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van Griethuysen PA, Redeker KR, MacFarlane SA, Neilson R, Hartley SE. Virus-induced changes in root volatiles attract soil nematode vectors to infected plants. New Phytol 2024; 241:2275-2286. [PMID: 38327027 DOI: 10.1111/nph.19518] [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] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/28/2023] [Indexed: 02/09/2024]
Abstract
Plant-derived volatiles mediate interactions among plants, pathogenic viruses, and viral vectors. These volatile-dependent mechanisms have not been previously demonstrated belowground, despite their likely significant role in soil ecology and agricultural pest impacts. We investigated how the plant virus, tobacco rattle virus (TRV), attracts soil nematode vectors to infected plants. We infected Nicotiana benthamiana with TRV and compared root growth relative to that of uninfected plants. We tested whether TRV-infected N. benthamiana was more attractive to nematodes 7 d post infection and identified a compound critical to attraction. We also infected N. benthamiana with mutated TRV strains to identify virus genes involved in vector nematode attraction. Virus titre and associated impacts on root morphology were greatest 7 d post infection. Tobacco rattle virus infection enhanced 2-ethyl-1-hexanol production. Nematode chemotaxis and 2-ethyl-1-hexanol production correlated strongly with viral load. Uninfected plants were more attractive to nematodes after the addition of 2-ethyl-1-hexanol than were untreated plants. Mutation of TRV RNA2-encoded genes reduced the production of 2-ethyl-1-hexanol and nematode attraction. For the first time, this demonstrates that virus-driven alterations in root volatile emissions lead to increased chemotaxis of the virus's nematode vector, a finding with implications for sustainable management of both nematodes and viral pathogens in agricultural systems.
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Affiliation(s)
| | - Kelly R Redeker
- Department of Biology, University of York, Heslington, York, YO1 5DD, UK
| | - Stuart A MacFarlane
- Cell and Molecular Sciences Department, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Roy Neilson
- Ecological Sciences Department, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Sue E Hartley
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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2
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Issitt T, Reilly M, Sweeney ST, Brackenbury WJ, Redeker KR. GC/MS analysis of hypoxic volatile metabolic markers in the MDA-MB-231 breast cancer cell line. Front Mol Biosci 2023; 10:1178269. [PMID: 37251079 PMCID: PMC10210155 DOI: 10.3389/fmolb.2023.1178269] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
Hypoxia in disease describes persistent low oxygen conditions, observed in a range of pathologies, including cancer. In the discovery of biomarkers in biological models, pathophysiological traits present a source of translatable metabolic products for the diagnosis of disease in humans. Part of the metabolome is represented by its volatile, gaseous fraction; the volatilome. Human volatile profiles, such as those found in breath, are able to diagnose disease, however accurate volatile biomarker discovery is required to target reliable biomarkers to develop new diagnostic tools. Using custom chambers to control oxygen levels and facilitate headspace sampling, the MDA-MB-231 breast cancer cell line was exposed to hypoxia (1% oxygen) for 24 h. The maintenance of hypoxic conditions in the system was successfully validated over this time period. Targeted and untargeted gas chromatography mass spectrometry approaches revealed four significantly altered volatile organic compounds when compared to control cells. Three compounds were actively consumed by cells: methyl chloride, acetone and n-Hexane. Cells under hypoxia also produced significant amounts of styrene. This work presents a novel methodology for identification of volatile metabolisms under controlled gas conditions with novel observations of volatile metabolisms by breast cancer cells.
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Affiliation(s)
- Theo Issitt
- Department of Biology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
| | - Matthew Reilly
- Department of Biology, University of York, York, United Kingdom
| | - Sean T. Sweeney
- Department of Biology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
| | - William J. Brackenbury
- Department of Biology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
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3
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Wiethase JH, Critchlow R, Foley C, Foley L, Kinsey EJ, Bergman BG, Osujaki B, Mbwambo Z, Kirway PB, Redeker KR, Hartley SE, Beale CM. Pathways of degradation in rangelands in Northern Tanzania show their loss of resistance, but potential for recovery. Sci Rep 2023; 13:2417. [PMID: 36813819 PMCID: PMC9946995 DOI: 10.1038/s41598-023-29358-6] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/02/2023] [Indexed: 02/24/2023] Open
Abstract
Semiarid rangelands are identified as at high risk of degradation due to anthropogenic pressure and climate change. Through tracking timelines of degradation we aimed to identify whether degradation results from a loss of resistance to environmental shocks, or loss of recovery, both of which are important prerequisites for restoration. Here we combined extensive field surveys with remote sensing data to explore whether long-term changes in grazing potential demonstrate loss of resistance (ability to maintain function despite pressure) or loss of recovery (ability to recover following shocks). To monitor degradation, we created a bare ground index: a measure of grazeable vegetation cover visible in satellite imagery, allowing for machine learning based image classification. We found that locations that ended up the most degraded tended to decline in condition more during years of widespread degradation but maintained their recovery potential. These results suggest that resilience in rangelands is lost through declines in resistance, rather than loss of recovery potential. We show that the long-term rate of degradation correlates negatively with rainfall and positively with human population and livestock density, and conclude that sensitive land and grazing management could enable restoration of degraded landscapes, given their retained ability to recover.
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Affiliation(s)
| | - Rob Critchlow
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Charles Foley
- Tanzania Conservation Research Program, Lincoln Park Zoo, Chicago, IL, 60614, USA
| | - Lara Foley
- Tanzania Conservation Research Program, Lincoln Park Zoo, Chicago, IL, 60614, USA
| | | | | | | | - Zawadi Mbwambo
- Tanzania Program, Zoological Society of London, London, NW1 4RY, UK
| | | | - Kelly R Redeker
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Susan E Hartley
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Colin M Beale
- Department of Biology, University of York, York, YO10 5DD, UK
- University of York, York Environmental Sustainability Institute, York, YO10 5DD, UK
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4
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Chadfield VGA, Hartley SE, Redeker KR. Associational resistance through intercropping reduces yield losses to soil-borne pests and diseases. New Phytol 2022; 235:2393-2405. [PMID: 35678712 PMCID: PMC9545407 DOI: 10.1111/nph.18302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 01/17/2022] [Accepted: 05/03/2022] [Indexed: 05/07/2023]
Abstract
Associational resistance to herbivore and pathogen attack is a well documented ecological phenomenon and, if applied to agriculture, may reduce impact of pests and diseases on crop yields without recourse to pesticides. The value of associational resistance through intercropping, planting multiple crops alongside each other, as a sustainable control method remains unclear, due to variable outcomes reported in the published literature. We performed a meta-analysis to provide a quantitative assessment of benefits of intercropping for target plant resistance to plant-parasitic nematodes and soil-borne diseases. We found that intercropping reduced damage to focal crops from nematodes by 40% and disease incidence by 55%. Intercropping efficacy varied with biological variables, such as field fertilisation status and intercrop family, and methodology, including whether study samples were potted or in fields. Nematode control using intercropping was sufficient to offset reductions in focal crop yield from intercrop presence, making intercropping a viable agricultural tool. We identify key drivers for underpinning the success of intercropping and indicate areas for future research to improve efficacy. This study also highlights the potential benefits of harnessing ecological knowledge on plant-enemy interactions for improving agricultural and landscape sustainability.
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Affiliation(s)
| | - Sue E. Hartley
- Department of BiologyUniversity of YorkWentworth WayYorkYO10 5DDUK
| | - Kelly R. Redeker
- Department of BiologyUniversity of YorkWentworth WayYorkYO10 5DDUK
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5
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Fulk EM, Gao X, Lu LC, Redeker KR, Masiello CA, Silberg JJ. Nondestructive Chemical Sensing within Bulk Soil Using 1000 Biosensors Per Gram of Matrix. ACS Synth Biol 2022; 11:2372-2383. [PMID: 35715210 DOI: 10.1021/acssynbio.2c00083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gene expression can be monitored in hard-to-image environmental materials using gas-reporting biosensors, but these outputs have only been applied in autoclaved matrices that are hydrated with rich medium. To better understand the compatibility of indicator gas reporting with environmental samples, we evaluated how matrix hydration affects the gas signal of an engineered microbe added to a sieved soil. A gas-reporting microbe presented a gas signal in a forest soil (Alfisol) when hydrated to an environmentally relevant osmotic pressure. When the gas signal was concentrated prior to analysis, a biosensor titer of 103 cells/gram of soil produced a significant signal when soil was supplemented with halides. A signal was also observed without halide amendment, but a higher cell titer (106 cells/gram of soil) was required. A sugar-regulated gas biosensor was able to report with a similar level of sensitivity when added to an unsterilized soil matrix, illustrating how gas concentration enables biosensing within a soil containing environmental microbes. These results establish conditions where engineered microbes can report on gene expression in living environmental matrices with decreased perturbation of the soil environment compared to previously reported approaches, using biosensor titers that are orders of magnitude lower than the number of cells typically observed in a gram of soil.
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Affiliation(s)
- Emily M Fulk
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, Texas 77005, United States
| | - Xiaodong Gao
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States
| | - Li Chieh Lu
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Kelly R Redeker
- Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Caroline A Masiello
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States.,Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States.,Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, Texas 77005, United States
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6
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Alessi AM, Redeker KR, Chong JPJ. A practical introduction to microbial molecular ecology through the use of isolation chips. Ecol Evol 2018; 8:12286-12298. [PMID: 30619545 PMCID: PMC6309002 DOI: 10.1002/ece3.4748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 10/23/2018] [Accepted: 10/31/2018] [Indexed: 12/20/2022] Open
Abstract
In the context of antimicrobial resistance as one of the most serious issues faced globally by health providers, we explored a practical introduction to molecular microbial ecology. We designed field work and practical experiments for third year members of a 4 year undergraduate Masters Program, in which the students employed traditional and novel isolation techniques to identify antimicrobial activities from soil dwelling microorganisms. Students gained experience in isolating DNA from complex microbial communities, amplifying 16S rRNA genes and applied richness/diversity indices as well as principal coordinate analyses to the interpretation of the data they obtained from high throughput sequencing. Our results confirmed that isolation chips facilitate the growth of a greater diversity and different species subset from the complex soil microorganism community than traditional plate spreading techniques. However, rarefaction of 16S rRNA amplicon sequencing data showed that the majority of observed species in soil remain unculturable by current methods. Based on the written reports produced by the students carrying out the work, we concluded that the described protocols are robust and informative, that these activities provide a good practical introduction to the theories and practice of molecular ecology and can be easily deployed to groups of six or more students in a cost-effective manner.
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7
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Redeker KR, Chong JPJ, Aguion A, Hodson A, Pearce DA. Microbial metabolism directly affects trace gases in (sub) polar snowpacks. J R Soc Interface 2018; 14:rsif.2017.0729. [PMID: 29263129 DOI: 10.1098/rsif.2017.0729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 11/29/2017] [Indexed: 11/12/2022] Open
Abstract
Concentrations of trace gases trapped in ice are considered to develop uniquely from direct snow/atmosphere interactions at the time of contact. This assumption relies upon limited or no biological, chemical or physical transformations occurring during transition from snow to firn to ice; a process that can take decades to complete. Here, we present the first evidence of environmental alteration due to in situ microbial metabolism of trace gases (methyl halides and dimethyl sulfide) in polar snow. We collected evidence for ongoing microbial metabolism from an Arctic and an Antarctic location during different years. Methyl iodide production in the snowpack decreased significantly after exposure to enhanced UV radiation. Our results also show large variations in the production and consumption of other methyl halides, including methyl bromide and methyl chloride, used in climate interpretations. These results suggest that this long-neglected microbial activity could constitute a potential source of error in climate history interpretations, by introducing a so far unappreciated source of bias in the quantification of atmospheric-derived trace gases trapped within the polar ice caps.
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Affiliation(s)
- K R Redeker
- Department of Biology, University of York, York, North Yorkshire, UK
| | - J P J Chong
- Department of Biology, University of York, York, North Yorkshire, UK
| | - A Aguion
- Department of Biology, University of York, York, North Yorkshire, UK
| | - A Hodson
- Department of Geography, University of Sheffield, Sheffield, UK.,Department of Arctic Geology, University Centre in Svalbard, Svalbard, Norway
| | - D A Pearce
- Department of Applied Sciences, Northumbria University, Ellison Building, Newcastle upon Tyne, NE66 1UG, UK
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8
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Redeker KR, Cai LL, Dumbrell AJ, Bardill A, Chong JP, Helgason T. Noninvasive Analysis of the Soil Microbiome: Biomonitoring Strategies Using the Volatilome, Community Analysis, and Environmental Data. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2018.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Abstract
MOTIVATION Next-generation sequencing methods are generating increasingly massive datasets, yet still do not fully capture genetic diversity in the richest environments. To understand such complicated and elusive systems, effective tools are needed to assist with delineating the differences found in and between community datasets. RESULTS The Small Subunit Markov Modeler (SSuMMo) was developed to probabilistically assign SSU rRNA gene fragments from any sequence dataset to recognized taxonomic clades, producing consistent, comparable cladograms. Accuracy tests predicted >90% of genera correctly for sequences downloaded from public reference databases. Sequences from a next-generation sequence dataset, sampled from lean, overweight and obese individuals, were analysed to demonstrate parallel visualization of comparable datasets. SSuMMo shows potential as a valuable curatorial tool, as numerous incorrect and outdated taxonomic entries and annotations were identified in public databases. AVAILABILITY AND IMPLEMENTATION SSuMMo is GPLv3 open source Python software, available at http://code.google.com/p/ssummo/. Taxonomy and HMM databases can be downloaded from http://bioltfws1.york.ac.uk/ssummo/. SUPPLEMENTARY INFORMATION Supplemental materials are available at Bioinformatics Online.
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Affiliation(s)
- Alex L B Leach
- Department of Biology, University of York, York YO10 5DD, UK.
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10
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Archbold ME, Redeker KR, Davis S, Elliot T, Kalin RM. A method for carbon stable isotope analysis of methyl halides and chlorofluorocarbons at pptv concentrations. Rapid Commun Mass Spectrom 2005; 19:337-342. [PMID: 15645502 DOI: 10.1002/rcm.1791] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A pre-concentration system has been validated for use with a gas chromatography/mass spectrometry/isotope ratio mass spectrometer (GC/MS/IRMS) to determine ambient air (13)C/(12)C ratios for methyl halides (MeCl and MeBr) and chlorofluorocarbons (CFCs). The isotopic composition of specific compounds can provide useful information on their atmospheric budgets and biogeochemistry that cannot be ascertained from abundance measurements alone. Although pre-concentration systems have been previously used with a GC/MS/IRMS for atmospheric trace gas analysis, this is the first study also to report system validation tests. Validation results indicate that the pre-concentration system and subsequent separation technologies do not significantly alter the stable isotopic ratios of the target methyl halides, CFC-12 (CCl(2)F(2)) and CFC-113 (C(2)Cl(3)F(3)). Significant, but consistent, isotopic shifts of -27.5 per thousand to -25.6 per thousand do occur within the system for CFC-11 (CCl(3)F), although the shift is correctible. The method presented has the capacity to separate these target halocarbons from more than 50 other compounds in ambient air samples. Separation allows for the determination of stable carbon isotope ratios of five of these six target trace atmospheric constituents within ambient air for large volume samples (</=10 L). Representative urban air analyses from Belfast City are also presented which give carbon isotope results similar to published values for (13)C/(12)C analysis of MeCl (-39.1 per thousand) and CFC-113 (-28.1 per thousand). However, this is the first paper reporting stable carbon isotope signatures for CFC-11 (-29.4 per thousand) and CFC-12 (-37.0 per thousand).
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Affiliation(s)
- Marie E Archbold
- Environmental Engineering Research Centre, School of Civil Engineering, Queen's University of Belfast, David Keir Building, Stranmillis Rd., Belfast BT9 5AG, UK.
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Abstract
Methyl halide gases are important sources of atmospheric inorganic halogen compounds, which in turn are central reactants in many stratospheric and tropospheric chemical processes. By observing emissions of methyl chloride, methyl bromide, and methyl iodide from flooded California rice fields, we estimate the impact of rice agriculture on the atmospheric budgets of these gases. Factors influencing methyl halide emissions are stage of rice growth, soil organic content, halide concentrations, and field-water management. Extrapolating our data implies that about 1 percent of atmospheric methyl bromide and 5 percent of methyl iodide arise from rice fields worldwide. Unplanted flooded fields emit as much methyl chloride as planted, flooded rice fields.
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Affiliation(s)
- K R Redeker
- Department of Earth System Science, Department of Chemistry, University of California, Irvine, CA 92697, USA
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