T.J. (2014) Genotypic variation in the ability of landraces and commercial cereal varieties to avoid manganese deficiency in soils with limited manganese availability: is there a role for root-exuded phytases?, Physiologia Plantarum, 151, 243-256.
- Holden, N.J.; Wright, F.; MacKenzie, K.; Marshall, J.; Mitchell, S.; Mahajan, A.; Wheatley, R.; Daniell, T.J. (2014) Prevalence and diversity of Escherichia coli isolated from a barley trial supplemented with bulky organic soil amendments: green compost and bovine slurry., Letters in Applied Microbiology, 58, 205-212.
- Bender, F.S.; Plantenga, F.; Neftel, A.; Jocher, M.; Oberholzer, H-R.; Kohl, L.; Giles, M.; Daniell, T.; Van der Heijden, M.G.A. (2014) Symbiotic relationships between soil fungi and plants reduce N2O emissions from soil., ISME Journal, 8, 1336-1345.
- Sun, B.; Roberts, D.M.; Dennis, P.G.; Caul, S.; Daniell, T.J.; Hallett, P.D.; Hopkins, D.W. (2014) Microbial properties and nitrogen contents of arable soils under different tillage regimes., Soil Use and Management, 30, 152-159.
- Vink, S.N.; Neilson, R.; Robinson, D.; Daniell, T. (2014) Temporal and land use effects on soil bacterial community structure of the machair, an EU Habitats Directive Annex I low-input agricultural system., Applied Soil Ecology, 73, 116-123.
- Bennett, A.E.; Daniell, T.J.; Opik, M.; Davison, J.; Moora, M.; Zobel, M.; Selosse, M-A.; Evans, D. (2013) Arbuscular mycorrhizal fungal networks vary throughout the growing season and between successional stages., PLoS ONE, 8, Article No. e83241.
- Griffiths, B.S.; Daniell, T.J.; Donn, S.; Neilson, R. (2012) Bioindication potential of using molecular characterisation of the nematode community: response to soil tillage., European Journal of Soil Biology, 49, 92-97.
- Giles, M.E.; Morley, N.; Baggs, E.M.; Daniell, T.J. (2012) Soil nitrate reducing processes - drivers, mechanisms for spatial variation, and significance for nitrous oxide production., Frontiers in Microbiology, 3, 407.
- Daniell, T.J.; Davidson, J.; Alexander, C.J.; Caul, S.; Roberts, D. (2012) Improved real-time PCR estimation of gene copy number in soil extracts using an artificial reference., Journal of Microbiological Methods, 91, 38-44.
- Dennis, P.G.; Rushton, S.P.; Laudicina, V.A.; Daniell, T.J.; Ord, V.; Newsham, K.K.; O'Donnell, A.G.; Hopkins, D.W. (2012) Soil fungal community composition does not alter along a latitudinal gradient through the maritime and sub-Antarctic., Fungal Ecology, 5, 403-408.
- Herold, M.B.; Baggs, E.M.; Daniell, T.J. (2012) Fungal and bacterial denitrification are differently affected by long-term pH amendment and cultivation of arable soil., Soil Biology and Biochemistry, 54, 25-35.
- Clark, E.L.; Daniell, T.J.; Wishart, J.; Hubbard, S.F.; Karley, A.J. (2012) How conserved are the bacterial communities associated with aphids? A detailed assessment of the cabbage aphid (Brevicoryne brassicae) using 16S rDNA., Environmental Entomology, 41, 1386-1397.
- Donn, S.; Neilson, R.; Griffiths, B.S.; Daniell, T.J. (2012) A novel molecular approach for rapid assessment of soil nematode assemblages û variation, validation and potential applications., Methods in Ecology and Evolution, 3, 12-23.
- Roberts, D.M.; Schofield, P.; Donn, S.; Daniell, T.J. (2012) Directed terminal restriction analysis tool (DRAT): an aid to enzyme selection for directed terminal restriction fragment length polymorphisms., Methods in Ecology and Evolution, 3, 24-28.
- Davison, J.; Opik, M.; Daniell, T.J.; Moora, M.; Zobel, M. (2011) Arbuscular mycorrhizal fungal communities in plant roots are not random assemblages., FEMS Microbiology Ecology, 78, 103-115.
- Skiba, M.W.; George, T.S.; Baggs, E.M.; Daniell, T.J. (2011) Plant influence on nitrification., Biochemical Society Transactions, 39, 275-278.
- Donn, S.; Neilson, R.; Griffiths, B.S.; Daniell, T.J. (2011) Greater coverage of the phylum Nematoda for SSU rDNA studies., Biology and Fertility of Soils, 47, 333-339.
- Sun, B.; Hallett, P.D.; Caul, S.; Daniell, T.J.; Hopkins, D.W. (2011) Distribution of soil carbon and microbial biomass in arable soils under different tillage regimes., Plant and Soil, 338, 17-25.
- Cooper, J.M.; Burton, D.; Daniell, T.J.; Griffiths, B.S.; Zebarth, B.J. (2011) Carbon mineralization kinetics and soil biological characteristics as influenced by manure addition in soil incubated at a range of temperatures., European Journal of Soil Biology, 47, 392-399.
- Griffiths, B.S.; Ball, B.C.; Daniell, T.J.; Hallett, P.D.; Neilson, R.; Wheatley, R.E.; Osler, G.; Bohanec, M. (2010) Integrating soil quality changes to arable agricultural systems following organic matter addition, or adoption of a ley-arable rotation., Applied Soil Ecology, 46, 43-53.
- Deng, H.; Zhang, B.; Yin, R.; Wang, H.L.; Mitchell, S.M.; Griffiths, B.S.; Daniell, T.J. (2010) Long-term effect of re-vegetation on the microbial community of a severely eroded soil in sub-tropical China., Plant and Soil, 328, 447-458.
- Hallett, P.D.; Caul, S.; Daniell, T.J.; Barre, P.; Paterson, E. (2010) The rheology of rhizosphere formation by root exudates and soil microbes., Proceedings of the 19th World Congress of Soil Science, Brisbane, Australia, 1-6 August 2010. (Poster)
- Bennett, A.E.; Daniell, T.J.; White, P.J. (2013) Benefits of breeding crops for yield response to soil organisms., In: de Bruijn, F.J. (ed.). Molecular Microbial Ecology of the Rhizosphere. Wiley-Blackwell, Hoboken, New Jersey. Volume 1, pp17-28.
- Daniell, T.J. (2011) Biodiversity in arable soil., In: Pakeman, R.J. (ed.). Biodiversity and Farming. A summary of research outputs from the Scottish Government's "Environment - Land Use and Rural Stewardship" research programme. Macaulay Land Use Research Institute, Aberdeen, 12-13.
- Neilson, R.; Donn, S.; Griffiths, B.S.; Daniell, T.J.; Rybarczyk, K.D.; van den Elsen, S.; Mooyman, P.; Helder, J. (2009) Molecular tools for analysing nematode assemblages., In: Wilson, M.J. & Kakouli-Duarte, T. (eds.). Nematodes as Environmental Indicators. CABI, Wallingford, pp188-207.
- Opik, M.; Saks, U.; Kennedy, J.; Daniell, T.J. (2008) Global diversity patterns of arbuscular mycorrhizal fungi - community composition and links with functionality., In: Varma, A. (ed.). Mycorrhiza: Genetics and Molecular Biology, ECO-function, Biotechnology, ECO-physiology, Structure and Systematics. Springer, Berlin, Heidelberg, 3rd edition, pp89-111.
- Walters, D.R.; Daniell, T.J. (2007) Microbial induction of resistance to pathogens., In: Walters, D.R., Newton, A.C. & Lyon, G.D. (eds.). Induced Resistance for Plant Defence: A Sustainable Approach to Crop Protection. Blackwell Publishing, Oxford, Chapter 8, 143-156.
- Whigham, D.F.; O'Neill, J.; McCormick, M.; Smith, C.; Rasmussen, H.; Caldwell, B.; Daniell, T.J. (2002) Interactions between decomposing wood, mycorrhizas, and terrestrial orchid seeds and protocorms., In: Kindlmann, P., Willems, J.H. & Whigham, D.F. (eds.). Trends and Fluctuations and Underlying Mechanisms in Terrestrial Orchid Populations. Backhuys Publishers, Leiden, The Netherlands, pp117-131.
- Clapp, J.P.; Helgason, T.; Daniell, T.J.; Young, J.P.W. (2002) Genetic studies of the structure and diversity of arbuscular mycorrhizal fungal communities., In: van der Heiden, M. & Sanders, I. (eds.). Mycorrhizal Ecology. Springer-Verlag, Heidelberg, pp201-221.
- Squire, G.; Cammarero, D.; Daniell, T.; Newton, A.C.; White, P.J. (2016) Agriculture and forestry climate change report card technical paper. 3. Arable Crops., Living With Environmental Change (LWEC) Network with additional support from the Scottish Government.
- Hough, R.L.; Bengough, A.G.; Chapman, S.J.; Daniell, T.; Matthews, R.; Squire, G.; Towers, W.; White, P.J. (2014) Heat in the soil form (NIA-NGGT0017)., Interim Report for National Grid.
- Rivington, M.; Dinnie, E.; Craig, T.; Heslop, S.; Slee, B.; Matthews, R.; Nijnik, M.; Morris, S.; Stewart, D.; Martin-Ortega, J.; Dawson, L.A.; Daniell, T. (2013) Climate: public understanding and policy implications., The James Hutton Institute response to the UK Parliament House of Commons Select Committee Inquiry, April 2013.
- Neilson, R.; Wiesel, L.; Daniell, T.J. (2012) Validation of a high-throughput nematode molecular tool as a bio-indicator of soil health and quality., Final Report for Genomia, 1-18.
- Neilson, R.; Donn, S.; Chen, X.Y.; Griffiths, B.S.; O'Flaherty, V.; Daniell, T.J. (2011) Molecular methods for monitoring soil nematodes and their potential use as biologicalindicators of soil health., Annual Report of the Scottish Crop Research Institute for 2010, pp37-38.
- Wheatley, R.E.; Hawes, C.; Daniell, T.J.; Birch, A.N.E. (2006) Management impacts on arable diversity and function., Annual Report of the Scottish Crop Research Institute for 2006, pp40-41.
- Forster, B.P.; Bengough, A.G.; Ellis, R.P.; Thomas, W.T.B.; Clark, S.; Gordon, D.C.; El-Meniae, R.; Keith, R.; Waugh, R.; Hedley, P.E.; Daniell, T.J. (2002) Genomics of the root-soil interface., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp153-154.
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