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Graf M, Greenfield LM, Reay MK, Bargiela R, Williams GB, Onyije C, Lloyd CEM, Bull ID, Evershed RP, Golyshin PN, Chadwick DR, Jones DL. Increasing concentration of pure micro- and macro-LDPE and PP plastic negatively affect crop biomass, nutrient cycling, and microbial biomass. J Hazard Mater 2023; 458:131932. [PMID: 37390687 DOI: 10.1016/j.jhazmat.2023.131932] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/29/2023] [Accepted: 06/23/2023] [Indexed: 07/02/2023]
Abstract
Over the last 50 years, the intense use of agricultural plastic in the form of mulch films has led to an accumulation of plastic in soil, creating a legacy of plastic in agricultural fields. Plastic often contains additives, however it is still largely unknown how these compounds affect soil properties, potentially influencing or masking effects of the plastic itself. Therefore, the aim of this study was to investigate the effects of pure plastics of varying sizes and concentrations, to improve our understanding of plastic-only interactions within soil-plant mesocosms. Maize (Zea mays L.) was grown over eight weeks following the addition of micro and macro low-density polyethylene and polypropylene at increasing concentrations (equivalent to 1, 10, 25, and 50 years mulch film use) and the effects of plastic on key soil and plant properties were measured. We found the effect of both macro and microplastic on soil and plant health is negligible in the short-term (1 to <10 years). However, ≥ 10 years of plastic application for both plastic types and sizes resulted in a clear negative effect on plant growth and microbial biomass. This study provides vital insight into the effect of both macro and microplastics on soil and plant properties.
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Affiliation(s)
- Martine Graf
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
| | - Lucy M Greenfield
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Michaela K Reay
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Rafael Bargiela
- Centre of Environmental Biotechnology, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Gwion B Williams
- Centre of Environmental Biotechnology, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Charles Onyije
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Charlotte E M Lloyd
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Ian D Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Peter N Golyshin
- Centre of Environmental Biotechnology, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - David R Chadwick
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Davey L Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; Centre of Environmental Biotechnology, Bangor University, Bangor, Gwynedd LL57 2UW, UK; SoilsWest, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
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2
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Zhao W, Whelton HL, Blong JC, Shillito LM, Jenkins DL, Bull ID. Volatile organic compounds (VOCs) as a rapid means for assessing the source of coprolites. iScience 2023; 26:106806. [PMID: 37255664 PMCID: PMC10225897 DOI: 10.1016/j.isci.2023.106806] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/22/2022] [Accepted: 05/01/2023] [Indexed: 06/01/2023] Open
Abstract
The odor of rehydrated coprolites can be used as an informal means of fecal identification. To date, the analysis of volatiles emitted by coprolites from different sources has not been attempted, and the possibility of utilizing volatile organic compounds (VOCs) as fecal biomarkers unexplored. VOCs released by coprolites from the Paisley Caves, were analyzed using solid-phase microextraction (SPME), to assess the variance of results from different coprolites (carnivores, herbivores, or humans). Coprolites from carnivores can be clearly distinguished from those produced by herbivores and humans; these latter two are separated to a lesser degree. Eight discriminatory compounds differentiated between the coprolite sources, and their identities were verified using reference standards. Coprolites and their associated sediments could not be differentiated between using this method, suggesting leaching of VOCs into the burial matrix. This work provides an alternative, more rapid way to assess coprolite origin.
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Affiliation(s)
- Wanyue Zhao
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - Helen L. Whelton
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - John C. Blong
- Department of Anthropology, Washington State University, College Hall, Pullman, WA 99164-4910, USA
| | - Lisa-Marie Shillito
- School of History, Classics and Archaeology, Armstrong Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Dennis L. Jenkins
- Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA
| | - Ian D. Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
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Reay MK, Pears KA, Kuhl A, Evershed RP, Murray PJ, Cardenas LM, Dungait JAJ, Bull ID. Mechanisms of nitrogen transfer in a model clover-ryegrass pasture: a 15N-tracer approach. Plant Soil 2022; 480:369-389. [PMID: 36466744 PMCID: PMC9705487 DOI: 10.1007/s11104-022-05585-0] [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] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/25/2022] [Indexed: 06/17/2023]
Abstract
PURPOSE Nitrogen (N) transfer from white clover (Trifolium repens cv.) to ryegrass (Lolium perenne cv.) has the potential to meet ryegrass N requirements. This study aimed to quantify N transfer in a mixed pasture and investigate the influence of the microbial community and land management on N transfer. METHODS Split root 15N-labelling of clover quantified N transfer to ryegrass via exudation, microbial assimilation, decomposition, defoliation and soil biota. Incorporation into the microbial protein pool was determined using compound-specific 15N-stable isotope probing approaches. RESULTS N transfer to ryegrass and soil microbial protein in the model system was relatively small, with one-third arising from root exudation. N transfer to ryegrass increased with no microbial competition but soil microbes also increased N transfer via shoot decomposition. Addition of mycorrhizal fungi did not alter N transfer, due to the source-sink nature of this pathway, whilst weevil grazing on roots decreased microbial N transfer. N transfer was bidirectional, and comparable on a short-term scale. CONCLUSIONS N transfer was low in a model young pasture established from soil from a permanent grassland with long-term N fertilisation. Root exudation and decomposition were major N transfer pathways. N transfer was influenced by soil biota (weevils, mycorrhizae) and land management (e.g. grazing). Previous land management and the role of the microbial community in N transfer must be considered when determining the potential for N transfer to ryegrass. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11104-022-05585-0.
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Affiliation(s)
- Michaela K. Reay
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS UK
| | - Katrina A. Pears
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS UK
| | - Alison Kuhl
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS UK
| | - Richard P. Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS UK
| | - Phillip J. Murray
- Department of Sustainable Agriculture Sciences, Rothamsted Research - North Wyke, Okehampton, EX20 2SB Devon UK
- Present Address: School of Agriculture, Food and Environment, Royal Agricultural University, Cirencester, GL7 6JS UK
| | - Laura M. Cardenas
- Department of Sustainable Agriculture Sciences, Rothamsted Research - North Wyke, Okehampton, EX20 2SB Devon UK
| | - Jennifer A. J. Dungait
- Department of Sustainable Agriculture Sciences, Rothamsted Research - North Wyke, Okehampton, EX20 2SB Devon UK
- Present Address: Carbon Management Center, SRUC - Scotland’s Rural College, Edinburgh, Scotland EH9 3JG UK
- Present Address: Geography, CLES - Amory Building, University of Exeter, Exeter, EX4 4RJ UK
| | - Ian D. Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS UK
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Al-Salihi SAA, Bull ID, Al-Salhi R, Gates PJ, Salih KSM, Bailey AM, Foster GD. Further Biochemical Profiling of Hypholoma fasciculare Metabolome Reveals Its Chemogenetic Diversity. Front Bioeng Biotechnol 2021; 9:567384. [PMID: 34109161 PMCID: PMC8181146 DOI: 10.3389/fbioe.2021.567384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 04/01/2021] [Indexed: 11/30/2022] Open
Abstract
Natural products with novel chemistry are urgently needed to battle the continued increase in microbial drug resistance. Mushroom-forming fungi are underutilized as a source of novel antibiotics in the literature due to their challenging culture preparation and genetic intractability. However, modern fungal molecular and synthetic biology tools have renewed interest in exploring mushroom fungi for novel therapeutic agents. The aims of this study were to investigate the secondary metabolites of nine basidiomycetes, screen their biological and chemical properties, and then investigate the genetic pathways associated with their production. Of the nine fungi selected, Hypholoma fasciculare was revealed to be a highly active antagonistic species, with antimicrobial activity against three different microorganisms: Bacillus subtilis, Escherichia coli, and Saccharomyces cerevisiae. Genomic comparisons and chromatographic studies were employed to characterize more than 15 biosynthetic gene clusters and resulted in the identification of 3,5-dichloromethoxy benzoic acid as a potential antibacterial compound. The biosynthetic gene cluster for this product is also predicted. This study reinforces the potential of mushroom-forming fungi as an underexplored reservoir of bioactive natural products. Access to genomic data, and chemical-based frameworks, will assist the development and application of novel molecules with applications in both the pharmaceutical and agrochemical industries.
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Affiliation(s)
| | - Ian D. Bull
- School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Raghad Al-Salhi
- Chemistry Department, University of Mustansiriyah, Baghdad, Iraq
| | - Paul J. Gates
- School of Chemistry, University of Bristol, Bristol, United Kingdom
| | | | - Andy M. Bailey
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Gary D. Foster
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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Lengger SK, Weber Y, Taylor KWR, Kopf SH, Berstan R, Bull ID, Mayser JP, Leavitt WD, Blewett J, Pearson A, Pancost RD. Determination of the δ 2 H values of high molecular weight lipids by high-temperature gas chromatography coupled to isotope ratio mass spectrometry. Rapid Commun Mass Spectrom 2021; 35:e8983. [PMID: 33068049 DOI: 10.1002/rcm.8983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE The hydrogen isotopic composition of lipids (δ2 Hlipid ) is widely used in food science and as a proxy for past hydrological conditions. Determining the δ2 H values of large, well-preserved triacylglycerides and other microbial lipids, such as glycerol dialkyl glycerol tetraether (GDGT) lipids, is thus of widespread interest but has so far not been possible due to their low volatility which prohibits analysis by traditional gas chromatography/pyrolysis/isotope ratio mass spectrometry (GC/P/IRMS). METHODS We determined the δ2 H values of large, polar molecules and applied high-temperature gas chromatography (HTGC) methods on a modified GC/P/IRMS system. The system used a high-temperature 7-m GC column, and a glass Y-splitter for low thermal mass. Methods were validated using authentic standards of large, functionalised molecules (triacylglycerides, TGs), purified standards of GDGTs. The results were compared with δ2 H values determined by high-temperature elemental analyser/pyrolysis/isotope ratio mass spectrometry (HTEA/P/IRMS), and subsequently applied to the analysis of GDGTs in a sample from a methane seep and a Welsh peat. RESULTS The δ2 H values of TGs agreed within error between HTGC/P/IRMS and HTEA/IRMS, with HTGC/P/IRMS showing larger errors. Archaeal lipid GDGTs with up to three cyclisations could be analysed: the δ2 H values were not significantly different between methods with standard deviations of 5 to 6 ‰. When environmental samples were analysed, the δ2 H values of isoGDGTs were 50 ‰ more negative than those of terrestrial brGDGTs. CONCLUSIONS Our results indicate that the HTGC/P/IRMS method developed here is appropriate to determine the δ2 H values of TGs, GDGTs with up to two cyclisations, and potentially other high molecular weight compounds. The methodology will widen the current analytical window for biomarker and food light stable isotope analyses. Moreover, our initial measurements suggest that bacterial and archaeal GDGT δ2 H values can record environmental and ecological conditions.
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Affiliation(s)
- Sabine K Lengger
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
- Biogeochemistry Research Centre, School of Geography, Earth and Environmental Science, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK
| | - Yuki Weber
- Department of Earth and Planetary Sciences, Harvard University, 20 Oxford St, Cambridge, MA, 02138, USA
| | - Kyle W R Taylor
- Elementar UK Ltd, Earl Road, Cheadle Hulme, Stockport, SK8 6PT, UK
| | - Sebastian H Kopf
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA
| | - Robert Berstan
- Elementar UK Ltd, Earl Road, Cheadle Hulme, Stockport, SK8 6PT, UK
| | - Ian D Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Jan-Peter Mayser
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - William D Leavitt
- Department of Earth Science, Department of Chemistry, Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Jerome Blewett
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, 20 Oxford St, Cambridge, MA, 02138, USA
| | - Richard D Pancost
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
- School of Earth Sciences and Cabot Institute for the Environment, University of Bristol, Queens Road, Bristol, BS8 1RL, UK
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Shillito LM, Whelton HL, Blong JC, Jenkins DL, Connolly TJ, Bull ID. Pre-Clovis occupation of the Americas identified by human fecal biomarkers in coprolites from Paisley Caves, Oregon. Sci Adv 2020; 6:eaba6404. [PMID: 32743069 PMCID: PMC7363456 DOI: 10.1126/sciadv.aba6404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
When and how people first settled in the Americas is an ongoing area of research and debate. The earliest sites typically only contain lithic artifacts that cannot be directly dated. The lack of human skeletal remains in these early contexts means that alternative sources of evidence are needed. Coprolites, and the DNA contained within them, are one such source, but unresolved issues concerning ancient DNA taphonomy and potential for contamination make this approach problematic. Here, we use fecal lipid biomarkers to demonstrate unequivocally that three coprolites dated to pre-Clovis are human, raise questions over the reliance on DNA methods, and present a new radiocarbon date on basketry further supporting pre-Clovis human occupation.
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Affiliation(s)
- Lisa-Marie Shillito
- School of History, Classics and Archaeology, Armstrong Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Helen L. Whelton
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - John C. Blong
- School of History, Classics and Archaeology, Armstrong Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Dennis L. Jenkins
- Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA
| | - Thomas J. Connolly
- Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA
| | - Ian D. Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
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Saitta ET, Liang R, Lau MCY, Brown CM, Longrich NR, Kaye TG, Novak BJ, Salzberg SL, Norell MA, Abbott GD, Dickinson MR, Vinther J, Bull ID, Brooker RA, Martin P, Donohoe P, Knowles TDJ, Penkman KEH, Onstott T. Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities. eLife 2019; 8:e46205. [PMID: 31210129 PMCID: PMC6581507 DOI: 10.7554/elife.46205] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/12/2019] [Indexed: 12/12/2022] Open
Abstract
Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These 'soft tissues' have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil 'soft tissues' differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize inorganic nutrients and complicate identification of original organic material. There exists potential post-burial taphonomic roles for subsurface microorganisms.
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Affiliation(s)
- Evan T Saitta
- Integrative Research Center, Section of Earth SciencesField Museum of Natural HistoryChicagoUnited States
| | - Renxing Liang
- Department of GeosciencesPrinceton UniversityPrincetonUnited States
| | - Maggie CY Lau
- Department of GeosciencesPrinceton UniversityPrincetonUnited States
- Institute of Deep-Sea Science and EngineeringChinese Academy of SciencesSanyaChina
| | - Caleb M Brown
- Royal Tyrrell Museum of PalaeontologyDrumhellerCanada
| | - Nicholas R Longrich
- Department of Biology and BiochemistryUniversity of BathBathUnited Kingdom
- Milner Centre for EvolutionUniversity of BathBathUnited Kingdom
| | - Thomas G Kaye
- Foundation for Scientific AdvancementSierra VistaUnited States
| | - Ben J Novak
- Revive and RestoreSan FranciscoUnited States
| | - Steven L Salzberg
- Department of Biomedical Engineering, Center for Computational Biology, McKusick-Nathans Institute of Genetic MedicineJohns Hopkins UniversityBaltimoreUnited States
- Department of Computer Science, Center for Computational Biology, McKusick-Nathans Institute of Genetic MedicineJohns Hopkins UniversityBaltimoreUnited States
- Department of Biostatistics, Center for Computational Biology, McKusick-Nathans Institute of Genetic MedicineJohns Hopkins UniversityBaltimoreUnited States
| | - Mark A Norell
- Division of PaleontologyAmerican Museum of Natural HistoryNew YorkUnited States
| | - Geoffrey D Abbott
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | | | - Jakob Vinther
- School of Earth SciencesUniversity of BristolBristolUnited Kingdom
- School of Biological SciencesUniversity of BristolBristolUnited Kingdom
| | - Ian D Bull
- School of ChemistryUniversity of BristolBristolUnited Kingdom
| | | | - Peter Martin
- School of PhysicsUniversity of BristolBristolUnited Kingdom
| | - Paul Donohoe
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Timothy DJ Knowles
- School of ChemistryUniversity of BristolBristolUnited Kingdom
- School of ArtsUniversity of BristolBristolUnited Kingdom
| | | | - Tullis Onstott
- Department of GeosciencesPrinceton UniversityPrincetonUnited States
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Nancolas B, Bull ID, Stenner R, Dufour V, Curnow P. Saccharomyces cerevisiae Atf1p is an alcohol acetyltransferase and a thioesterase in vitro. Yeast 2017; 34:239-251. [PMID: 28160314 PMCID: PMC5484351 DOI: 10.1002/yea.3229] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 07/05/2016] [Revised: 01/30/2017] [Accepted: 02/01/2017] [Indexed: 11/09/2022] Open
Abstract
The alcohol-O-acyltransferases are bisubstrate enzymes that catalyse the transfer of acyl chains from an acyl-coenzyme A (CoA) donor to an acceptor alcohol. In the industrial yeast Saccharomyces cerevisiae this reaction produces acyl esters that are an important influence on the flavour of fermented beverages and foods. There is also a growing interest in using acyltransferases to produce bulk quantities of acyl esters in engineered microbial cell factories. However, the structure and function of the alcohol-O-acyltransferases remain only partly understood. Here, we recombinantly express, purify and characterize Atf1p, the major alcohol acetyltransferase from S. cerevisiae. We find that Atf1p is promiscuous with regard to the alcohol cosubstrate but that the acyltransfer activity is specific for acetyl-CoA. Additionally, we find that Atf1p is an efficient thioesterase in vitro with specificity towards medium-chain-length acyl-CoAs. Unexpectedly, we also find that mutating the supposed catalytic histidine (H191) within the conserved HXXXDG active site motif only moderately reduces the thioesterase activity of Atf1p. Our results imply a role for Atf1p in CoA homeostasis and suggest that engineering Atf1p to reduce the thioesterase activity could improve product yields of acetate esters from cellular factories. © 2017 The Authors. Yeast published by John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Ian D Bull
- School of Chemistry, University of Bristol, Bristol, UK
| | - Richard Stenner
- School of Biochemistry, University of Bristol, Bristol, UK.,Bristol Centre for Functional Nanomaterials, University of Bristol, Bristol, UK
| | - Virginie Dufour
- School of Biochemistry, University of Bristol, Bristol, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, Bristol, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol, UK
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Masson M, Bereczki Z, Molnár E, Donoghue HD, Minnikin DE, Lee OYC, Wu HH, Besra GS, Bull ID, Pálfi G. 7000 year-old tuberculosis cases from Hungary – Osteological and biomolecular evidence. Tuberculosis (Edinb) 2015; 95 Suppl 1:S13-7. [DOI: 10.1016/j.tube.2015.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Molnár E, Donoghue HD, Lee OYC, Wu HH, Besra GS, Minnikin DE, Bull ID, Llewellyn G, Williams CM, Spekker O, Pálfi G. Morphological and biomolecular evidence for tuberculosis in 8th century AD skeletons from Bélmegyer-Csömöki domb, Hungary. Tuberculosis (Edinb) 2015; 95 Suppl 1:S35-41. [DOI: 10.1016/j.tube.2015.02.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Donoghue HD, Michael Taylor G, Marcsik A, Molnár E, Pálfi G, Pap I, Teschler-Nicola M, Pinhasi R, Erdal YS, Velemínsky P, Likovsky J, Belcastro MG, Mariotti V, Riga A, Rubini M, Zaio P, Besra GS, Lee OYC, Wu HHT, Minnikin DE, Bull ID, O'Grady J, Spigelman M. A migration-driven model for the historical spread of leprosy in medieval Eastern and Central Europe. Infect Genet Evol 2015; 31:250-6. [PMID: 25680828 DOI: 10.1016/j.meegid.2015.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 02/01/2015] [Accepted: 02/03/2015] [Indexed: 11/26/2022]
Abstract
Leprosy was rare in Europe during the Roman period, yet its prevalence increased dramatically in medieval times. We examined human remains, with paleopathological lesions indicative of leprosy, dated to the 6th-11th century AD, from Central and Eastern Europe and Byzantine Anatolia. Analysis of ancient DNA and bacterial cell wall lipid biomarkers revealed Mycobacterium leprae in skeletal remains from 6th-8th century Northern Italy, 7th-11th century Hungary, 8th-9th century Austria, the Slavic Greater Moravian Empire of the 9th-10th century and 8th-10th century Byzantine samples from Northern Anatolia. These data were analyzed alongside findings published by others. M. leprae is an obligate human pathogen that has undergone an evolutionary bottleneck followed by clonal expansion. Therefore M. leprae genotypes and sub-genotypes give information about the human populations they have infected and their migration. Although data are limited, genotyping demonstrates that historical M. leprae from Byzantine Anatolia, Eastern and Central Europe resembles modern strains in Asia Minor rather than the recently characterized historical strains from North West Europe. The westward migration of peoples from Central Asia in the first millennium may have introduced different M. leprae strains into medieval Europe and certainly would have facilitated the spread of any existing leprosy. The subsequent decline of M. leprae in Europe may be due to increased host resistance. However, molecular evidence of historical leprosy and tuberculosis co-infections suggests that death from tuberculosis in leprosy patients was also a factor.
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Affiliation(s)
- Helen D Donoghue
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, UK.
| | - G Michael Taylor
- Department of Microbial and Cellular Science, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Antónia Marcsik
- University of Szeged, Mályva utca 23, H-6771 Szeged, Hungary
| | - Erika Molnár
- Department of Biological Anthropology, University of Szeged, Hungary
| | - Gyorgy Pálfi
- Department of Biological Anthropology, University of Szeged, Hungary
| | - Ildikó Pap
- Department of Anthropology, Natural History Museum, Budapest, Hungary
| | | | - Ron Pinhasi
- School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
| | - Yilmaz S Erdal
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Petr Velemínsky
- Department of Anthropology, National Museum, Prague, Czech Republic
| | - Jakub Likovsky
- Department of the Archaeology of Landscape and Archaeobiology, Institute of Archaeology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Maria Giovanna Belcastro
- Laboratorio di Bioarcheologia e Osteologia Forense, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Via Selmi 3, 40126 Bologna, Italy; Centro Fermi, Piazza del Viminale 1, 00184 Rome, Italy
| | - Valentina Mariotti
- Laboratorio di Bioarcheologia e Osteologia Forense, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Via Selmi 3, 40126 Bologna, Italy; ADES, UMR 7268 CNRS/Université de la Méditerranée/EFS, Université de la Méditerranée, CS80011, Bd Pierre Dramard,13344 Marseille Cedex 15, France
| | - Alessandro Riga
- Laboratorio di Bioarcheologia e Osteologia Forense, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Via Selmi 3, 40126 Bologna, Italy
| | - Mauro Rubini
- Department of Archaeology, Foggia University, Tivoli, Italy; Anthropological Service of S.B.A.L. (Ministry of Culture), Rome, Italy
| | - Paola Zaio
- Department of Archaeology, Foggia University, Tivoli, Italy
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Oona Y-C Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Houdini H T Wu
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - David E Minnikin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Ian D Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
| | - Justin O'Grady
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, UK
| | - Mark Spigelman
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, UK; Department of Anatomy and Anthropology Sackler Medical School, Tel Aviv University, Israel
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Knight MJ, Bull ID, Curnow P. The yeast enzyme Eht1 is an octanoyl-CoA:ethanol acyltransferase that also functions as a thioesterase. Yeast 2014; 31:463-74. [PMID: 25308280 PMCID: PMC4282330 DOI: 10.1002/yea.3046] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/18/2014] [Accepted: 10/04/2014] [Indexed: 11/17/2022] Open
Abstract
Fatty acid ethyl esters are secondary metabolites that are produced during microbial fermentation, in fruiting plants and in higher organisms during ethanol stress. In particular, volatile medium-chain fatty acid ethyl esters are important flavour compounds that impart desirable fruit aromas to fermented beverages, including beer and wine. The biochemical synthesis of medium-chain fatty acid ethyl esters is poorly understood but likely involves acyl-CoA:ethanol O-acyltransferases. Here, we characterize the enzyme ethanol hexanoyl transferase 1 (Eht1) from the brewer's yeast Saccharomyces cerevisiae. Full-length Eht1 was successfully overexpressed from a recombinant yeast plasmid and purified at the milligram scale after detergent solubilization of sedimenting membranes. Recombinant Eht1 was functional as an acyltransferase and, unexpectedly, was optimally active toward octanoyl-CoA, with kcat = 0.28 ± 0.02/s and KM = 1.9 ± 0.6 μm. Eht1 was also revealed to be active as a thioesterase but was not able to hydrolyse p-nitrophenyl acyl esters, in contrast to the findings of a previous study. Low-resolution structural data and site-directed mutagenesis provide experimental support for a predicted α/β-hydrolase domain featuring a Ser–Asp–His catalytic triad. The S. cerevisiae gene YBR177C/EHT1 should thus be reannotated as coding for an octanoyl-CoA:ethanol acyltransferase that can also function as a thioesterase. © 2014 The Authors. Yeast published by John Wiley & Sons, Ltd.
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Masson M, Molnár E, Donoghue HD, Besra GS, Minnikin DE, Wu HHT, Lee OYC, Bull ID, Pálfi G. Osteological and biomolecular evidence of a 7000-year-old case of hypertrophic pulmonary osteopathy secondary to tuberculosis from neolithic hungary. PLoS One 2013; 8:e78252. [PMID: 24205173 PMCID: PMC3813517 DOI: 10.1371/journal.pone.0078252] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 09/04/2013] [Indexed: 11/19/2022] Open
Abstract
Seventy-one individuals from the late Neolithic population of the 7000-year-old site of Hódmezővásárhely-Gorzsa were examined for their skeletal palaeopathology. This revealed numerous cases of infections and non-specific stress indicators in juveniles and adults, metabolic diseases in juveniles, and evidence of trauma and mechanical changes in adults. Several cases showed potential signs of tuberculosis, particularly the remains of the individual HGO-53. This is an important finding that has significant implications for our understanding of this community. The aim of the present study was to seek biomolecular evidence to confirm this diagnosis. HGO-53 was a young male with a striking case of hypertrophic pulmonary osteopathy (HPO), revealing rib changes and cavitations in the vertebral bodies. The initial macroscopic diagnosis of HPO secondary to tuberculosis was confirmed by analysis of Mycobacterium tuberculosis complex specific cell wall lipid biomarkers and corroborated by ancient DNA (aDNA) analysis. This case is the earliest known classical case of HPO on an adult human skeleton and is one of the oldest palaeopathological and palaeomicrobiological tuberculosis cases to date.
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Affiliation(s)
- Muriel Masson
- Archaeology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
- * E-mail:
| | - Erika Molnár
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - Helen D. Donoghue
- Centre for Clinical Microbiology and Centre for the History of Medicine, University College London, London, United Kingdom
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Egbaston, Birmingham, United Kingdom
| | - David E. Minnikin
- School of Biosciences, University of Birmingham, Egbaston, Birmingham, United Kingdom
| | - Houdini H. T. Wu
- School of Biosciences, University of Birmingham, Egbaston, Birmingham, United Kingdom
| | - Oona Y-C. Lee
- School of Biosciences, University of Birmingham, Egbaston, Birmingham, United Kingdom
| | - Ian D. Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - György Pálfi
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
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14
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McCartney CA, Bull ID, Waters SM, Dewhurst RJ. Technical note: Comparison of biomarker and molecular biological methods for estimating methanogen abundance. J Anim Sci 2013; 91:5724-8. [PMID: 24146154 DOI: 10.2527/jas.2013-6513] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Quantitative real-time PCR (qPCR) has become a popular method for estimation of methanogen abundance in the ruminant digestive tract. However, there is no established method in terms of primer choice and quantification, which means that results are variable and not directly comparable between studies. Archaeol has been proposed as an alternative marker for methanogen abundance, as it is ubiquitous in methanogenic Archaea, and can be quantified by gas chromatography-mass spectrometry (GC-MS). The aim of this experiment was to compare total methanogen populations estimated using the new archaeol approach with estimates based on qPCR. Specific primer sets and probes were used to detect dominant ruminal methanogen species Methanobrevibacter ruminantium, Methanobrevibacter smithii, Methanosphaera stadtmanae, and total methanogen populations. There was variation in the relationships among total methanogen abundance estimates based on archaeol and qPCR. In addition, the universal methanogen primers appeared to preferentially amplify genes from M. smithii. Archaeol had the strongest relationship with the dominant rumen methanogen M. ruminantium, whereas the total methanogen primers had a comparatively weak relationship with archaeol. Archaeol analysis was a useful adjunct to molecular biology methods, but it seems that a valid specific primer for M. ruminantium would be more useful than a biased primer for total methanogens.
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Affiliation(s)
- C A McCartney
- Teagasc Animal and Grassland Research and Innovation Centre, Grange, Dunsany, Co., Meath, Ireland
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15
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Lee OYC, Wu HHT, Donoghue HD, Spigelman M, Greenblatt CL, Bull ID, Rothschild BM, Martin LD, Minnikin DE, Besra GS. Mycobacterium tuberculosis complex lipid virulence factors preserved in the 17,000-year-old skeleton of an extinct bison, Bison antiquus. PLoS One 2012; 7:e41923. [PMID: 22860031 PMCID: PMC3408397 DOI: 10.1371/journal.pone.0041923] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [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: 04/24/2012] [Accepted: 06/29/2012] [Indexed: 12/22/2022] Open
Abstract
Tracing the evolution of ancient diseases depends on the availability and accessibility of suitable biomarkers in archaeological specimens. DNA is potentially information-rich but it depends on a favourable environment for preservation. In the case of the major mycobacterial pathogens, Mycobacterium tuberculosis and Mycobacterium leprae, robust lipid biomarkers are established as alternatives or complements to DNA analyses. A DNA report, a decade ago, suggested that a 17,000-year-old skeleton of extinct Bison antiquus, from Natural Trap Cave, Wyoming, was the oldest known case of tuberculosis. In the current study, key mycobacterial lipid virulence factor biomarkers were detected in the same two samples from this bison. Fluorescence high-performance liquid chromatography (HPLC) indicated the presence of mycolic acids of the mycobacterial type, but they were degraded and could not be precisely correlated with tuberculosis. However, pristine profiles of C29, C30 and C32 mycocerosates and C27 mycolipenates, typical of the Mycobacterium tuberculosis complex, were recorded by negative ion chemical ionization gas chromatography mass spectrometry of pentafluorobenzyl ester derivatives. These findings were supported by the detection of C34 and C36 phthiocerols, which are usually esterified to the mycocerosates. The existence of Pleistocene tuberculosis in the Americas is confirmed and there are many even older animal bones with well-characterised tuberculous lesions similar to those on the analysed sample. In the absence of any evidence of tuberculosis in human skeletons older than 9,000 years BP, the hypothesis that this disease evolved as a zoonosis, before transfer to humans, is given detailed consideration and discussion.
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Affiliation(s)
- Oona Y-C. Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Houdini H. T. Wu
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Helen D. Donoghue
- Centre for Clinical Microbiology (M9), Royal Free Campus, University College London, London, United Kingdom
- Centre for the History of Medicine, University College London, London, United Kingdom
| | - Mark Spigelman
- Centre for Clinical Microbiology (M9), Royal Free Campus, University College London, London, United Kingdom
- Kuvin Center for the Study of Infectious and Tropical Diseases and Ancient DNA, Hadassah Medical School, Hebrew University, Jerusalem, Israel
| | - Charles L. Greenblatt
- Kuvin Center for the Study of Infectious and Tropical Diseases and Ancient DNA, Hadassah Medical School, Hebrew University, Jerusalem, Israel
| | - Ian D. Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Bruce M. Rothschild
- Department of Medicine, Northeast Ohio Medical University, Rootstown, Ohio, United States of America
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Larry D. Martin
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - David E. Minnikin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- * E-mail:
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16
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Chivall D, Berstan R, Bull ID, Evershed RP. Isotope effects associated with the preparation and methylation of fatty acids by boron trifluoride in methanol for compound-specific stable hydrogen isotope analysis via gas chromatography/thermal conversion/isotope ratio mass spectrometry. Rapid Commun Mass Spectrom 2012; 26:1232-1240. [PMID: 22499199 DOI: 10.1002/rcm.6188] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE Compound-specific stable hydrogen isotope analysis of fatty acids is being used increasingly as a means of deriving information from a diverse range of materials of archaeological, geological and environmental interest. Preparative steps required prior to isotope ratio mass spectrometry (IRMS) analysis have the potential to alter determined δD values and hence must be accounted for if accurate δD values for target compounds are to be obtained. METHODS Myristic, palmitic, stearic, arachidic and behenic saturated fatty acids were derivatised to their respective fatty acid methyl esters (FAMEs), using 14% (w/v) boron trifluoride in methanol then analysed by gas chromatography/thermal conversion/IRMS (GC/TC/IRMS). FAMEs generated from fatty acid sodium salts of unknown δD values were then used to test a correction factor determined for this method of derivatisation. RESULTS Derivatisation was found to alter the hydrogen isotopic composition of FAMEs although this effect was reproducible and can be accounted for. The difference between the mean corrected and mean bulk δD values was always less than 6.7 ‰. Extraction of saturated fatty acids and acyl lipids from samples, subsequent hydrolysis, then separation on a solid-phase extraction cartridge, was found to alter the determined δD values by less than one standard deviation. CONCLUSIONS Overall, it has been shown that for natural abundance hydrogen isotope determinations, the isolation and derivatisation of extracted fatty acids alters the determined δD values only by a numerical increment comparable with the experimental error. This supports the use of the described analytical protocol as an effective means of determining fatty acid δD values by GC/TC/IRMS.
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Affiliation(s)
- David Chivall
- Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, Bristol, UK
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17
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Hansel FA, Bull ID, Evershed RP. Gas chromatographic mass spectrometric detection of dihydroxy fatty acids preserved in the 'bound' phase of organic residues of archaeological pottery vessels. Rapid Commun Mass Spectrom 2011; 25:1893-1898. [PMID: 21638365 DOI: 10.1002/rcm.5038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A methodology is presented for the determination of dihydroxy fatty acids preserved in the 'bound' phase of organic residues preserved in archaeological potsherds. The method comprises saponification, esterification, silica gel column chromatographic fractionation, and analysis by gas chromatography/mass spectrometry. The electron ionisation mass spectra of the trimethylsilyl ether methyl ester derivatives are characterised by fragment ions arising from cleavage of the bond between the two vicinal trimethylsiloxy groups. Other significant fragment ions are [M-15](+.), [M-31](+.), m/z 147 and ions characteristic of vicinal disubstituted (trimethylsiloxy) TMSO- groups (Δ(7,8), Δ(9,10), Δ(11,12) and Δ(13,14): m/z 304, 332, 360 and 388, respectively). The dihydroxy fatty acids identified in archaeological extracts exhibited carbon numbers ranging from C(16) to C(22) and concentrations varying from 0.05 to 14.05 µg g(-1) . The wide range of dihydroxy fatty acids observed indicates that this approach may be applied confidently in screening archaeological potsherds for the degradation products of monounsaturated fatty acids derived from commodities processed in archaeological pottery vessels.
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Affiliation(s)
- Fabricio A Hansel
- Organic Geochemistry Unit, Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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18
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Rujiralai T, Bull ID, Llewellyn N, Evershed RP. In situ polar organic chemical integrative sampling (POCIS) of steroidal estrogens in sewage treatment works discharge and river water. ACTA ACUST UNITED AC 2011; 13:1427-34. [DOI: 10.1039/c0em00537a] [Citation(s) in RCA: 30] [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: 11/21/2022]
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Wurster CM, Bird MI, Bull ID, Creed F, Bryant C, Dungait JAJ, Paz V. Forest contraction in north equatorial Southeast Asia during the Last Glacial Period. Proc Natl Acad Sci U S A 2010; 107:15508-11. [PMID: 20660748 PMCID: PMC2932586 DOI: 10.1073/pnas.1005507107] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Today, insular Southeast Asia is important for both its remarkably rich biodiversity and globally significant roles in atmospheric and oceanic circulation. Despite the fundamental importance of environmental history for diversity and conservation, there is little primary evidence concerning the nature of vegetation in north equatorial Southeast Asia during the Last Glacial Period (LGP). As a result, even the general distribution of vegetation during the Last Glacial Maximum is debated. Here we show, using the stable carbon isotope composition of ancient cave guano profiles, that there was a substantial forest contraction during the LGP on both peninsular Malaysia and Palawan, while rainforest was maintained in northern Borneo. These results directly support rainforest "refugia" hypotheses and provide evidence that environmental barriers likely reduced genetic mixing between Borneo and Sumatra flora and fauna. Moreover, it sheds light on possible early human dispersal events.
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Affiliation(s)
- Christopher M Wurster
- School of Geography and Geosciences, University of St. Andrews, St. Andrews, Fife KY16 9AL, United Kingdom.
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20
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Dungait JAJ, Bol R, Lopez-Capel E, Bull ID, Chadwick D, Amelung W, Granger SJ, Manning DAC, Evershed RP. Applications of stable isotope ratio mass spectrometry in cattle dung carbon cycling studies. Rapid Commun Mass Spectrom 2010; 24:495-500. [PMID: 20112271 DOI: 10.1002/rcm.4332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Understanding the fate of dung carbon (C) in soils is challenging due to the ubiquitous presence of the plant-derived organic matter (OM), the source material from which both dung-derived OM and soil organic matter (SOM) predominantly originate. A better understanding of the fate of specific components of this substantial source of OM, and thereby its contribution to C cycling in terrestrial ecosystems, can only be achieved through the use of labelled dung treatments. In this short review, we consider analytical approaches using bulk and compound-specific stable carbon isotope analysis that have been utilised to explore the fate of dung-derived C in soils. Bulk stable carbon isotope analyses are now used routinely to explore OM matter cycling in soils, and have shown that up to 20% of applied dung C may be incorporated into the surface soil horizons several weeks after application, with up to 8% remaining in the soil profile after one year. However, whole soil delta(13)C values represent the average of a wide range of organic components with varying delta(13)C values and mean residence times in soils. Several stable (13)C isotope ratio mass spectrometric methods have been developed to qualify and quantify different fractions of OM in soils and other complex matrices. In particular, thermogravimetry-differential scanning calorimetry-isotope ratio mass spectrometry (TG-DSC-IRMS) and gas chromatography-combustion-IRMS (GC-C-IRMS) analyses have been applied to determine the incorporation and turnover of polymeric plant cell wall materials from C(4) dung into C(3) grassland soils using natural abundance (13)C isotope labelling. Both approaches showed that fluxes of C derived from polysaccharides, i.e. as cellulose or monosaccharide components, were more similar to the behaviour of bulk dung C in soil than lignin. However, lignin and its 4-hydroxypropanoid monomers were unexpectedly dynamic in soil. These findings provide further evidence for emerging themes in biogeochemical investigations of soil OM dynamics that challenge perceived concepts of recalcitrance of C pools in soils, which may have profound implications for the assessment of the potential of agricultural soils to influence terrestrial C sinks.
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Dickson L, Bull ID, Gates PJ, Evershed RP. A simple modification of a silicic acid lipid fractionation protocol to eliminate free fatty acids from glycolipid and phospholipid fractions. J Microbiol Methods 2009; 78:249-54. [DOI: 10.1016/j.mimet.2009.05.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 05/21/2009] [Indexed: 11/17/2022]
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22
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Karaca F, Morgan TJ, George A, Bull ID, Herod AA, Millan M, Kandiyoti R. Molecular mass ranges of coal tar pitch fractions by mass spectrometry and size-exclusion chromatography. Rapid Commun Mass Spectrom 2009; 23:2087-2098. [PMID: 19489019 DOI: 10.1002/rcm.4104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A coal tar pitch was fractionated by solvent solubility into heptane-solubles, heptane-insoluble/toluene-solubles (asphaltenes), and toluene-insolubles (preasphaltenes). The aim of the work was to compare the mass ranges of the different fractions by several different techniques. Thermogravimetric analysis, size-exclusion chromatography (SEC) and UV-fluorescence spectroscopy showed distinct differences between the three fractions in terms of volatility, molecular size ranges and the aromatic chromophore sizes present. The mass spectrometric methods used were gas chromatography/mass spectrometry (GC/MS), pyrolysis/GC/MS, electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) and laser desorption time-of-flight mass spectrometry (LD-TOFMS). The first three techniques gave good mass spectra only for the heptane-soluble fraction. Only LDMS gave signals from the toluene-insolubles, indicating that the molecules were too involatile for GC and too complex to pyrolyze into small molecules during pyrolysis/GC/MS. ESI-FTICRMS gave no signal for toluene-insolubles probably because the fraction was insoluble in the methanol or acetonitrile, water and formic acid mixture used as solvent to the ESI source. LDMS was able to generate ions from each of the fractions. Fractionation of complex samples is necessary to separate smaller molecules to allow the use of higher laser fluences for the larger molecules and suppress the formation of ionized molecular clusters. The upper mass limit of the pitch was determined as between 5000 and 10,000 u. The pitch asphaltenes showed a peak of maximum intensity in the LDMS spectra at around m/z 400, in broad agreement with the estimate from SEC. The mass ranges of the toluene-insoluble fraction found by LDMS and SEC (400-10,000 u with maximum intensity around 2000 u by LDMS and 100-9320 u with maximum intensity around 740 u by SEC) are higher than those for the asphaltene fraction (200-4000 u with maximum intensity around 400 u by LDMS and 100-2680 u with maximum intensity around 286 u by SEC) and greater than values considered appropriate for petroleum asphaltenes (300-1200 u with maximum intensity near 700 u).
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Affiliation(s)
- F Karaca
- Department of Chemical Engineering, Marmara University, Goztepe Campus, 34722 Kadikoy, Istanbul, Turkey
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23
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Evershed RP, Crossman ZM, Bull ID, Mottram H, Dungait JAJ, Maxfield PJ, Brennand EL. 13C-Labelling of lipids to investigate microbial communities in the environment. Curr Opin Biotechnol 2006; 17:72-82. [PMID: 16423522 DOI: 10.1016/j.copbio.2006.01.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [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: 11/14/2005] [Revised: 12/01/2005] [Accepted: 01/06/2006] [Indexed: 11/23/2022]
Abstract
The introduction of (13)C-labelled substrates to soils, sediments or cultures followed by (13)C analysis of phospholipid fatty acids (PLFAs) provides quantitative and chemotaxonomic information for the groups of microorganisms utilizing a given substrate. Gas chromatography-combustion-isotope ratio mass spectrometry has provided the high precision necessary to measure small isotopic changes (differences in the relative abundances of (13)C to (12)C expressed as delta(13)C values) for nanogram amounts of individual compounds, such as microbial PLFAs. This methodology constitutes a powerful new culture-independent method for investigating microbial communities in the environment. The information obtained is highly complementary to that obtained from gene-probe-based methods, and considerable possibilities exist to extend this methodology to include other biochemical components of microorganisms.
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Affiliation(s)
- Richard P Evershed
- Organic Geochemistry Unit, Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
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24
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Chamberlain PM, Bull ID, Black HIJ, Ineson P, Evershed RP. Lipid content and carbon assimilation in Collembola: implications for the use of compound-specific carbon isotope analysis in animal dietary studies. Oecologia 2004; 139:325-35. [PMID: 14997374 DOI: 10.1007/s00442-003-1422-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [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: 01/02/2003] [Accepted: 10/01/2003] [Indexed: 11/30/2022]
Abstract
In an effort to understand the relationships between both the lipid content and delta13C values of Collembola and their diet, isotopically labelled (C3 and C4) bakers' yeasts were cultured and fed to two Collembolan species, Folsomia candida and Proisotoma minuta. The fatty acid composition of Collembola generally reflected that of the diet with the addition of the polyunsaturated components 18:2(n-6), 20:4(n-6) and 20:5(n-3), which appeared to be biosynthesised by the Collembola. Whilst ergosterol was the only sterol detected in the yeast diets, only cholesterol was detected in Collembola, and although the delta13C values of diet and consumer sterols differed by >2 per thousand, the delta13C values indicated that cholesterol was derived entirely from dietary sterol. The bulk delta13C values of Collembola were similar to those of the diets, but fatty acid delta13C values did not necessarily reflect those of the dietary fatty acids, indicating significant de novo biosynthesis of fatty acids within Collembola. Switching the Collembola from C3 to C4 yeast enabled the determination of the rates of incorporation of dietary carbon into Collembolan lipids, and showed that half-lives of the incorporation of dietary carbon varied between 1.5 and 5.8 days at 20 degrees C. Cholesterol exhibited the slowest rate of incorporation in both species, while bulk carbon in F. candida possessed an intermediate rate. These results demonstrate that an understanding of the sources of isotopic fractionation and the role of biochemistry in regulating the delta13C values of individual compounds is important in the application of compound-specific isotopic analysis to the study of animal trophic activities.
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Affiliation(s)
- Paul M Chamberlain
- Organic Geochemistry Unit, Biogeochemistry Research Centre, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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25
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Affiliation(s)
- Ian D Bull
- Biogeochemistry Research Centre, School Chemistry, University of Bristol, Cantock's Close, UK
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26
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Abstract
Well-drained non-agricultural soils mediate the oxidation of methane directly from the atmosphere, contributing 5 to 10% towards the global methane sink. Studies of methane oxidation kinetics in soil infer the activity of two methanotrophic populations: one that is only active at high methane concentrations (low affinity) and another that tolerates atmospheric levels of methane (high affinity). The activity of the latter has not been demonstrated by cultured laboratory strains of methanotrophs, leaving the microbiology of methane oxidation at atmospheric concentrations unclear. Here we describe a new pulse-chase experiment using long-term enrichment with 12CH4 followed by short-term exposure to 13CH4 to isotopically label methanotrophs in a soil from a temperate forest. Analysis of labelled phospholipid fatty acids (PLFAs) provided unambiguous evidence of methane assimilation at true atmospheric concentrations (1.8-3.6 p.p.m.v.). High proportions of 13C-labelled C18 fatty acids and the co-occurrence of a labelled, branched C17 fatty acid indicated that a new methanotroph, similar at the PLFA level to known type II methanotrophs, was the predominant soil micro-organism responsible for atmospheric methane oxidation.
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Affiliation(s)
- I D Bull
- School of Chemistry, University of Bristol, Cantock's Close, UK
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Simpson IA, Bol R, Bull ID, Evershed RP, Petzke K, Dockrill SJ. Interpreting early land management through compound specific stable isotope analyses of archaeological soils. Rapid Commun Mass Spectrom 1999; 13:1315-1319. [PMID: 10407317 DOI: 10.1002/(sici)1097-0231(19990715)13:13<1315::aid-rcm629>3.0.co;2-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Compound specific stable isotope analyses of managed soils using isotope ratio mass spectrometry have been undertaken as a means of determining early land use practices. delta (15)N amino acid signals demonstrate differences between manured grassland, unmanured grassland and continuous cereal cultivation under long-term experimental land use control conditions, with delta (15)N in hydrophobic amino acids providing the most distinctive signals. Analysis of early modern/medieval and of Bronze age anthropogenic soils from Orkney demonstrates that such signals are retained in archaeological contexts. delta (13)C analyses of n- alkanoic acid components of the fossil, Bronze Age, anthropogenic soils suggest a major terrestrial input to these soils, with uniform composition of formation materials. Surficial soils demonstrate the assimilation of isotopically lighter carbon, providing a means of assessing the mobility of the n- alkanoic acids within soils and sediments. Copyright 1999 John Wiley & Sons, Ltd.
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Affiliation(s)
- IA Simpson
- Department of Environmental Science, University of Stirling, Stirling FK9 4LA, Scotland, UK
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