Dr Tim Daniell
Department of Animal and Plant Sciences
N8 Chair in Soil Microbiology
+44 114 222 0137
Full contact details
Department of Animal and Plant Sciences
Arthur Willis Environment Centre
- 2016-present: N8 Chair in Soil Microbiology, Department of Animal and Plant Sciences, University of Sheffield
- 2016-present: Research Leader in Soil Ecology (Grade G), The James Hutton Institute, Invergowrie, Dundee
- 2015-2016: Adjunct Chair in Rhizosphere Interactions, Department of Animal and Plant Sciences, University of Sheffield
- 2013-2016: Theme Leader – Sustainable Production Systems, (Grade G) The James Hutton Institute, Invergowrie, Dundee
- 2011-2013: Research Leader in Soil Ecology (Grade F), The James Hutton Institute, Invergowrie, Dundee
- 2009-2011: Research Leader in Soil Ecology (Grade F), Scottish Crop Research Institute (SCRI), Invergowrie, Dundee
- 2000-2009: Research Leader in Soil Ecology (Grade 5/E), Scottish Crop Research Institute (SCRI), Invergowrie, Dundee
- 1997-2000: Research Fellow, Department of Biology, University of York
- 1995-1997: Senior Research Assistant, Biological Sciences, Lancaster University
- 1992-1995: Research Associate, Biological Sciences, University of Durham
- 1992: PhD, Department of Biological Sciences, University of Warwick: Regulation of expression of the glutamine synthetase gln-α gene of Phaseolus vulgaris L., Supervisor: Dr Julie Cullimore
- 1988: BSc (Hons), Biological Sciences, University of Nottingham
- Research interests
Arbuscular mycorrhizal ecology
For many years I have been involved in mycorrhizal ecology focusing 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. My work has focused on the impact of arable farming on AM fungi with published work highlighting the depauperate nature of the group under conventional farming. In addition, work in grasslands discovered both host preference and links to bacterial communities and recent research in a boreal system (in collaboration with Maarja Öpike and others at the University of Tartu) 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 with Alison Bennett and Dave Johnson at the 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 Sheffield, I have become involved in the area of microbial nitrogen cycling in soil. This work has expanded - mainly through a collaboration with Liz Baggs at Aberdeen and 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 key group with representation at most trophic levels within that 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.
Suzanne Donnn (funded by the BBSRC and supervised jointly with Roy Neilson and Bryan Griffiths (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.
This methodology has been tested in other systems as part of joint student projects undertaken by Xiaoyun Chen, in Ireland (co-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).
Most recently, we have employed Lea Wiesel to explore spatial structure in a sand dune system to further test and develop the methodology.
This person does not have any publications available.
- Role of microbial communities in conferring resistance and resilience of soil carbon and nitrogen cycling following contrasting stresses. European Journal of Soil Biology, 104.
- Impact of land use and management practices on soil nematode communities of Machair, a low-input calcareous ecosystem of conservation importance. Science of The Total Environment. View this article in WRRO
- Mycorrhizas for a changing world: Sustainability, conservation, and society. Plants, People, Planet, 2(2), 98-103. View this article in WRRO
- Does reduced usage of antibiotics in livestock production mitigate the spread of antibiotic resistance in soil, earthworm guts, and the phyllosphere?. Environment International, 136. View this article in WRRO
- A commercial arbuscular mycorrhizal inoculum increases root colonisation across wheat cultivars but does not increase assimilation of mycorrhiza-acquired nutrients. Plants, People, Planet. View this article in WRRO
- Phyllosphere of staple crops under pig manure fertilization, a reservoir of antibiotic resistance genes. Environmental Pollution, 252(Part A), 227-235. View this article in WRRO
- Mineral and organic fertilization alters the microbiome of a soil nematode Dorylaimus stagnalis and its resistome. The Science of The Total Environment, 680, 70-78. View this article in WRRO
- The Effects of Arbuscular Mycorrhizal Fungal Colonisation on Nutrient Status, Growth, Productivity, and Canker Resistance of Apple (Malus pumila). Frontiers in Microbiology, 9. View this article in WRRO
- Effect of model root exudate on denitrifier community dynamics and activity at different water-filled pore space levels in a fertilised soil. Soil Biology & Biochemistry, 120, 70-79. View this article in WRRO
- Variable response of nirK and nirS containing denitrifier communities to long term pH manipulation and cultivation. Fems Microbiology Letters. View this article in WRRO
- Ensuring water resource security in China; the need for advances in evidence based policy to support sustainable management.. Environmental Science & Policy, 75, 65-69. View this article in WRRO
- DNA Barcoding and Morphological Identification of Benthic Nematodes Assemblages of Estuarine Intertidal Sediments: Advances in Molecular Tools for Biodiversity Assessment. Frontiers in Marine Science. View this article in WRRO
- 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. View this article in WRRO
- Alternate thermoregulation and functional binding of Escherichia coli type 1 fimbriae in environmental and animal isolates. FEMS Microbiology Letters, 363(22). View this article in WRRO
- Arbuscular mycorrhizal hyphae promote priming of native soil organic matter mineralisation. Plant and Soil, 408(1), 243-254.
- Soil carbon and nitrogen and barley yield responses to repeated additions of compost and slurry. The Journal of Agricultural Science, 1-15.
- Organic matter chemistry controls greenhouse gas emissions from permafrost peatlands. Soil Biology and Biochemistry, 98, 42-53.
- Using nematode communities to test a European scale soil biological monitoring programme for policy development. Applied Soil Ecology, 97, 78-85.
- Preceding crop and weed management history affect denitrification and denitrifier community structure throughout the development of durum wheat. Agriculture, Ecosystems & Environment, 212, 49-63.
- Probing soil physical and biological resilience data from a broad sampling of arable farms in Scotland. Soil Use and Management, 31(4), 491-503.
- Corrigendum to “Microbial and microfaunal communities in phosphorus limited, grazed grassland change composition but maintain homeostatic nutrient stoichiometry” [Soil Biol. Biochem. 75 (2014) 94–101]. Soil Biology and Biochemistry, 85, 21-21.
- Improving intercropping: a synthesis of research in agronomy, plant physiology and ecology. New Phytologist, 206(1), 107-117.
- Determination of the optimal soil sample size to accurately characterise nematode communities in soil. Soil Biology and Biochemistry, 80, 89-91.
- Microbial and microfaunal communities in phosphorus limited, grazed grassland change composition but maintain homeostatic nutrient stoichiometry. Soil Biology and Biochemistry, 75, 94-101.
- 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(3), 243-256.
- Symbiotic relationships between soil fungi and plants reduce N2O emissions from soil. The ISME Journal, 8, 1336-1345.
- Prevalence and diversity ofEscherichia coliisolated from a barley trial supplemented with bulky organic soil amendments: green compost and bovine slurry. Letters in Applied Microbiology, 58(3), 205-212.
- Microbial properties and nitrogen contents of arable soils under different tillage regimes. Soil Use and Management, 30(1), 152-159.
- 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.
- How Conserved Are the Bacterial Communities Associated With Aphids? A Detailed Assessment of the Brevicoryne brassicae (Hemiptera: Aphididae) Using 16S rDNA. Environmental Entomology, 41(6), 1386-1397.
- Corrigendum to “Soil fungal community composition does not alter along a latitudinal gradient through the maritime and sub-Antarctic” Fungal Ecology (2012) 5 (4) 403–408. Fungal Ecology, 5(6), 759-759.
- Fungal and bacterial denitrification are differently affected by long-term pH amendment and cultivation of arable soil. Soil Biology and Biochemistry, 54, 25-35.
- Improved real-time PCR estimation of gene copy number in soil extracts using an artificial reference. Journal of Microbiological Methods, 91(1), 38-44.
- Bioindication potential of using molecular characterisation of the nematode community: Response to soil tillage. European Journal of Soil Biology, 49, 92-97.
- Directed terminal restriction analysis tool (DRAT): an aid to enzyme selection for directed terminal-restriction fragment length polymorphisms. Methods in Ecology and Evolution, 3(1), 24-28.
- A novel molecular approach for rapid assessment of soil nematode assemblages - variation, validation and potential applications. Methods in Ecology and Evolution, 3(1), 12-23.
- 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(6), 392-399.
- Arbuscular mycorrhizal fungal communities in plant roots are not random assemblages. FEMS Microbiology Ecology, 78(1), 103-115.
- Greater coverage of the phylum Nematoda in SSU rDNA studies. Biology and Fertility of Soils, 47(3), 333-339.
- Plant influence on nitrification. Biochemical Society Transactions, 39(1), 275-278.
- Distribution of soil carbon and microbial biomass in arable soils under different tillage regimes. Plant and Soil, 338(1-2), 17-25.
- Integrating soil quality changes to arable agricultural systems following organic matter addition, or adoption of a ley-arable rotation. Applied Soil Ecology, 46(1), 43-53.
- A comparison of molecular methods for monitoring soil nematodes and their use as biological indicators. European Journal of Soil Biology, 46(5), 319-324.
- Pathogenesis, parasitism and mutualism in the trophic space of microbe–plant interactions. Trends in Microbiology, 18(8), 365-373.
- Plant treatment, pollutant load, and soil type effects in rhizosphere ecology of trace element polluted soils. Ecotoxicology and Environmental Safety, 73(5), 970-981.
- Does microbial habitat or community structure drive the functional stability of microbes to stresses following re-vegetation of a severely degraded soil?. Soil Biology and Biochemistry, 42(5), 850-859.
- Long-term effect of re-vegetation on the microbial community of a severely eroded soil in sub-tropical China. Plant and Soil, 328(1-2), 447-458.
- Extracellular release of a heterologous phytase from roots of transgenic plants: does manipulation of rhizosphere biochemistry impact microbial community structure?. FEMS Microbiology Ecology, 70(3), 433-445.
- Differential effect of arbuscular mycorrhizal fungal communities from ecosystems along management gradient on the growth of forest understorey plant species. Soil Biology and Biochemistry, 41(10), 2141-2146.
- Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytologist, 184(2), 424-437.
- Viruses in soils: morphological diversity and abundance in the rhizosphere. Annals of Applied Biology, 155(1), 51-60.
- Using molecular phylogeny to investigate the bacteria associated with the cabbage aphid (Brevicoryne brassicae). Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 153(2), S47-S47.
- Gas chromatographic metabolic profiling: A sensitive tool for functional microbial ecology. Journal of Microbiological Methods, 75(3), 491-500.
- High diversity of arbuscular mycorrhizal fungi in a boreal herb-rich coniferous forest. New Phytologist, 179(3), 867-876.
- DNA extraction from soil nematodes for multi-sample community studies. Applied Soil Ecology, 38(1), 20-26.
- Relationship between assemblages of mycorrhizal fungi and bacteria on grass roots. Environmental Microbiology, 10(2), 534-541.
- Spatial pattern and species richness of boreonemoral forest understorey and its determinants—A comparison of differently managed forests. Forest Ecology and Management, 250(1-2), 64-70.
- Molecular sequencing and morphological analysis of a nematode community. Applied Soil Ecology, 32(3), 325-337.
- Three-dimensional Microorganization of the Soil–Root–Microbe System. Microbial Ecology, 52(1), 151-158.
- Links between Plant and Rhizoplane Bacterial Communities in Grassland Soils, Characterized Using Molecular Techniques. Applied and Environmental Microbiology, 71(11), 6784-6792.
- Community-level responses of metabolically-active soil microorganisms to the quantity and quality of substrate inputs. Soil Biology and Biochemistry, 36(5), 841-848.
- Linking the bacterial community in pea aphids with host-plant use and natural enemy resistance. Ecological Entomology, 29(1), 60-65.
- Does the presence of glomalin relate to reduced water infiltration through hydrophobicity?. Canadian Journal of Soil Science, 84(4), 365-372.
- Microbial population dynamics related to temporal variations in nitrification in three arable fields. European Journal of Soil Science, 54(4), 707-714.
- Diversity of Bacteria Associated with Natural Aphid Populations. Applied and Environmental Microbiology, 69(12), 7216-7223.
- Arbuscular mycorrhizal community composition associated with two plant species in a grassland ecosystem. Molecular Ecology, 11(8), 1555-1564.
- Isolation and identification of synthetic pyrethroid-degrading bacteria. Journal of Applied Microbiology, 92(3), 534-540.
- Molecular diversity of arbuscular mycorrhizal fungi colonising arable crops. FEMS Microbiology Ecology, 36(2-3), 203-209.
- Development of a genetically modified bacteriophage for use in tracing sources of pollution. Journal of Applied Microbiology, 88(5), 860-869.
- How many fungi does it take to change a plant community?. Trends in Plant Science, 4(3), 81-82.
- Resource sharing in plant–fungus communities: did the carbon move for you?. Trends in Ecology & Evolution, 14(2), 70-70.
- Ploughing up the wood-wide web?. Nature, 394(6692), 431-431.
- Methylation reactions and the phytoalexin response in alfalfa suspension cultures. Planta, 201(3), 359-367.
- Alfalfa cell cultures treated with a fungal elicitor accumulate flavone metabolites rather than isoflavones in the presence of the methylation inhibitor tubericidin. Phytochemistry, 44(2), 285-291.
- Changes in protein methylation associated with the elicitation response in cell cultures of alfalfa (Medicago sativa L.). FEBS Letters, 360(1), 57-61.
- Arbuscular Mycorrhizal Fungal Networks Vary throughout the Growing Season and between Successional Stages. PLoS ONE, 8(12), e83241-e83241.
- Soil nitrate reducing processes – drivers, mechanisms for spatial variation, and significance for nitrous oxide production. Frontiers in Microbiology, 3. View this article in WRRO
- Whole plant-environment microscopy reveals how Bacillus subtilis utilises the soil pore space to colonise plant roots.
- Molecular tools for analysing nematode assemblages., Nematodes as environmental indicators (pp. 188-207). CABI
- The use of arbuscular mycorrhizal fungi to improve root function and nutrient use efficiency In Gregory P (Ed.), Understanding and improving crop root function
Conference proceedings papers
- Soil fungal community composition does not alter along a latitudinal gradient through the maritime and sub-Antarctic. Fungal Ecology, Vol. 5(4) (pp 403-408)
- EARTH'S FRAGILE SYSTEMS: THE MACHAIR OF SCOTLAND - A CASE STUDY.. JOURNAL OF NEMATOLOGY, Vol. 41(4) (pp 391-392)
- T-RFLP approaches to nematode assemblage analysis.. JOURNAL OF NEMATOLOGY, Vol. 39(1) (pp 81-81)
- Dna extraction from soil fauna.. JOURNAL OF NEMATOLOGY, Vol. 39(1) (pp 81-81)
- Novel application of T-RFLP techniques to characterise the diet of three species of predatory Mononchidae.. JOURNAL OF NEMATOLOGY, Vol. 38(2) (pp 285-285)
- Interactions between decomposing wood, mycorrhizas, and terrestrial orchid seeds and protocorms. TRENDS AND FLUCTUATIONS AND UNDERLYING MECHANISMS IN TERRESTRIAL ORCHID POPULATIONS (pp 117-131)
- Inducibility of the glutamine synthetase gene family in Phaseolus vulgaris L. (pp 79-96)
- Professional activities
- Editorial Board: FEMS Microbiology Letters (Section editor for Environmental Microbiology) and Frontiers in Microbiology
- Committee memberships: BES special interest group “Plants, Soils, Ecosystems”
- Honorary Lecturer, University of Dundee
- European Science Foundation – Review panel member
- Member of BBSRC pool of experts