Professor Tim Daniell
School of Biosciences
Chair
t.j.daniell@sheffield.ac.uk
+44 114 222 0137
+44 114 222 0137
A05, Arthur Willis Environment Centre
Full contact details
Professor Tim Daniell
School of Biosciences
A05
Arthur Willis Environment Centre
Maxfield Avenue
Sheffield
S10 1AE
School of Biosciences
A05
Arthur Willis Environment Centre
Maxfield Avenue
Sheffield
S10 1AE
- Profile
-
- 2016-present: N8 Chair in Soil Microbiology, School of Biosciences, University of Sheffield
- 2016-2019: 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
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Arbuscular mycorrhizal ecology
My work was amongst the first to apply molecular techniques to the study of this important, but poorly studied, group of fungi. I have demonstrated that diversity is heavily impacted by arable practice, there is host preference in the symbiosis and that mycorrhiza can impact other soil processes. Currently I am involved in projects exploring the dynamics of AM fungal communities across disturbance gradients, the interplay between AMF and fine root endophyte fungi in the arbuscular symbiosis and the role that this symbiosis could play in sustainable agricultural systems.
Soil nitrogen dynamics
I am interested in soil N dynamics with a particular focus on agricultural systems. This has led to an increased understanding of the role of fungi in denitrification dynamics, the role of management in denitrifier and nitrifier community size and structure, the impact of different substrates and to the role of plants and their mycorrhizal status in moderating nitrification and denitrification rates. Much of this work is now reaching fruition with data from projects investigating the role of root exudates and land use in driving N dynamics. Current projects and applications are exploring the possibility that detrimental impacts of agriculture can be mitigated through crop breeding and/or changes in fertilisation practice.
- Publications
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Journal articles
- Preferential nitrogen and carbon exchange dynamics in Mucoromycotina “fine root endophyte”-plant symbiosis. Current Biology.
- Plant pests influence the movement of plant-fixed carbon and fungal-acquired nutrients through arbuscular mycorrhizal networks. Functional Ecology.
- Measuring the transition to regenerative agriculture in the UK with a co-designed experiment: design, methods and expected outcomes. Environmental Research: Food Systems, 1(2), 025007-025007.
- Mobility and growth in confined spaces are important mechanisms for the establishment of Bacillus subtilis in the rhizosphere. Microbiology, 170(8).
- The functionality of arbuscular mycorrhizal networks across
scales of experimental complexity and ecological relevance. Functional Ecology. View this article in WRRO
- Organic fertilization reduces nitrous oxide emission by altering nitrogen cycling microbial guilds favouring complete denitrification at soil aggregate scale. Science of The Total Environment, 174178-174178.
- Correction to: Patterns and determinants of microbial- and plant-derived carbon contributions to soil organic carbon in tea plantation chronosequence. Plant and Soil, 1-1.
- Patterns and determinants of microbial- and plant-derived carbon contributions to soil organic carbon in tea plantation chronosequence. Plant and Soil, 1-15.
- Awakening soil microbial utilization of nitrate by carbon regulation to lower nitrogen pollution. Agriculture, Ecosystems & Environment, 362, 108848-108848.
- Phyllosphere antibiotic resistome in a natural primary vegetation across a successional sequence after glacier retreat. Environment International, 174, 107903-107903.
- The potential role of Mucoromycotina ‘fine root endophytes’ in plant nitrogen nutrition. Physiologia Plantarum.
- Collective movement by soil bacteria during the colonisation of the rhizosphere.
- Variation in mycorrhizal growth response among a spring wheat mapping population shows potential to breed for symbiotic benefit. Food and Energy Security. View this article in WRRO
- A widely distributed phosphate-insensitive phosphatase presents a route for rapid organophosphorus remineralization in the biosphere. Proceedings of the National Academy of Sciences, 119(5).
- Evidence of a plant genetic basis for maize roots impacting soil organic matter mineralization. Soil Biology and Biochemistry, 161, 108402-108402.
- Mycorrhizal mediation of sustainable development goals. Plants, People, Planet, 3(5), 430-432. View this article in WRRO
- How does partial substitution of chemical fertiliser with organic forms increase sustainability of agricultural production?. Science of The Total Environment, 149933-149933.
- Insights into the mechanism of the interference of sulfadiazine on soil microbial community and function. Journal of Hazardous Materials, 126388.
- 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.
- Linking biogeochemical variability and microbial community structure in forest soils: Abies pinsapo-fir forests as a study case. Ecosistemas, 18(2), 91-102.
- Gas chromatographic metabolic profiling: A sensitive tool for functional microbial ecology. Journal of Microbiological Methods, 75(3), 491-500.
- Restoration of soil physical and biological stability are not coupled in response to plants and earthworms. Ecological Restoration, 26(2), 102-104.
- 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.
- 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.
- Session 13 Primary metabolism. Biologia plantarum, 36(Suppl.1), S213-S223.
- Mitigating Contaminant-Driven Risks for the Safe Expansion of the Agricultural─Sanitation Circular Economy in an Urbanizing World. ACS ES&T Water.
- Space controlled environment agriculture offers pathways to improve the sustainability of controlled environmental agriculture on Earth. Nature Food.
- Smart soils track the formation of pH gradients across the rhizosphere. Plant and Soil.
- Biological nitrogen fixation by soybean (Glycine max [L.] Merr.), a novel, high protein crop in Scotland, requires inoculation with non-native bradyrhizobia. Frontiers in Agronomy, 5, 1196873.
- Soil pH moderates the resistance and resilience of C and N cycling to transient and persistent stress. Applied Soil Ecology.
- Novel form of collective movement by soil bacteria. The ISME Journal.
- 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
- Towards greater sustainability - how investing in soil health may enhance maize productivity in southern Africa. Renewable Agriculture and Food Systems.
- Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere. PNAS.
- Smart soils to observe hidden rhizosphere processes.
Chapters
- Benefits of Breeding Crops for Yield Response to Soil Organisms, Molecular Microbial Ecology of the Rhizosphere (pp. 17-27).
- Global diversity patterns of arbuscular mycorrhizal fungi-community composition and links with functionality, Mycorrhiza: State of the Art, Genetics and Molecular Biology, Eco-Function, Biotechnology, Eco-Physiology, Structure and Systematics (Third Edition) (pp. 89-111).
- Microbial Induction of Resistance to Pathogens, Induced Resistance for Plant Defence: A Sustainable Approach to Crop Protection (pp. 143-156).
- Genetic Studies of the Structure and Diversity of Arbuscular Mycorrhizal Fungal Communities, Ecological Studies (pp. 201-224). Springer Berlin Heidelberg
- 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)
Preprints
- Preferential assimilation, metabolism, and transfer of organic nitrogen to host plants by Mucoromycotina ‘fine root endophytes’, Cold Spring Harbor Laboratory.
- Hybrid xyloglucan utilisation loci are prevalent among plant-associated Bacteroidota, Cold Spring Harbor Laboratory.
- Development of a novel molecular tool for the rapid assessment of changes in biodiversity of benthic nematodes assemblages, PeerJ.
- Development of a novel molecular tool for the rapid assessment of changes in biodiversity of benthic nematodes assemblages, PeerJ.
- A highly active phosphate-insensitive phosphatase is widely distributed in nature, Cold Spring Harbor Laboratory.
- Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere.
- Preferential nitrogen and carbon exchange dynamics in Mucoromycotina “fine root endophyte”-plant symbiosis. Current Biology.
- Research group
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Postdocs
Sara Moeskjaer 2021 – to present
NERC Newton Funding on two projects: MIDST-CZ – Maximising Impact by Decision Support Tools for sustainable soil and water through UK-China Critical Zone Science and PARAMO – Provisioning of ecosystem services And cultuRAl values in the MOntane tropics.
Anne Cotton 2018 – to present
BBSRC Harnessing integrating disease suppressive microbes and synthetic soils for sustainable, low input horticulture.
PhD students
Saifrun Pervin (Co-Supervisor) Interaction between rice and the nitrogen cycle in paddy soil University of Sheffield Doctoral Academy Fellowship. Registered at the University of Sheffield with Duncan Cameron.
Luke Fountain (Principal supervisor) Promoting microbial nitrogen cycling to improve crop nitrogen availability White Rose BBSRC DTP Studentship with Julie Gray and Duncan Cameron.
Robel Patwary (Principal supervisor) Understanding how the soil microbiome can be used to control greenhouse gas emissions from arable agriculture. Bangladeshi Government Scholarship with Duncan Cameron.
Grace Wardell (Co-supervisor) NERC Exploring the ecological and evolutionary impacts of novel agricultural probiotics on naive microbial communities ACCE Studentship with Ellie Harrison and Euan James (Hutton)..
Nathan Howard (Co-supervisor) Structure and function of mucoromycotina fungi in plants ERC associated studentship with Katie Field.
Emily Magkourilou (Co-supervisor) The role of fungal networks in modulating plant symbioses with competing root symbionts White Rose BBSRC DTP Studentship with Katie Field and Peter Urwin (Leeds).
Yu Zhao (Co-supervisor) Application of earthworm eDNA to assess soil health Self-Funded with Penny Watt.
Technician
Sue Colby NERC Newton MIDST-CZ – Maximising Impact by Decision Support Tools for sustainable soil and water through UK-China Critical Zone Science.
- Professional activities and memberships
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- Section Editor for Environmental Microbiology for FEMS Microbiology Letters
- Member of BBSRC pool of experts
- European Science Foundation – Review panel member