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Neal AL, Barrat HA, Bacq-Lebreuil A, Qin Y, Zhang X, Takahashi T, Rubio V, Hughes D, Clark IM, Cárdenas LM, Gardiner LJ, Krishna R, Glendining ML, Ritz K, Mooney SJ, Crawford JW. Arable soil nitrogen dynamics reflect organic inputs via the extended composite phenotype. Nat Food 2023; 4:51-60. [PMID: 37118575 DOI: 10.1038/s43016-022-00671-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/14/2022] [Indexed: 04/30/2023]
Abstract
Achieving food security requires resilient agricultural systems with improved nutrient-use efficiency, optimized water and nutrient storage in soils, and reduced gaseous emissions. Success relies on understanding coupled nitrogen and carbon metabolism in soils, their associated influences on soil structure and the processes controlling nitrogen transformations at scales relevant to microbial activity. Here we show that the influence of organic matter on arable soil nitrogen transformations can be decoded by integrating metagenomic data with soil structural parameters. Our approach provides a mechanistic explanation of why organic matter is effective in reducing nitrous oxide losses while supporting system resilience. The relationship between organic carbon, soil-connected porosity and flow rates at scales relevant to microbes suggests that important increases in nutrient-use efficiency could be achieved at lower organic carbon stocks than currently envisaged.
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Affiliation(s)
- Andrew L Neal
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke, UK.
| | - Harry A Barrat
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke, UK
- The Carbon Trust, London, UK
| | - Aurélie Bacq-Lebreuil
- School of Biosciences, The University of Nottingham, Sutton Bonington, UK
- Genesis, Lisors, France
| | - Yuwei Qin
- Department of Environmental Sciences, Wageningen University, Wageningen, The Netherlands
| | - Xiaoxian Zhang
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | - Taro Takahashi
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke, UK
- Bristol Veterinary School, University of Bristol, Langford, UK
| | - Valentina Rubio
- Programa de Producción y Sustentabilidad Ambiental, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA La Estanzuela, Colonia, Uruguay
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - David Hughes
- Intelligent Data Ecosystems, Rothamsted Research, Harpenden, UK
| | - Ian M Clark
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | - Laura M Cárdenas
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke, UK
| | | | - Ritesh Krishna
- IBM Research Europe - Daresbury, The Hartree Centre, Warrington, UK
| | | | - Karl Ritz
- School of Biosciences, The University of Nottingham, Sutton Bonington, UK
| | - Sacha J Mooney
- School of Biosciences, The University of Nottingham, Sutton Bonington, UK
| | - John W Crawford
- Adam Smith Business School, University of Glasgow, Glasgow, UK
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2
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Canisares LP, Rosolem CA, Momesso L, Crusciol CAC, Villegas DM, Arango J, Ritz K, Cantarella H. Maize-Brachiaria intercropping: A strategy to supply recycled N to maize and reduce soil N 2O emissions? Agric Ecosyst Environ 2021; 319:107491. [PMID: 34602686 PMCID: PMC8363933 DOI: 10.1016/j.agee.2021.107491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
Nitrogen use in agriculture directly impacts food security, global warming, and environmental degradation. Forage grasses intercropped with maize produce feed for animals and or mulch for no-till systems. Forage grasses may exude nitrification inhibitors. It was hypothesized that brachiaria intercropping increases N recycling and maize grain yield and reduces nitrous oxide (N2O) emissions from soil under maize cropping. A field experiment was set up in December 2016 to test three cropping system (maize monocropped, maize intercropped with Brachiaria brizantha or with B. humidicola) and two N rates (0 or 150 kg ha-1). The grasses were sown with maize, but B. humidicola did not germinate well in the first year. B. brizantha developed slowly during the maize cycle because of shading but expanded after maize was harvested. The experiment was repeated in 2017/2018 when B. humidicola was replanted. N2O and carbon dioxide (CO2) emissions, maize grain yield and N content were measured during the two seasons. After the first maize harvest, the above- and below-ground biomass, C and N content of B. brizantha grown during fall-winter, and the biological nitrification inhibition potential of B. brizantha were evaluated. Maize yield responded to N fertilization (5.1 vs. 9.8 t ha-1) but not to brachiaria intercropping. B. brizantha recycled approximately 140 kg N ha-1 and left 12 t dry matter ha-1 for the second maize crop. However, the 2017/18 maize yields were not affected by the N recycled by B. brizantha, whereas N2O emissions were higher in the plots with brachiaria, suggesting that part of the recycled N was released too early after desiccation. Brachiarias showed no evidence of causing nitrification inhibition. The strategy of intercropping brachiarias did not increase maize yield, although it added C and recycled N in the system.
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Affiliation(s)
| | - Ciro Antonio Rosolem
- São Paulo State University, College of Agricultural Sciences, Botucatu, São Paulo 18603-970, Brazil
| | - Letusa Momesso
- São Paulo State University, College of Agricultural Sciences, Botucatu, São Paulo 18603-970, Brazil
| | | | | | - Jacobo Arango
- International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
| | - Karl Ritz
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicester LE12 5RD, UK
| | - Heitor Cantarella
- Agronomic Institute of Campinas, Campinas, São Paulo 13012-970, Brazil
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3
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Hand LH, Marshall SJ, Dougan C, Nichols C, Kende A, Ritz K, Oliver RG. The Impact of Disturbed Soil Structure on the Degradation of 2 Fungicides Under Constant and Variable Moisture. Environ Toxicol Chem 2021; 40:2715-2725. [PMID: 34288074 DOI: 10.1002/etc.5167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 06/18/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Degradation of agrochemicals in soil is frequently faster under field conditions than in laboratory studies. Field studies are carried out on relatively undisturbed soil, whereas laboratory studies typically use sieved soil, which can have a significant impact on the physical and microbial nature of the soil and may contribute to differences in degradation between laboratory and field studies. A laboratory study was therefore conducted to determine the importance of soil structure and variable soil moisture on the degradation of 2 fungicides (azoxystrobin and paclobutrazol) that show significant differences between laboratory and field degradation rates in regulatory studies. Degradation rates were measured in undisturbed cores of a sandy clay loam soil (under constant or variable moisture contents) and in sieved soil. For azoxystrobin, degradation rates under all conditions were similar (median degradation time [DegT50] 34-37 d). However, for paclobutrazol, degradation was significantly faster in undisturbed cores (DegT50 255 d in sieved soil and 63 d in undisturbed cores). Varying the moisture content did not further enhance degradation of either fungicide. Further examination into the impact of soil structure on paclobutrazol degradation, comparing undisturbed and sieved/repacked cores, revealed that the impact of sieving could not be mitigated by repacking the soil to a realistic bulk density. Examination of fungal and bacterial community structure using automated ribosomal spacer analysis showed significant initial differences between sieved/repacked and intact soil cores, although such differences were reduced at the end of the study (70 d). The present study demonstrates that disruption of soil structure significantly impacts microbial community structure, and for some compounds this may explain the differences between laboratory and field degradation rates. Environ Toxicol Chem 2021;40:2715-2725. © 2021 SETAC.
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Affiliation(s)
- Laurence H Hand
- Product Safety Department, Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, United Kingdom
| | - Samantha J Marshall
- Product Safety Department, Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, United Kingdom
| | - Christine Dougan
- Product Safety Department, Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, United Kingdom
| | - Carol Nichols
- Product Safety Department, Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, United Kingdom
| | - Aniko Kende
- Product Safety Department, Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, United Kingdom
| | - Karl Ritz
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
| | - Robin G Oliver
- Product Safety Department, Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, United Kingdom
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4
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Hickman DT, Rasmussen A, Ritz K, Birkett MA, Neve P. Review: Allelochemicals as multi-kingdom plant defence compounds: towards an integrated approach. Pest Manag Sci 2021; 77:1121-1131. [PMID: 32902160 PMCID: PMC7891363 DOI: 10.1002/ps.6076] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 05/05/2023]
Abstract
The capability of synthetic pesticides to manage weeds, insect pests and pathogens in crops has diminished due to evolved resistance. Sustainable management is thus becoming more challenging. Novel solutions are needed and, given the ubiquity of biologically active secondary metabolites in nature, such compounds require further exploration as leads for novel crop protection chemistry. Despite improving understanding of allelochemicals, particularly in terms of their potential for use in weed control, their interactions with multiple biotic kingdoms have to date largely been examined in individual compounds and not as a recurrent phenomenon. Here, multi-kingdom effects in allelochemicals are introduced by defining effects on various organisms, before exploring current understanding of the inducibility and possible ecological roles of these compounds with regard to the evolutionary arms race and dose-response relationships. Allelochemicals with functional benefits in multiple aspects of plant defence are described. Gathering these isolated areas of science under the unified umbrella of multi-kingdom allelopathy encourages the development of naturally-derived chemistries conferring defence to multiple discrete biotic stresses simultaneously, maximizing benefits in weed, insect and pathogen control, while potentially circumventing resistance. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Darwin T Hickman
- Rothamsted Research, HarpendenHertfordshireUK
- University of Nottingham, Sutton BoningtonLeicestershireUK
| | | | - Karl Ritz
- University of Nottingham, Sutton BoningtonLeicestershireUK
| | | | - Paul Neve
- Rothamsted Research, HarpendenHertfordshireUK
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5
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Burr-Hersey JE, Ritz K, Bengough GA, Mooney SJ. Reorganisation of rhizosphere soil pore structure by wild plant species in compacted soils. J Exp Bot 2020; 71:6107-6115. [PMID: 32668003 PMCID: PMC7541912 DOI: 10.1093/jxb/eraa323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Soil compaction represents a major impediment to plant growth, yet wild plants are often observed thriving in soil of high bulk density in non-agricultural settings. We analysed the root growth of three non-cultivated species often found growing in compacted soils in the natural environment. Plants of ribwort plantain (Plantago lanceolata), dandelion (Taraxacum officinale), and spear thistle (Cirsium vulgare) were grown for 28 d in a sandy loam soil compacted to 1.8 g cm-3 with a penetration resistance of 1.55 MPa. X-Ray computed tomography was used to observe root architecture in situ and to visualise changes in rhizosphere porosity (at a resolution of 35 μm) at 14 d and 28 d after sowing. Porosity of the soil was analysed within four incremental zones up to 420 μm from the root surface. In all species, the porosity of the rhizosphere was greatest closest to the root and decreased with distance from the root surface. There were significant differences in rhizosphere porosity between the three species, with Cirsium plants exhibiting the greatest structural genesis across all rhizosphere zones. This creation of pore space indicates that plants can self-remediate compacted soil via localised structural reorganisation in the rhizosphere, which has potential functional implications for both plant and soil.
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Affiliation(s)
- Jasmine E Burr-Hersey
- Division of Agricultural & Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
- The James Hutton Institute, Invergowrie, Dundee, UK
| | - Karl Ritz
- Division of Agricultural & Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - Glyn A Bengough
- The James Hutton Institute, Invergowrie, Dundee, UK
- School of Science and Engineering, University of Dundee, Dundee, UK
| | - Sacha J Mooney
- Division of Agricultural & Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
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7
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Dhandapani S, Ritz K, Evers S, Yule CM, Sjögersten S. Are secondary forests second-rate? Comparing peatland greenhouse gas emissions, chemical and microbial community properties between primary and secondary forests in Peninsular Malaysia. Sci Total Environ 2019; 655:220-231. [PMID: 30471590 DOI: 10.1016/j.scitotenv.2018.11.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/02/2018] [Accepted: 11/04/2018] [Indexed: 06/09/2023]
Abstract
Tropical peatlands are globally important ecosystems with high C storage and are endangered by anthropogenic disturbances. Microbes in peatlands play an important role in sustaining the functions of peatlands as a C sink, yet their characteristics in these habitats are poorly understood. This research aimed to elucidate the responses of these complex ecosystems to disturbance by exploring greenhouse gas (GHG) emissions, nutrient contents, soil microbial communities and the functional interactions between these components in a primary and secondary peat swamp forest in Peninsular Malaysia. GHG measurements using closed chambers, and peat sampling were carried out in both wet and dry seasons. Microbial community phenotypes and nutrient content were determined using phospholipid fatty acid (PLFA) and inductively-coupled plasma mass spectrometry (ICP-MS) analyses respectively. CO2 emissions in the secondary peat swamp forest were > 50% higher than in the primary forest. CH4 emission rates were ca. 2 mg m-2 h-1 in the primary forest but the secondary forest was a CH4 sink, showing no seasonal variations in GHG emissions. Almost all the nutrient concentrations were significantly lower in the secondary forest, postulated to be due to nutrient leaching via drainage and higher rates of decomposition. Cu and Mo concentrations were negatively correlated with CO2 and CH4 emissions respectively. Microbial community structure was overwhelmingly dominated by bacteria in both forest types, however it was highly sensitive to land-use change and season. Gram-positive and Gram-negative relative abundance were positively correlated with CO2 and CH4 emissions respectively. Drainage related disturbances increased CO2 emissions, by reducing the nutrient content including some with known antimicrobial properties (Cu & Na) and by favouring Gram-positive bacteria over Gram-negative bacteria. These results suggest that the biogeochemistry of secondary peat swamp forest is fundamentally different from that of primary peat swamp forest, and these differences have significant functional impacts on their respective environments.
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Affiliation(s)
| | - Karl Ritz
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Stephanie Evers
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK; School of Biosciences, University of Nottingham Malaysia Campus, Semenyih, Malaysia; Tropical Catchment Research Initiative (TROCARI), Malaysia
| | - Catherine M Yule
- School of Science, University of the Sunshine Coast, Queensland, Australia; School of Science, Monash University, Malaysia
| | - Sofie Sjögersten
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
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8
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Bacq-Labreuil A, Crawford J, Mooney SJ, Neal AL, Akkari E, McAuliffe C, Zhang X, Redmile-Gordon M, Ritz K. Effects of cropping systems upon the three-dimensional architecture of soil systems are modulated by texture. Geoderma 2018; 332:73-83. [PMID: 30559518 PMCID: PMC6088510 DOI: 10.1016/j.geoderma.2018.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/28/2018] [Accepted: 07/02/2018] [Indexed: 05/21/2023]
Abstract
Soil delivers fundamental ecosystem functions via interactions between physical and biological processes mediated by soil structure. The structure of soil is also dynamic and modified by natural factors and management intervention. The aim of this study was to investigate the effects of different cropping systems on soil structure at contrasting spatial scales. Three systems were studied in replicated plot field experiments involving varying degrees of plant-derived inputs to the soil, viz. perennial (grassland), annual (arable), and no-plant control (bare fallow), associated with two contrasting soil textures (clayey and sandy). We hypothesized the presence of plants results in a greater range (diversity) of pore sizes and that perennial cropping systems invoke greater structural heterogeneity. Accordingly, the nature of the pore systems was visualised and quantified in 3D by X-ray Computed Tomography at the mm and μm scale. Plants did not affect the porosity of clay soil at the mm scale, but at the μm scale, annual and perennial plant cover resulted in significantly increased porosity, a wider range of pore sizes and greater connectivity compared to bare fallow soil. However, the opposite occurred in the sandy soil, where plants decreased the porosity and pore connectivity at the mm scale but had no significant structural effect at the μm scale. These data reveal profound effects of different agricultural management systems upon soil structural modification, which are strongly modulated by the extent of plant presence and also contingent on the inherent texture of the soil.
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Affiliation(s)
- Aurelie Bacq-Labreuil
- Division of Agriculture & Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
- Corresponding author.
| | - John Crawford
- Sustainable Agriculture Science, Rothamsted Research, West Common, Harpenden, AL5 2JQ, UK
| | - Sacha J. Mooney
- Division of Agriculture & Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
| | - Andrew L. Neal
- Sustainable Agriculture Science, Rothamsted Research, West Common, Harpenden, AL5 2JQ, UK
| | - Elsy Akkari
- Sustainable Agriculture Science, Rothamsted Research, West Common, Harpenden, AL5 2JQ, UK
| | - Cormac McAuliffe
- Sustainable Agriculture Science, Rothamsted Research, West Common, Harpenden, AL5 2JQ, UK
| | - Xiaoxian Zhang
- Sustainable Agriculture Science, Rothamsted Research, West Common, Harpenden, AL5 2JQ, UK
| | - Marc Redmile-Gordon
- Sustainable Agriculture Science, Rothamsted Research, West Common, Harpenden, AL5 2JQ, UK
| | - Karl Ritz
- Division of Agriculture & Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
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9
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Abstract
Microbial community profiling via phospholipid fatty-acid (PLFA) analysis is an insightful technique which elucidates the phenotypic structure of microbial assemblages within soil. Previous iterations of PLFA analysis have used large quantities of chemicals and can take extended periods of time to perform. Another barrier to the implementation of this method is the cost and availability of specialised machinery. We report on a high-throughput method which reduces both the time to extract PLFAs from soil and reduces the quantity of chemicals required.
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10
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Todman LC, Fraser FC, Corstanje R, Harris JA, Pawlett M, Ritz K, Whitmore AP. Evidence for functional state transitions in intensively-managed soil ecosystems. Sci Rep 2018; 8:11522. [PMID: 30068982 PMCID: PMC6070522 DOI: 10.1038/s41598-018-29925-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 07/17/2018] [Indexed: 11/16/2022] Open
Abstract
Soils are fundamental to terrestrial ecosystem functioning and food security, thus their resilience to disturbances is critical. Furthermore, they provide effective models of complex natural systems to explore resilience concepts over experimentally-tractable short timescales. We studied soils derived from experimental plots with different land-use histories of long-term grass, arable and fallow to determine whether regimes of extreme drying and re-wetting would tip the systems into alternative stable states, contingent on their historical management. Prior to disturbance, grass and arable soils produced similar respiration responses when processing an introduced complex carbon substrate. A distinct respiration response from fallow soil here indicated a different prior functional state. Initial dry:wet disturbances reduced the respiration in all soils, suggesting that the microbial community was perturbed such that its function was impaired. After 12 drying and rewetting cycles, despite the extreme disturbance regime, soil from the grass plots, and those that had recently been grass, adapted and returned to their prior functional state. Arable soils were less resilient and shifted towards a functional state more similar to that of the fallow soil. Hence repeated stresses can apparently induce persistent shifts in functional states in soils, which are influenced by management history.
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Affiliation(s)
- L C Todman
- Rothamsted Research, Harpenden, AL5 2JQ, UK.
| | - F C Fraser
- Cranfield University, Cranfield, Bedford, MK43 0AL, UK
| | - R Corstanje
- Cranfield University, Cranfield, Bedford, MK43 0AL, UK
| | - J A Harris
- Cranfield University, Cranfield, Bedford, MK43 0AL, UK
| | - M Pawlett
- Cranfield University, Cranfield, Bedford, MK43 0AL, UK
| | - K Ritz
- Cranfield University, Cranfield, Bedford, MK43 0AL, UK
- The University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, UK
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11
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Ashekuzzaman SM, Richards K, Ellis S, Tyrrel S, O'Leary E, Griffiths B, Ritz K, Fenton O. Risk Assessment of E. coli Survival Up to the Grazing Exclusion Period After Dairy Slurry, Cattle Dung, and Biosolids Application to Grassland. Front Sustain Food Syst 2018. [DOI: 10.3389/fsufs.2018.00034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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12
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Burr-Hersey JE, Mooney SJ, Bengough AG, Mairhofer S, Ritz K. Correction: Developmental morphology of cover crop species exhibit contrasting behaviour to changes in soil bulk density, revealed by X-ray computed tomography. PLoS One 2018; 13:e0190759. [PMID: 29293668 PMCID: PMC5749865 DOI: 10.1371/journal.pone.0190759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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13
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Armenise E, Simmons RW, Ahn S, Garbout A, Doerr SH, Mooney SJ, Sturrock CJ, Ritz K. Soil seal development under simulated rainfall: Structural, physical and hydrological dynamics. J Hydrol (Amst) 2018; 556:211-219. [PMID: 29332951 PMCID: PMC5761063 DOI: 10.1016/j.jhydrol.2017.10.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
This study delivers new insights into rainfall-induced seal formation through a novel approach in the use of X-ray Computed Tomography (CT). Up to now seal and crust thickness have been directly quantified mainly through visual examination of sealed/crusted surfaces, and there has been no quantitative method to estimate this important property. X-ray CT images were quantitatively analysed to derive formal measures of seal and crust thickness. A factorial experiment was established in the laboratory using open-topped microcosms packed with soil. The factors investigated were soil type (three soils: silty clay loam - ZCL, sandy silt loam - SZL, sandy loam - SL) and rainfall duration (2-14 min). Surface seal formation was induced by applying artificial rainfall events, characterised by variable duration, but constant kinetic energy, intensity, and raindrop size distribution. Soil porosities derived from CT scans were used to quantify the thickness of the rainfall-induced surface seals and reveal temporal seal micro-morphological variations with increasing rainfall duration. In addition, the water repellency and infiltration dynamics of the developing seals were investigated by measuring water drop penetration time (WDPT) and unsaturated hydraulic conductivity (Kun). The range of seal thicknesses detected varied from 0.6 to 5.4 mm. Soil textural characteristics and OM content played a central role in the development of rainfall-induced seals, with coarser soil particles and lower OM content resulting in thicker seals. Two different trends in soil porosity vs. depth were identified: i) for SL soil porosity was lowest at the immediate soil surface, it then increased constantly with depth till the median porosity of undisturbed soil was equalled; ii) for ZCL and SL the highest reduction in porosity, as compared to the median porosity of undisturbed soil, was observed in a well-defined zone of maximum porosity reduction c. 0.24-0.48 mm below the soil surface. This contrasting behaviour was related to different dynamics and processes of seal formation which depended on the soil properties. The impact of rainfall-induced surface sealing on the hydrological behaviour of soil (as represented by WDTP and Kun) was rapid and substantial: an average 60% reduction in Kun occurred for all soils between 2 and 9 min rainfall, and water repellent surfaces were identified for SZL and ZCL. This highlights that the condition of the immediate surface of agricultural soils involving rainfall-induced structural seals has a strong impact in the overall ability of soil to function as water reservoir.
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Affiliation(s)
- Elena Armenise
- School of Energy, Environment, and Agrifood, Cranfield University, Bedford, UK
- Corresponding authors at: Environment Agency, Guildbourne House, Chatsworth Road, Worthing, Sussex, BN11 1LD, UK (E. Armenise). Cranfield University, School of Water, Energy and Environment, Building 52a, Cranfield, Bedfordshire, MK43 0AL, UK (R.W. Simmons).
| | - Robert W. Simmons
- School of Energy, Environment, and Agrifood, Cranfield University, Bedford, UK
- Corresponding authors at: Environment Agency, Guildbourne House, Chatsworth Road, Worthing, Sussex, BN11 1LD, UK (E. Armenise). Cranfield University, School of Water, Energy and Environment, Building 52a, Cranfield, Bedfordshire, MK43 0AL, UK (R.W. Simmons).
| | - Sujung Ahn
- Department of Geography, College of Science, Swansea University, Singleton Park, UK
| | - Amin Garbout
- School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
| | - Stefan H. Doerr
- Department of Geography, College of Science, Swansea University, Singleton Park, UK
| | - Sacha J. Mooney
- School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
| | - Craig J. Sturrock
- School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
| | - Karl Ritz
- School of Energy, Environment, and Agrifood, Cranfield University, Bedford, UK
- School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
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14
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Tsiafouli MA, Drakou EG, Orgiazzi A, Hedlund K, Ritz K. Editorial: Optimizing the Delivery of Multiple Ecosystem Goods and Services in Agricultural Systems. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Burr-Hersey JE, Mooney SJ, Bengough AG, Mairhofer S, Ritz K. Developmental morphology of cover crop species exhibit contrasting behaviour to changes in soil bulk density, revealed by X-ray computed tomography. PLoS One 2017; 12:e0181872. [PMID: 28753645 PMCID: PMC5533331 DOI: 10.1371/journal.pone.0181872] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/07/2017] [Indexed: 11/18/2022] Open
Abstract
Plant roots growing through soil typically encounter considerable structural heterogeneity, and local variations in soil dry bulk density. The way the in situ architecture of root systems of different species respond to such heterogeneity is poorly understood due to challenges in visualising roots growing in soil. The objective of this study was to visualise and quantify the impact of abrupt changes in soil bulk density on the roots of three cover crop species with contrasting inherent root morphologies, viz. tillage radish (Raphanus sativus), vetch (Vicia sativa) and black oat (Avena strigosa). The species were grown in soil columns containing a two-layer compaction treatment featuring a 1.2 g cm-3 (uncompacted) zone overlaying a 1.4 g cm-3 (compacted) zone. Three-dimensional visualisations of the root architecture were generated via X-ray computed tomography, and an automated root-segmentation imaging algorithm. Three classes of behaviour were manifest as a result of roots encountering the compacted interface, directly related to the species. For radish, there was switch from a single tap-root to multiple perpendicular roots which penetrated the compacted zone, whilst for vetch primary roots were diverted more horizontally with limited lateral growth at less acute angles. Black oat roots penetrated the compacted zone with no apparent deviation. Smaller root volume, surface area and lateral growth were consistently observed in the compacted zone in comparison to the uncompacted zone across all species. The rapid transition in soil bulk density had a large effect on root morphology that differed greatly between species, with major implications for how these cover crops will modify and interact with soil structure.
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Affiliation(s)
- Jasmine E. Burr-Hersey
- Division of Agricultural & Environmental Science, School of Bioscience, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Sacha J. Mooney
- Division of Agricultural & Environmental Science, School of Bioscience, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - A. Glyn Bengough
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
- School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Stefan Mairhofer
- School of Computer Science, University of Nottingham, Nottingham, United Kingdom
| | - Karl Ritz
- Division of Agricultural & Environmental Science, School of Bioscience, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
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16
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Fraser F, Todman L, Corstanje R, Deeks L, Harris J, Pawlett M, Whitmore A, Ritz K. Distinct respiratory responses of soils to complex organic substrate are governed predominantly by soil architecture and its microbial community. Soil Biol Biochem 2016; 103:493-501. [PMID: 27917005 PMCID: PMC5113515 DOI: 10.1016/j.soilbio.2016.09.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/13/2016] [Accepted: 09/17/2016] [Indexed: 06/06/2023]
Abstract
Factors governing the turnover of organic matter (OM) added to soils, including substrate quality, climate, environment and biology, are well known, but their relative importance has been difficult to ascertain due to the interconnected nature of the soil system. This has made their inclusion in mechanistic models of OM turnover or nutrient cycling difficult despite the potential power of these models to unravel complex interactions. Using high temporal-resolution respirometery (6 min measurement intervals), we monitored the respiratory response of 67 soils sampled from across England and Wales over a 5 day period following the addition of a complex organic substrate (green barley powder). Four respiratory response archetypes were observed, characterised by different rates of respiration as well as different time-dependent patterns. We also found that it was possible to predict, with 95% accuracy, which type of respiratory behaviour a soil would exhibit based on certain physical and chemical soil properties combined with the size and phenotypic structure of the microbial community. Bulk density, microbial biomass carbon, water holding capacity and microbial community phenotype were identified as the four most important factors in predicting the soils' respiratory responses using a Bayesian belief network. These results show that the size and constitution of the microbial community are as important as physico-chemical properties of a soil in governing the respiratory response to OM addition. Such a combination suggests that the 'architecture' of the soil, i.e. the integration of the spatial organisation of the environment and the interactions between the communities living and functioning within the pore networks, is fundamentally important in regulating such processes.
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Affiliation(s)
- F.C. Fraser
- School of Water, Energy, and Environment, Cranfield University, Bedford, MK43 0AL, UK
| | - L.C. Todman
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - R. Corstanje
- School of Water, Energy, and Environment, Cranfield University, Bedford, MK43 0AL, UK
| | - L.K. Deeks
- School of Water, Energy, and Environment, Cranfield University, Bedford, MK43 0AL, UK
| | - J.A. Harris
- School of Water, Energy, and Environment, Cranfield University, Bedford, MK43 0AL, UK
| | - M. Pawlett
- School of Water, Energy, and Environment, Cranfield University, Bedford, MK43 0AL, UK
| | - A.P. Whitmore
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - K. Ritz
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, UK
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17
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Fraser F, Corstanje R, Deeks L, Harris J, Pawlett M, Todman L, Whitmore A, Ritz K. On the origin of carbon dioxide released from rewetted soils. Soil Biol Biochem 2016; 101:1-5. [PMID: 27698513 PMCID: PMC5012885 DOI: 10.1016/j.soilbio.2016.06.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 06/24/2016] [Accepted: 06/28/2016] [Indexed: 05/19/2023]
Abstract
When dry soils are rewetted a pulse of CO2 is invariably released, and whilst this phenomenon has been studied for decades, the precise origins of this CO2 remain obscure. We postulate that it could be of chemical (i.e. via abiotic pathways), biochemical (via free enzymes) or biological (via intact cells) origin. To elucidate the relative contributions of the pathways, dry soils were either sterilised (double autoclaving) or treated with solutions of inhibitors (15% trichloroacetic acid or 1% silver nitrate) targeting the different modes. The rapidity of CO2 release from the soils after the drying:rewetting (DRW) cycle was remarkable, with maximal rates of evolution within 6 min, and 41% of the total efflux over 96 h released within the first 24 h. The complete cessation of CO2 eflux following sterilisation showed there was no abiotic (dissolution of carbonates) contribution to the CO2 release on rewetting, and clear evidence for an organismal or biochemical basis to the flush. Rehydration in the presence of inhibitors indicated that there were approximately equal contributions from biochemical (outside membranes) and organismal (inside membranes) sources within the first 24 h after rewetting. This suggests that some of the flux was derived from microbial respiration, whilst the remainder was a consequence of enzyme activity, possibly through remnant respiratory pathways in the debris of dead cells.
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Affiliation(s)
- F.C. Fraser
- School of Energy, Environment, and Agrifood, Cranfield University, Bedford, UK
- Corresponding author.
| | - R. Corstanje
- School of Energy, Environment, and Agrifood, Cranfield University, Bedford, UK
| | - L.K. Deeks
- School of Energy, Environment, and Agrifood, Cranfield University, Bedford, UK
| | - J.A. Harris
- School of Energy, Environment, and Agrifood, Cranfield University, Bedford, UK
| | - M. Pawlett
- School of Energy, Environment, and Agrifood, Cranfield University, Bedford, UK
| | | | | | - K. Ritz
- School of Biosciences, University of Nottingham, Nottingham, UK
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18
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Todman LC, Fraser FC, Corstanje R, Deeks LK, Harris JA, Pawlett M, Ritz K, Whitmore AP. Defining and quantifying the resilience of responses to disturbance: a conceptual and modelling approach from soil science. Sci Rep 2016; 6:28426. [PMID: 27329053 PMCID: PMC4916505 DOI: 10.1038/srep28426] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/02/2016] [Indexed: 12/22/2022] Open
Abstract
There are several conceptual definitions of resilience pertaining to environmental systems and, even if resilience is clearly defined in a particular context, it is challenging to quantify. We identify four characteristics of the response of a system function to disturbance that relate to "resilience": (1) degree of return of the function to a reference level; (2) time taken to reach a new quasi-stable state; (3) rate (i.e. gradient) at which the function reaches the new state; (4) cumulative magnitude of the function (i.e. area under the curve) before a new state is reached. We develop metrics to quantify these characteristics based on an analogy with a mechanical spring and damper system. Using the example of the response of a soil function (respiration) to disturbance, we demonstrate that these metrics effectively discriminate key features of the dynamic response. Although any one of these characteristics could define resilience, each may lead to different insights and conclusions. The salient properties of a resilient response must thus be identified for different contexts. Because the temporal resolution of data affects the accurate determination of these metrics, we recommend that at least twelve measurements are made over the temporal range for which the response is expected.
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Affiliation(s)
| | - F. C. Fraser
- Cranfield University, Cranfield, Bedford MK43 0AL, UK
| | - R. Corstanje
- Cranfield University, Cranfield, Bedford MK43 0AL, UK
| | - L. K. Deeks
- Cranfield University, Cranfield, Bedford MK43 0AL, UK
| | - J. A. Harris
- Cranfield University, Cranfield, Bedford MK43 0AL, UK
| | - M. Pawlett
- Cranfield University, Cranfield, Bedford MK43 0AL, UK
| | - K. Ritz
- Cranfield University, Cranfield, Bedford MK43 0AL, UK
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
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19
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York LM, Carminati A, Mooney SJ, Ritz K, Bennett MJ. The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots. J Exp Bot 2016; 67:3629-43. [PMID: 26980751 DOI: 10.1093/jxb/erw108] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Despite often being conceptualized as a thin layer of soil around roots, the rhizosphere is actually a dynamic system of interacting processes. Hiltner originally defined the rhizosphere as the soil influenced by plant roots. However, soil physicists, chemists, microbiologists, and plant physiologists have studied the rhizosphere independently, and therefore conceptualized the rhizosphere in different ways and using contrasting terminology. Rather than research-specific conceptions of the rhizosphere, the authors propose a holistic rhizosphere encapsulating the following components: microbial community gradients, macroorganisms, mucigel, volumes of soil structure modification, and depletion or accumulation zones of nutrients, water, root exudates, volatiles, and gases. These rhizosphere components are the result of dynamic processes and understanding the integration of these processes will be necessary for future contributions to rhizosphere science based upon interdisciplinary collaborations. In this review, current knowledge of the rhizosphere is synthesized using this holistic perspective with a focus on integrating traditionally separated rhizosphere studies. The temporal dynamics of rhizosphere activities will also be considered, from annual fine root turnover to diurnal fluctuations of water and nutrient uptake. The latest empirical and computational methods are discussed in the context of rhizosphere integration. Clarification of rhizosphere semantics, a holistic model of the rhizosphere, examples of integration of rhizosphere studies across disciplines, and review of the latest rhizosphere methods will empower rhizosphere scientists from different disciplines to engage in the interdisciplinary collaborations needed to break new ground in truly understanding the rhizosphere and to apply this knowledge for practical guidance.
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Affiliation(s)
- Larry M York
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Andrea Carminati
- Division of Soil Hydrology, Georg-August University of Göttingen, 37077 Göttingen, Germany
| | - Sacha J Mooney
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Karl Ritz
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
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20
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Durenkamp M, Pawlett M, Ritz K, Harris JA, Neal AL, McGrath SP. Nanoparticles within WWTP sludges have minimal impact on leachate quality and soil microbial community structure and function. Environ Pollut 2016; 211:399-405. [PMID: 26799000 DOI: 10.1016/j.envpol.2015.12.063] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/03/2015] [Accepted: 12/31/2015] [Indexed: 05/23/2023]
Abstract
One of the main pathways by which engineered nanoparticles (ENPs) enter the environment is through land application of waste water treatment plant (WWTP) sewage sludges. WWTP sludges, enriched with Ag and ZnO ENPs or their corresponding soluble metal salts during anaerobic digestion and subsequently mixed with soil (targeting a final concentration of 1400 and 140 mg/kg for Zn and Ag, respectively), were subjected to 6 months of ageing and leaching in lysimeter columns outdoors. Amounts of Zn and Ag leached were very low, accounting for <0.3% and <1.4% of the total Zn and Ag, respectively. No differences in total leaching rates were observed between treatments of Zn or Ag originally input to WWTP as ENP or salt forms. Phospholipid fatty acid profiling indicated a reduction in the fungal component of the soil microbial community upon metal exposure. However, overall, the leachate composition and response of the soil microbial community following addition of sewage sludge enriched either with ENPs or metal salts was very similar.
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Affiliation(s)
- Mark Durenkamp
- Department of Sustainable Soils and Grassland Systems, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom.
| | - Mark Pawlett
- Environmental Science and Technology Department, School of Energy Environment and Agrifood, Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, United Kingdom
| | - Karl Ritz
- Environmental Science and Technology Department, School of Energy Environment and Agrifood, Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, United Kingdom
| | - Jim A Harris
- Environmental Science and Technology Department, School of Energy Environment and Agrifood, Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, United Kingdom
| | - Andrew L Neal
- Department of Sustainable Soils and Grassland Systems, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom
| | - Steve P McGrath
- Department of Sustainable Soils and Grassland Systems, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom
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21
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Gregory AS, Ritz K, McGrath SP, Quinton JN, Goulding KWT, Jones RJA, Harris JA, Bol R, Wallace P, Pilgrim ES, Whitmore AP. A review of the impacts of degradation threats on soil properties in the UK. Soil Use Manag 2015; 31:1-15. [PMID: 27667890 PMCID: PMC5014291 DOI: 10.1111/sum.12212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 07/31/2015] [Indexed: 05/20/2023]
Abstract
National governments are becoming increasingly aware of the importance of their soil resources and are shaping strategies accordingly. Implicit in any such strategy is that degradation threats and their potential effect on important soil properties and functions are defined and understood. In this paper, we aimed to review the principal degradation threats on important soil properties in the UK, seeking quantitative data where possible. Soil erosion results in the removal of important topsoil and, with it, nutrients, C and porosity. A decline in soil organic matter principally affects soil biological and microbiological properties, but also impacts on soil physical properties because of the link with soil structure. Soil contamination affects soil chemical properties, affecting nutrient availability and degrading microbial properties, whilst soil compaction degrades the soil pore network. Soil sealing removes the link between the soil and most of the 'spheres', significantly affecting hydrological and microbial functions, and soils on re-developed brownfield sites are typically degraded in most soil properties. Having synthesized the literature on the impact on soil properties, we discuss potential subsequent impacts on the important soil functions, including food and fibre production, storage of water and C, support for biodiversity, and protection of cultural and archaeological heritage. Looking forward, we suggest a twin approach of field-based monitoring supported by controlled laboratory experimentation to improve our mechanistic understanding of soils. This would enable us to better predict future impacts of degradation processes, including climate change, on soil properties and functions so that we may manage soil resources sustainably.
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Affiliation(s)
- A. S. Gregory
- Department of Sustainable Soils and Grassland SystemsRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
| | - K. Ritz
- Division of Agricultural and Environmental SciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLeicestershireLE12 5RDUK
| | - S. P. McGrath
- Department of Sustainable Soils and Grassland SystemsRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
| | - J. N. Quinton
- Lancaster Environment CentreLancaster UniversityLancasterLA1 4YQUK
| | - K. W. T. Goulding
- Department of Sustainable Soils and Grassland SystemsRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
| | - R. J. A. Jones
- School of Energy, Environment and AgrifoodCranfield UniversityCranfieldBedfordshireMK43 0ALUK
| | - J. A. Harris
- School of Energy, Environment and AgrifoodCranfield UniversityCranfieldBedfordshireMK43 0ALUK
| | - R. Bol
- Terrestrial Biogeochemistry GroupInstitute of Bio‐ and Geosciences IBG‐3: AgrosphereForschungszentrum Jülich GmbHJülich52425Germany
| | - P. Wallace
- Phil Wallace LtdWestlandMartlesham HeathIpswichSuffolkIP5 3SUUK
| | - E. S. Pilgrim
- University of ExeterAmory BuildingRennes DriveExeterEX4 4RJUK
| | - A. P. Whitmore
- Department of Sustainable Soils and Grassland SystemsRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
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22
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Van der Donckt C, Roth L, Vanhoutte G, Blockx I, Bink D, Ritz K, Pintelon I, Timmermans JP, Bauters D, Martinet W, Daemen M, Verhoye M, De Meyer G. Fibrillin-1 impairment enhances blood–brain barrier permeability and xanthoma formation in brains of apolipoprotein E-deficient mice. Neuroscience 2015; 295:11-22. [DOI: 10.1016/j.neuroscience.2015.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/27/2015] [Accepted: 03/11/2015] [Indexed: 01/14/2023]
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23
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Schaefer A, te Riet J, Ritz K, Hoogenboezem M, Anthony EC, Mul FPJ, de Vries CJ, Daemen MJ, Figdor CG, van Buul JD, Hordijk PL. Actin-binding proteins differentially regulate endothelial cell stiffness, ICAM-1 function and neutrophil transmigration. Development 2014. [DOI: 10.1242/dev.118497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Denswil NP, Van Der Wal AC, De Boer OJ, Van Der Loos CM, Ritz K, Aronica E, Troost D, Daemen MJAP. Advanced intracranial atherosclerosis is present in asymptomatic patients, but is almost devoid of microvessels. Eur Heart J 2013. [DOI: 10.1093/eurheartj/eht308.p2407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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25
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Pawlett M, Ritz K, Dorey RA, Rocks S, Ramsden J, Harris JA. The impact of zero-valent iron nanoparticles upon soil microbial communities is context dependent. Environ Sci Pollut Res Int 2013; 20:1041-9. [PMID: 23007947 DOI: 10.1007/s11356-012-1196-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 09/12/2012] [Indexed: 05/20/2023]
Abstract
Nanosized zero-valent iron (nZVI) is an effective land remediation tool, but there remains little information regarding its impact upon and interactions with the soil microbial community. nZVI stabilised with sodium carboxymethyl cellulose was applied to soils of three contrasting textures and organic matter contents to determine impacts on soil microbial biomass, phenotypic (phospholipid fatty acid (PLFA)), and functional (multiple substrate-induced respiration (MSIR)) profiles. The nZVI significantly reduced microbial biomass by 29 % but only where soil was amended with 5 % straw. Effects of nZVI on MSIR profiles were only evident in the clay soils and were independent of organic matter content. PLFA profiling indicated that the soil microbial community structure in sandy soils were apparently the most, and clay soils the least, vulnerable to nZVI suggesting a protective effect imparted by clays. Evidence of nZVI bactericidal effects on Gram-negative bacteria and a potential reduction of arbuscular mycorrhizal fungi are presented. Data imply that the impact of nZVI on soil microbial communities is dependent on organic matter content and soil mineral type. Thereby, evaluations of nZVI toxicity on soil microbial communities should consider context. The reduction of AM fungi following nZVI application may have implications for land remediation.
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Affiliation(s)
- Mark Pawlett
- School of Applied Sciences, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK.
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26
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Butler E, Whelan MJ, Ritz K, Sakrabani R, van Egmond R. The effect of triclosan on microbial community structure in three soils. Chemosphere 2012; 89:1-9. [PMID: 22551872 DOI: 10.1016/j.chemosphere.2012.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 03/22/2012] [Accepted: 04/03/2012] [Indexed: 05/31/2023]
Abstract
The application of sewage sludge to land can expose soils to a range of associated chemical toxicants. In this paper we explore the effects of the broad spectrum anti-microbial compound triclosan on the phenotypic composition of the microbial communities of three soils of contrasting texture (loamy sand, sandy loam and clay) using phospholipid fatty-acid (PLFA) analysis. Each soil type was dosed and subsequently re-dosed 6 weeks later with triclosan at five nominal concentrations in microcosms (10, 100, 500, 1000 mg kg(-1) and a zero-dose control). PLFA profiles were analysed using multivariate statistics focussing on changes in the soil phenotypic community structure. Additionally, ratios of fungal:bacterial PLFA indicators and cyclo:mono-unsaturated PLFAs (a common stress indicator) were calculated. It was hypothesised that triclosan addition would alter the community structure in each soil with a particular effect on the fungal:bacterial ratio, since bacteria are likely to be more susceptible to triclosan than fungi. It was also hypothesised that the PLFA response to re-dosing would be suppressed due to acclimation. Although the microbial community structure changed over the course of the experiment, the response was complex. Soil type and time emerged as the most important explanatory factors. Principal component analysis was used to detect phenotypic responses to different doses of triclosan in each soil. As expected, there was a significant increase in the fungal:bacterial ratio with triclosan dose especially in treatments with the highest nominal concentrations. Furthermore, the PLFA response to re-dosing was negligible in all soils confirming the acclimation hypothesis.
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Affiliation(s)
- E Butler
- Department of Environmental Science and Technology, School of Applied Sciences, Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK
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27
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Philippot L, Ritz K, Pandard P, Hallin S, Martin-Laurent F. Standardisation of methods in soil microbiology: progress and challenges. FEMS Microbiol Ecol 2012; 82:1-10. [DOI: 10.1111/j.1574-6941.2012.01436.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 04/22/2012] [Accepted: 06/15/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
| | - Karl Ritz
- Department of Environmental Science and Technology; School of Applied Sciences; National Soil Resources Institute; Cranfield University; Cranfield; UK
| | - Pascal Pandard
- INERIS; Parc Technologique ALATA; Verneuil en Halatte; France
| | - Sara Hallin
- Department of Microbiology; Swedish University of Agricultural Sciences; Uppsala; Sweden
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28
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Crawford JW, Deacon L, Grinev D, Harris JA, Ritz K, Singh BK, Young I. Microbial diversity affects self-organization of the soil-microbe system with consequences for function. J R Soc Interface 2011; 9:1302-10. [PMID: 22158839 DOI: 10.1098/rsif.2011.0679] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Soils are complex ecosystems and the pore-scale physical structure regulates key processes that support terrestrial life. These include maintaining an appropriate mixture of air and water in soil, nutrient cycling and carbon sequestration. There is evidence that this structure is not random, although the organizing mechanism is not known. Using X-ray microtomography and controlled microcosms, we provide evidence that organization of pore-scale structure arises spontaneously out of the interaction between microbial activity, particle aggregation and resource flows in soil. A simple computational model shows that these interactions give rise to self-organization involving both physical particles and microbes that gives soil unique material properties. The consequence of self-organization for the functioning of soil is determined using lattice Boltzmann simulation of fluid flow through the observed structures, and predicts that the resultant micro-structural changes can significantly increase hydraulic conductivity. Manipulation of the diversity of the microbial community reveals a link between the measured change in micro-porosity and the ratio of fungal to bacterial biomass. We suggest that this behaviour may play an important role in the way that soil responds to management and climatic change, but that this capacity for self-organization has limits.
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Affiliation(s)
- John W Crawford
- Faculty of Agriculture, Food and Natural Resources, University of Sydney, Sydney, New South Wales 2006, Australia.
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Abstract
The antimicrobial substance triclosan has widespread use in personal care products and can enter the terrestrial environment if sewage sludge is applied to soil. The inhibitory effects of triclosan on basal and substrate-induced respiration (SIR) of three different soils were investigated. Soils were dosed and later redosed with four nominal triclosan concentrations, and respiration rates were measured over time. In each soil, a significant depression in basal respiration was noted after initial dosing, followed by a recovery. The initial extent of respiration inhibition was positively related to the triclosan dose, i.e., respiration was most inhibited at highest triclosan concentration. Differences in respiration inhibition between soils at equivalent dose were inversely correlated with organic matter and clay content, suggesting that the bioavailability of triclosan might have been reduced by sorption to organic carbon or by physical protection in micropores. Substrate-induced respiration was also reduced by the addition of triclosan and subsequently recovered. After redosing with triclosan, basal respiration was enhanced in all soils, suggesting that it was acting as a substrate. However, redosing resulted in SIR inhibition in all treatments above 10 mg triclosan kg(-1) in all three soils, although all soils appeared to be more resistant to perturbation than following initial dosing. The present study suggests that triclosan inhibits soil respiration but that a subsequent acclimation of the microbial community occurs.
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Affiliation(s)
- Emma Butler
- Cranfield University, Cranfield, Bedfordshire, United Kingdom.
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30
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Weininger M, Ritz K, Ritter CO, Hahn D, Beissert M. Koronares Kalzium-Scoring in der CT: Ergeben verschiedene Analyseprogramme vergleichbare Ergebnisse? – Bestimmung des koronaren Kalzium-Scores. ROFO-FORTSCHR RONTG 2010. [DOI: 10.1055/s-0029-1247988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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31
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Ritz K, Gerrits MCF, Foncke EMJ, van Ruissen F, van der Linden C, Vergouwen MDI, Bloem BR, Vandenberghe W, Crols R, Speelman JD, Baas F, Tijssen MAJ. Myoclonus-dystonia: clinical and genetic evaluation of a large cohort. J Neurol Neurosurg Psychiatry 2009; 80:653-8. [PMID: 19066193 DOI: 10.1136/jnnp.2008.162099] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Myoclonus-dystonia (M-D) is an autosomal dominant inherited movement disorder. Various mutations within the epsilon-sarcoglycan (SGCE) gene have been associated with M-D, but mutations are detected in only about 30% of patients. The lack of stringent clinical inclusion criteria and limitations of mutation screens by direct sequencing might explain this observation. METHODS Eighty-six M-D index patients from the Dutch national referral centre for M-D underwent neurological examination and were classified according to previously published criteria into definite, probable and possible M-D. Sequence analysis of the SGCE gene and screening for copy number variations were performed. In addition, screening was carried out for the 3 bp deletion in exon 5 of the DYT1 gene. RESULTS Based on clinical examination, 24 definite, 23 probable and 39 possible M-D patients were detected. Thirteen of the 86 M-D index patients carried a SGCE mutation: seven nonsense mutations, two splice site mutations, three missense mutations (two within one patient) and one multiexonic deletion. In the definite M-D group, 50% carried an SGCE mutation and one single patient in the probable group (4%). One possible M-D patient showed a 4 bp deletion in the DYT1 gene (c.934_937delAGAG). CONCLUSIONS Mutation carriers were mainly identified in the definite M-D group. However, in half of definite M-D cases, no mutation could be identified. Copy-number variations did not play a major role in the large cohort.
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Affiliation(s)
- K Ritz
- Department of Neurology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
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32
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Abstract
Soil health is presented as an integrative property that reflects the capacity of soil to respond to agricultural intervention, so that it continues to support both the agricultural production and the provision of other ecosystem services. The major challenge within sustainable soil management is to conserve ecosystem service delivery while optimizing agricultural yields. It is proposed that soil health is dependent on the maintenance of four major functions: carbon transformations; nutrient cycles; soil structure maintenance; and the regulation of pests and diseases. Each of these functions is manifested as an aggregate of a variety of biological processes provided by a diversity of interacting soil organisms under the influence of the abiotic soil environment. Analysis of current models of the soil community under the impact of agricultural interventions (particularly those entailing substitution of biological processes with fossil fuel-derived energy or inputs) confirms the highly integrative pattern of interactions within each of these functions and leads to the conclusion that measurement of individual groups of organisms, processes or soil properties does not suffice to indicate the state of the soil health. A further conclusion is that quantifying the flow of energy and carbon between functions is an essential but non-trivial task for the assessment and management of soil health.
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Affiliation(s)
- M.G Kibblewhite
- National Soil Resources Institute, School of Applied Sciences, Cranfield UniversityCranfield MK43 0AL, UK
| | - K Ritz
- National Soil Resources Institute, School of Applied Sciences, Cranfield UniversityCranfield MK43 0AL, UK
| | - M.J Swift
- Tropical Soil Biology and Fertility Institute of CIATPO Box 30677, Nairobi, Kenya
- Department of Biological Sciences, University of EssexColchester CO4 3SQ, UK
- Author and address for correspondence: Via Carlo Conti Rossini 115, Int 12, 00147 Roma, Italy ()
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33
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Affiliation(s)
- Karl Ritz
- National Soil Resources Institute, Cranfield University, Cranfield, UK.
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34
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Ritz K, Vergouwen M, Gerrits M, van Ruissen F, Baas F, Tijssen M. 1.306 Two novel epsilon-sarcoglycan mutations within one patient with myoclonus–dystonia. Parkinsonism Relat Disord 2007. [DOI: 10.1016/s1353-8020(08)70541-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Boswell GP, Jacobs H, Ritz K, Gadd GM, Davidson FA. The Development of Fungal Networks in Complex Environments. Bull Math Biol 2006; 69:605-34. [PMID: 16841267 DOI: 10.1007/s11538-005-9056-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Accepted: 05/17/2005] [Indexed: 11/29/2022]
Abstract
Fungi are of fundamental importance in terrestrial ecosystems playing important roles in decomposition, nutrient cycling, plant symbiosis and pathogenesis, and have significant potential in several areas of environmental biotechnology such as biocontrol and bioremediation. In all of these contexts, the fungi are growing in environments exhibiting spatio-temporal nutritional and structural heterogeneities. In this work, a discrete mathematical model is derived that allows detailed understanding of how events at the hyphal level are influenced by the nature of various environmental heterogeneities. Mycelial growth and function is simulated in a range of environments including homogeneous conditions, nutritionally-heterogeneous conditions and structurally-heterogeneous environments, the latter emulating porous media such as soils. Our results provide further understanding of the crucial processes involved in fungal growth, nutrient translocation and concomitant functional consequences, e.g. acidification, and have implications for the biotechnological application of fungi.
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Affiliation(s)
- Graeme P Boswell
- Department of Mathematics, University of Dundee, Dundee, DD1 4HN, UK.
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36
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Feeney DS, Crawford JW, Daniell T, Hallett PD, Nunan N, Ritz K, Rivers M, Young IM. Three-dimensional microorganization of the soil-root-microbe system. Microb Ecol 2006; 52:151-8. [PMID: 16680511 DOI: 10.1007/s00248-006-9062-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Accepted: 01/18/2006] [Indexed: 05/04/2023]
Abstract
Soils contain the greatest reservoir of biodiversity on Earth, and the functionality of the soil ecosystem sustains the rest of the terrestrial biosphere. This functionality results from complex interactions between biological and physical processes that are strongly modulated by the soil physical structure. Using a novel combination of biochemical and biophysical indicators and synchrotron microtomography, we have discovered that soil microbes and plant roots microengineer their habitats by changing the porosity and clustering properties (i.e., spatial correlation) of the soil pores. Our results indicate that biota act to significantly alter their habitat toward a more porous, ordered, and aggregated structure that has important consequences for functional properties, including transport processes. These observations support the hypothesis that the soil-plant-microbe complex is self-organized.
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Affiliation(s)
- Debbie S Feeney
- Scottish Informatics Mathematics Biology and Statistics (SIMBIOS) Centre, University of Abertay, Bell Street, Dundee, DD1 1HG, UK
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37
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Ritz K, Griffiths B, Torsvik V, Hendriksen N. Analysis of soil and bacterioplankton community DNA by melting profiles and reassociation kinetics. FEMS Microbiol Lett 2006. [DOI: 10.1111/j.1574-6968.1997.tb10322.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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38
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Griffiths B, Dı́az-Raviña M, Ritz K, McNicol J, Ebblewhite N, Bååth E. Community DNA hybridisation and %G+C profiles of microbial communities from heavy metal polluted soils. FEMS Microbiol Ecol 2006. [DOI: 10.1111/j.1574-6941.1997.tb00427.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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39
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Crawford JW, Harris JA, Ritz K, Young IM. Towards an evolutionary ecology of life in soil. Trends Ecol Evol 2004; 20:81-7. [PMID: 16701347 DOI: 10.1016/j.tree.2004.11.014] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2004] [Revised: 11/01/2004] [Accepted: 11/29/2004] [Indexed: 11/21/2022]
Abstract
The soil-microbe system is one of the most diverse components of the terrestrial ecosystem. The origin of this diversity, and its relation to the life-sustaining processes that are mediated by the resident microbial community, is still poorly understood. The inherent complexities necessitate a theoretical framework that integrates ecological and evolutionary approaches and which embraces the physical heterogeneity of the soil environment. Such a framework is currently lacking, although recent advances in theory and experimentation are beginning to identify the essential ingredients. Here, we review and evaluate the relevance of current modelling approaches, and propose a new synthesis of an evolutionary ecology of life in soil. Key elements include an account of dispersal, horizontal gene transfer, and the consideration of the physical and biological components of soil as an integrated complex adaptive system.
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Affiliation(s)
- John W Crawford
- SIMBIOS Center, University of Abertay Dundee, Bell Street, Dundee, UK, DD1 1HG.
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40
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Jacobs H, Boswell GP, Scrimgeour CM, Davidson FA, Gadd GM, Ritz K. Translocation of carbon by Rhizoctonia solani in nutritionally-heterogeneous microcosms. ACTA ACUST UNITED AC 2004; 108:453-62. [PMID: 15209285 DOI: 10.1017/s0953756204009840] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Responses of Rhizoctonia solani to spatial heterogeneity in sources of carbon, and associated translocation of carbon (C), were studied in a simple microcosm system comprising two discrete domains of agar gels separated on a glass slide and overlain with a porous membrane. Two arrangements of the gel pairs were used, one containing two equally large resources (representing 'homogeneous' conditions) and one containing a large and a negligible resource (representing 'heterogeneous' conditions). The nutrient sources were a standard mineral salt medium with or without glucose as sole C source. The fungus was inoculated onto one domain and growth responses determined by direct measurement of biomass. Translocation of C was quantified by use of 13C-enriched glucose. This substrate was either added to the agar at the outset, when studying newly developing colonies, or as a pulse into already established colonies. When growing in heterogeneous conditions, the fungus actively translocated C from a glucose-containing domain to sustain growth in the adjacent region lacking such a resource. In homogeneous conditions there was evidence of passive translocation (diffusion), but the fungus preferentially used local resource to maintain growth. Active translocation was only observed in newly growing colonies, whereas passive translocation occurred in both growing and established colonies. When the fungus was pulsed with a 13C-enriched glucose solution after 10 d growth, 2.5 times more 13C was taken up by the fungus grown in heterogeneous than homogeneous conditions, suggesting uptake exceeded local demands. In heterogeneous conditions, the total amount of 13C enriched glucose taken up by the fungus was independent of the location of the enriched glucose in the underlying medium. When the nylon membrane was replaced by Cellophane (an additional C source), degradation of the membrane and an increase in biomass occurred only in the heterogeneous system. The possible implications for these results in soil systems are discussed.
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Affiliation(s)
- Helen Jacobs
- Division of Environmental and Applied Biology, Biological Sciences Institute, School of Life Sciences, University of Dundee, Dundee DD1 4HN, UK
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41
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Griffiths BS, Kuan HL, Ritz K, Glover LA, McCaig AE, Fenwick C. The relationship between microbial community structure and functional stability, tested experimentally in an upland pasture soil. Microb Ecol 2004; 47:104-13. [PMID: 15259275 DOI: 10.1007/s00248-002-2043-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Soil collected from an upland pasture was manipulated experimentally in ways shown previously to alter microbial community structure. One set of soil was subjected to chloroform fumigation for 0, 0.5, 2, or 24 h and the other was sterilised by gamma-irradiation and inoculated with a 10(-2), 10(-4), 10(-6), or 10(-8) dilution of a soil suspension prepared from unsterilized soil. Following incubation for 8 months, to allow for the stabilization of microbial biomass and activity, the resulting microbial community structure (determined by PCR-DGGE of bacterial specific amplification products of total soil DNA) was assessed. In addition, the functional stability (defined here as the resistance and resilience of short-term decomposition of plant residues to a transient heat or a persistent copper perturbation) was determined. Changes in the active bacterial population following perturbation (determined by RT-PCR-DGGE of total soil RNA) were also monitored. The manipulations resulted in distinct shifts in microbial community structure as shown by PCR-DGGE profiles, but no significant decreases in the number of bands. These shifts in microbial community structure were associated with a reduction in functional stability. The clear correlation between altered microbial community structure and functional stability observed in this upland pasture soil was not evident when the same protocols were applied to soils in other studies. RT-PCR-DGGE profiles only detected a shift in the active bacterial population following heat, but not copper, perturbation. We conclude that the functional stability of decomposition is related to specific components of the microbial community.
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Affiliation(s)
- B S Griffiths
- Plant-Soil Interface Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK.
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42
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Abstract
Metal-contaminated soils often contain a spatially heterogeneous distribution of metal concentrations, and the ability of fungi to colonize such metal-contaminated domains will be influenced by the nutritional resources available. An experimental system based upon tessellated agar tiles was used to study the influence of nutrients upon the ability of soil fungi Trichoderma virens and Clonostachys rosea to colonize spatially discrete toxic metal (copper and cadmium) containing domains. The growth parameters recorded demonstrated a decrease in apparent metal toxicity with increasing concentration of available carbon source. It was shown that maximum hyphal extension rates and the efficacy of carbon substrate utilization of both species decreased with increasing concentration of toxic metals. It was also observed that in the gap between metal-free and metal-containing tiles, the presence of toxic metals led to negative chemotropic reactions and cessation of growth, swelling and lysis of some hyphal tips. Penetration of the hyphae into the metal-containing domain was often followed by the formation of very dense mycelia or mycelial 'bushes' representing an associative (constraining, exploitative or 'phalanx') growth strategy of the mycelial system. After the fungi entered the toxic metal-containing domains, they often produced long sparsely-branched or branchless explorative hyphae representing a dissociative (expansive, explorative or 'guerrilla') growth strategy. Our data therefore demonstrate that fungi efficiently use both 'phalanx' and 'guerrilla' states of the mycelial system as well as shifts in these growth strategies as a response to toxic metal stress combined with nutritionally-poor conditions.
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Affiliation(s)
- Marina Fomina
- Division of Environmental and Applied Biology, Biological Sciences Institute, School of Life Sciences, University of Dundee, Dundee DD1 4HN, UK
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43
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Nunan N, Wu K, Young IM, Crawford JW, Ritz K. Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil. FEMS Microbiol Ecol 2003; 44:203-15. [DOI: 10.1016/s0168-6496(03)00027-8] [Citation(s) in RCA: 261] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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44
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Harris K, Young IM, Gilligan CA, Otten W, Ritz K. Effect of bulk density on the spatial organisation of the fungus Rhizoctonia solani in soil. FEMS Microbiol Ecol 2003; 44:45-56. [DOI: 10.1111/j.1574-6941.2003.tb01089.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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45
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Abstract
As decomposer organisms, pathogens, plant symbionts and nutrient cyclers, fungi are of fundamental importance in the terrestrial environment. Moreover, in addition to their well-known applications in industry, many species also have great potential in environmental biotechnology. The study of this important class of organisms is difficult through experimental means alone due to the heterogeneity of their natural growth habitat and the microscopic scale of growth. In this work we present a mathematical model for colony expansion that is derived through consideration of the growth characteristics on the microscale. The model equations are of mixed hyperbolic-parabolic type and are treated with a numerical scheme that preserves positivity and conserves mass. The numerical solutions are compared against experimental results in a variety of environments. Thus the effect of different translocation mechanisms on fungal growth and function are identified. The derivation and analysis of an approximation to the full model yields further results concerning basic properties of mycelial growth. Finally, the acidification of the growth habitat is considered and the model thus provides important predictions on the functional consequences of the redistribution of internally-located material.
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Affiliation(s)
- Graeme P Boswell
- Department of Mathematics, University of Dundee, Dundee DD1 4HN, UK
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46
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Griffiths BS, Ritz K, Bardgett RD, Cook R, Christensen S, Ekelund F, Sørensen SJ, Bååth E, Bloem J, De Ruiter PC, Dolfing J, Nicolardot B. Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship. OIKOS 2003. [DOI: 10.1034/j.1600-0706.2000.900208.x] [Citation(s) in RCA: 464] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Nunan N, Wu K, Young IM, Crawford JW, Ritz K. In situ spatial patterns of soil bacterial populations, mapped at multiple scales, in an arable soil. Microb Ecol 2002; 44:296-305. [PMID: 12375095 DOI: 10.1007/s00248-002-2021-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2002] [Accepted: 07/30/2002] [Indexed: 05/23/2023]
Abstract
Very little is known about the spatial organization of soil microbes across scales that are relevant both to microbial function and to field-based processes. The spatial distributions of microbes and microbially mediated activity have a high intrinsic variability. This can present problems when trying to quantify the effects of disturbance, management practices, or climate change on soil microbial systems and attendant function. A spatial sampling regime was implemented in an arable field. Cores of undisturbed soil were sampled from a 3 x 3 x 0.9 m volume of soil (topsoil and subsoil) and a biological thin section, in which the in situ distribution of bacteria could be quantified, prepared from each core. Geostatistical analysis was used to quantify the nature of spatial structure from micrometers to meters and spatial point pattern analysis to test for deviations from complete spatial randomness of mapped bacteria. Spatial structure in the topsoil was only found at the microscale (micrometers), whereas evidence for nested scales of spatial structure was found in the subsoil (at the microscale, and at the centimeter to meter scale). Geostatistical ranges of spatial structure at the micro scale were greater in the topsoil and tended to decrease with depth in the subsoil. Evidence for spatial aggregation in bacteria was stronger in the topsoil and also decreased with depth in the subsoil, though extremely high degrees of aggregation were found at very short distances in the deep subsoil. The data suggest that factors that regulate the distribution of bacteria in the subsoil operate at two scales, in contrast to one scale in the topsoil, and that bacterial patches are larger and more prevalent in the topsoil.
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Affiliation(s)
- N Nunan
- Soil-Plant Dynamics Unit, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK.
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48
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Abstract
Fungi are of fundamental importance for plant and microbial nutrition with primary roles in decomposition and nutrient recycling. They also have great potential for use in areas of biotechnology such as bioremediation of organic and inorganic pollutants and biocontrol of plant pathogens. In all these contexts, environmental heterogeneity has a strong influence on growth and function. A large class of fungi overcome the difficulties encountered in such environments by the mechanism of translocation which results in the internal redistribution of nutrients within the fungal mycelium. In this paper, we use a combination of experimental techniques and mathematical modelling to examine fungal growth in general, and in particular, translocation in the common soil saprophytic fungus Rhizoctonia solani. A detailed mathematical model is presented where translocation is considered to have both diffusive and metabolically-driven components. A calibration experiment provided the necessary parameter values. Growth experiments were compared with model solutions and thus we provide strong evidence that diffusion is the dominant mechanism for translocation in homogeneous environments. In heterogeneous environments, we conclude that diffusion is still vital for exploration, i.e. the expansion of the fungal network into the surrounding area. However, we also conclude that localized resources may be utilized faster if energy is invested, i.e. when exploitation of the fungal microenvironment is enhanced by metabolically driven translocation.
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Affiliation(s)
- Graeme P Boswell
- Department of Mathematics, University of Dundee, Dundee, DD1 4HN, UK.
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49
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Jacobs H, Boswell GP, Ritz K, Davidson FA, Gadd GM. Solubilization of calcium phosphate as a consequence of carbon translocation by Rhizoctonia solani. FEMS Microbiol Ecol 2002; 40:65-71. [DOI: 10.1111/j.1574-6941.2002.tb00937.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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50
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Sturrock CJ, Ritz K, Samson WB, Bown JL, Staines HJ, Palfreyman JW, Crawford JW, White NA. The effects of fungal inoculum arrangement (scale and context) on emergent community development in an agar model system. FEMS Microbiol Ecol 2002; 39:9-16. [PMID: 19709179 DOI: 10.1111/j.1574-6941.2002.tb00901.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Abstract Consequences of initial spatial organisation of model fungal communities upon their spatio-temporal development were investigated. Dynamics of prescribed two- and three-species 'communities' developing on tessellated agar tile model systems were analysed in terms of literal maps, principal component analyses, or as the proportion of species extant within tiles. It was established that for two-species interactions of equal patch size, large-scale (i.e. many constituent tiles) behaviour could be extrapolated from the relevant small-scale (i.e. pairs of tiles) interactions. However, relative patch sizes (scale) of species within tessellations influenced the times taken by individuals to colonise tiles and, hence, temporal behaviour of the system. Outcome of arrangements involving three species of equal patch size and inoculum potential, and prescribed with different mixing patterns, could not be directly extrapolated by reference to the outcome of pair-wise interactions between constituent species. Three-species arrangements attempt to limit assembly of lateral aggregates of individuals (patch size) and hence any effects of tile colonisation times, so as to reveal effects of nearest neighbour context within the complex community. Such arrangements indicate that spatial configuration of inoculum influences community development and reproducibility. They also suggest that spatial distribution of species affects persistence of individuals, which would otherwise be expected to be eliminated from the system. Two-species interactions appeared generally more reproducible than those comprising three species, and the sensitivity of fungal community development to temperature was not solely associated with influence on colony extension rate.
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Affiliation(s)
- Craig J Sturrock
- SIMBIOS, University of Abertay Dundee, Kydd Building, Dundee DD1 1HG, UK
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