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Broadbent AAD, Newbold LK, Pritchard WJ, Michas A, Goodall T, Cordero I, Giunta A, Snell HSK, Pepper VVLH, Grant HK, Soto DX, Kaufmann R, Schloter M, Griffiths RI, Bahn M, Bardgett RD. Climate change disrupts the seasonal coupling of plant and soil microbial nutrient cycling in an alpine ecosystem. Glob Chang Biol 2024; 30:e17245. [PMID: 38511487 DOI: 10.1111/gcb.17245] [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: 09/21/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
The seasonal coupling of plant and soil microbial nutrient demands is crucial for efficient ecosystem nutrient cycling and plant production, especially in strongly seasonal alpine ecosystems. Yet, how these seasonal nutrient cycling processes are modified by climate change and what the consequences are for nutrient loss and retention in alpine ecosystems remain unclear. Here, we explored how two pervasive climate change factors, reduced snow cover and shrub expansion, interactively modify the seasonal coupling of plant and soil microbial nitrogen (N) cycling in alpine grasslands, which are warming at double the rate of the global average. We found that the combination of reduced snow cover and shrub expansion disrupted the seasonal coupling of plant and soil N-cycling, with pronounced effects in spring (shortly after snow melt) and autumn (at the onset of plant senescence). In combination, both climate change factors decreased plant organic N-uptake by 70% and 82%, soil microbial biomass N by 19% and 38% and increased soil denitrifier abundances by 253% and 136% in spring and autumn, respectively. Shrub expansion also individually modified the seasonality of soil microbial community composition and stoichiometry towards more N-limited conditions and slower nutrient cycling in spring and autumn. In winter, snow removal markedly reduced the fungal:bacterial biomass ratio, soil N pools and shifted bacterial community composition. Taken together, our findings suggest that interactions between climate change factors can disrupt the temporal coupling of plant and soil microbial N-cycling processes in alpine grasslands. This could diminish the capacity of these globally widespread alpine ecosystems to retain N and support plant productivity under future climate change.
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Affiliation(s)
- Arthur A D Broadbent
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
- Biological & Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | | | - William J Pritchard
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Antonios Michas
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
- Chair for Environmental Microbiology, Technical University of Munich, Freising, Germany
| | - Tim Goodall
- UK Centre for Ecology & Hydrology, Wallingford, Oxfordshire, UK
| | - Irene Cordero
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
- Swiss Federal Institute for Forest, Snow and Landscape Research, WSL, Birmensdorf, Switzerland
| | - Andrew Giunta
- Institut für Ökologie, Universität Innsbruck, Innsbruck, Austria
| | - Helen S K Snell
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | | | - Helen K Grant
- National Environmental Isotope Facility, UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, UK
| | - David X Soto
- National Environmental Isotope Facility, UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, UK
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
- Chair for Environmental Microbiology, Technical University of Munich, Freising, Germany
| | | | - Michael Bahn
- Institut für Ökologie, Universität Innsbruck, Innsbruck, Austria
| | - Richard D Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
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2
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Thorpe AC, Mackay EB, Goodall T, Bendle JA, Thackeray SJ, Maberly SC, Read DS. Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long-term microscopy-based monitoring of the phytoplankton community. Mol Ecol Resour 2024; 24:e13903. [PMID: 37994249 DOI: 10.1111/1755-0998.13903] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/26/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Palaeolimnological records provide valuable information about how phytoplankton respond to long-term drivers of environmental change. Traditional palaeolimnological tools such as microfossils and pigments are restricted to taxa that leave sub-fossil remains, and a method that can be applied to the wider community is required. Sedimentary DNA (sedDNA), extracted from lake sediment cores, shows promise in palaeolimnology, but validation against data from long-term monitoring of lake water is necessary to enable its development as a reliable record of past phytoplankton communities. To address this need, 18S rRNA gene amplicon sequencing was carried out on lake sediments from a core collected from Esthwaite Water (English Lake District) spanning ~105 years. This sedDNA record was compared with concurrent long-term microscopy-based monitoring of phytoplankton in the surface water. Broadly comparable trends were observed between the datasets, with respect to the diversity and relative abundance and occurrence of chlorophytes, dinoflagellates, ochrophytes and bacillariophytes. Up to 20% of genera were successfully captured using both methods, and sedDNA revealed a previously undetected community of phytoplankton. These results suggest that sedDNA can be used as an effective record of past phytoplankton communities, at least over timescales of <100 years. However, a substantial proportion of genera identified by microscopy were not detected using sedDNA, highlighting the current limitations of the technique that require further development such as reference database coverage. The taphonomic processes which may affect its reliability, such as the extent and rate of deposition and DNA degradation, also require further research.
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Affiliation(s)
- Amy C Thorpe
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, UK
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | | | - Tim Goodall
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, UK
| | - James A Bendle
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | | | | | - Daniel S Read
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, UK
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3
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Lavallee JM, Chomel M, Alvarez Segura N, de Castro F, Goodall T, Magilton M, Rhymes JM, Delgado-Baquerizo M, Griffiths RI, Baggs EM, Caruso T, de Vries FT, Emmerson M, Johnson D, Bardgett RD. Land management shapes drought responses of dominant soil microbial taxa across grasslands. Nat Commun 2024; 15:29. [PMID: 38167688 PMCID: PMC10762234 DOI: 10.1038/s41467-023-43864-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
Soil microbial communities are dominated by a relatively small number of taxa that may play outsized roles in ecosystem functioning, yet little is known about their capacities to resist and recover from climate extremes such as drought, or how environmental context mediates those responses. Here, we imposed an in situ experimental drought across 30 diverse UK grassland sites with contrasting management intensities and found that: (1) the majority of dominant bacterial (85%) and fungal (89%) taxa exhibit resistant or opportunistic drought strategies, possibly contributing to their ubiquity and dominance across sites; and (2) intensive grassland management decreases the proportion of drought-sensitive and non-resilient dominant bacteria-likely via alleviation of nutrient limitation and pH-related stress under fertilisation and liming-but has the opposite impact on dominant fungi. Our results suggest a potential mechanism by which intensive management promotes bacteria over fungi under drought with implications for soil functioning.
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Affiliation(s)
- J M Lavallee
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
- Environmental Defense Fund, 257 Park Ave S, New York, NY, 10010, USA.
| | - M Chomel
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- FiBL France, Research Institute of Organic Agriculture, 26400, Eurre, France
| | - N Alvarez Segura
- Institute of Biological and Environmental Sciences, University of Aberdeen, St Machar Dr, Old Aberdeen, Aberdeen, AB24 3UL, UK
- EURECAT-Centre Tecnològic de Catalunya, C/ de Bilbao, 72, 08005, Barcelona, Spain
| | - F de Castro
- School of Biological Sciences and Institute for Global Food Security, Queen's University of Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
- AgriFood & Biosciences Institute, 18a Newforge Ln, Belfast, BT9 5PX, UK
| | - T Goodall
- UK Centre for Ecology & Hydrology Wallingford, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
| | - M Magilton
- School of Biological Sciences and Institute for Global Food Security, Queen's University of Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK
| | - J M Rhymes
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Centre for Ecology & Hydrology Bangor, Environment Centre Wales, Deiniol Road, Bangor, LL57 2UW, UK
| | - M Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - R I Griffiths
- UK Centre for Ecology & Hydrology Wallingford, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UR, UK
| | - E M Baggs
- Global Academy of Agriculture and Food Systems, Royal (Dick) School of Veterinary Studies, Easter Bush Campus, Charnock Bradley Building, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - T Caruso
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - F T de Vries
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE, Amsterdam, Netherlands
| | - M Emmerson
- School of Biological Sciences and Institute for Global Food Security, Queen's University of Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - D Johnson
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - R D Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
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4
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Chau KK, Goodall T, Bowes M, Easterbrook K, Brett H, Hughes J, Crook DW, Read DS, Walker AS, Stoesser N. High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent. Microb Genom 2023; 9. [PMID: 37145848 DOI: 10.1099/mgen.0.000983] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
Wastewater-based epidemiology (WBE) for population-level surveillance of antimicrobial resistance (AMR) is gaining significant traction, but the impact of wastewater sampling methods on results is unclear. In this study, we characterized taxonomic and resistome differences between single-timepoint-grab and 24 h composites of wastewater influent from a large UK-based wastewater treatment work [WWTW (population equivalent: 223 435)]. We autosampled hourly influent grab samples (n=72) over three consecutive weekdays, and prepared additional 24 h composites (n=3) from respective grabs. For taxonomic profiling, metagenomic DNA was extracted from all samples and 16S rRNA gene sequencing was performed. One composite and six grabs from day 1 underwent metagenomic sequencing for metagenomic dissimilarity estimation and resistome profiling. Taxonomic abundances of phyla varied significantly across hourly grab samples but followed a repeating diurnal pattern for all 3 days. Hierarchical clustering grouped grab samples into four time periods dissimilar in both 16S rRNA gene-based profiles and metagenomic distances. 24H-composites resembled mean daily phyla abundances and showed low variability of taxonomic profiles. Of the 122 AMR gene families (AGFs) identified across all day 1 samples, single grab samples identified a median of six (IQR: 5-8) AGFs not seen in the composite. However, 36/36 of these hits were at lateral coverage <0.5 (median: 0.19; interquartile range: 0.16-0.22) and potential false positives. Conversely, the 24H-composite identified three AGFs not seen in any grab with higher lateral coverage (0.82; 0.55-0.84). Additionally, several clinically significant human AGFs (bla VIM, bla IMP, bla KPC) were intermittently or completely missed by grab sampling but captured by the 24 h composite. Wastewater influent undergoes significant taxonomic and resistome changes on short timescales potentially affecting interpretation of results based on sampling strategy. Grab samples are more convenient and potentially capture low-prevalence/transient targets but are less comprehensive and temporally variable. Therefore, we recommend 24H-composite sampling where feasible. Further validation and optimization of WBE methods is vital for its development into a robust AMR surveillance approach.
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Affiliation(s)
- Kevin K Chau
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
| | - T Goodall
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - M Bowes
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - K Easterbrook
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - H Brett
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - J Hughes
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - D W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- Department of Microbiology/Infectious diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
| | - D S Read
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - A S Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
| | - N Stoesser
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- Department of Microbiology/Infectious diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
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5
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Semeraro S, Kergunteuil A, Moreno SS, Puissant J, Goodall T, Griffiths R, Rasmann S. Relative contribution of high and low elevation soil microbes and nematodes to ecosystem functioning. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Sarah Semeraro
- Institute of Biology University of Neuchâtel Rue Emile‐Argand 11 2000 Neuchâtel Switzerland
| | | | - Sara Sánchez Moreno
- Department of the Environment and Agronomy National Centre Institute for Agricultural and Food Research and Technology INIA‐CSIC 28040 Madrid Spain
| | | | - Tim Goodall
- UK Centre for Ecology & Hydrology Wallingford UK
| | | | - Sergio Rasmann
- Institute of Biology University of Neuchâtel Rue Emile‐Argand 11 2000 Neuchâtel Switzerland
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6
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Broadbent AAD, Bahn M, Pritchard WJ, Newbold LK, Goodall T, Guinta A, Snell HSK, Cordero I, Michas A, Grant HK, Soto DX, Kaufmann R, Schloter M, Griffiths RI, Bardgett RD. Shrub expansion modulates belowground impacts of changing snow conditions in alpine grasslands. Ecol Lett 2021; 25:52-64. [PMID: 34708508 DOI: 10.1111/ele.13903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/03/2021] [Revised: 06/18/2021] [Accepted: 10/06/2021] [Indexed: 11/28/2022]
Abstract
Climate change is disproportionately impacting mountain ecosystems, leading to large reductions in winter snow cover, earlier spring snowmelt and widespread shrub expansion into alpine grasslands. Yet, the combined effects of shrub expansion and changing snow conditions on abiotic and biotic soil properties remains poorly understood. We used complementary field experiments to show that reduced snow cover and earlier snowmelt have effects on soil microbial communities and functioning that persist into summer. However, ericaceous shrub expansion modulates a number of these impacts and has stronger belowground effects than changing snow conditions. Ericaceous shrub expansion did not alter snow depth or snowmelt timing but did increase the abundance of ericoid mycorrhizal fungi and oligotrophic bacteria, which was linked to decreased soil respiration and nitrogen availability. Our findings suggest that changing winter snow conditions have cross-seasonal impacts on soil properties, but shifts in vegetation can modulate belowground effects of future alpine climate change.
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Affiliation(s)
- Arthur A D Broadbent
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Michael Bahn
- Institut für Ökologie, Universität Innsbruck, Innsbruck, Austria
| | - William J Pritchard
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | | | - Tim Goodall
- UK Centre for Ecology & Hydrology, Wallingford, Oxfordshire, UK
| | - Andrew Guinta
- Institut für Ökologie, Universität Innsbruck, Innsbruck, Austria
| | - Helen S K Snell
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Irene Cordero
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Antonios Michas
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany.,Chair for Soil Science, Technical University of Munich, Freising, Germany
| | - Helen K Grant
- National Environmental Isotope Facility, UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, UK
| | - David X Soto
- National Environmental Isotope Facility, UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, UK
| | - Rüdiger Kaufmann
- Institut für Ökologie, Universität Innsbruck, Innsbruck, Austria
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany.,Chair for Soil Science, Technical University of Munich, Freising, Germany
| | - Robert I Griffiths
- UK Centre for Ecology & Hydrology, Environment Centre Wales, Gwynedd, UK
| | - Richard D Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
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7
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Jones B, Goodall T, George PBL, Gweon HS, Puissant J, Read DS, Emmett BA, Robinson DA, Jones DL, Griffiths RI. Beyond Taxonomic Identification: Integration of Ecological Responses to a Soil Bacterial 16S rRNA Gene Database. Front Microbiol 2021; 12:682886. [PMID: 34349739 PMCID: PMC8326369 DOI: 10.3389/fmicb.2021.682886] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. However, current analytical approaches are of limited use in formalizing syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterize taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth CS) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from survey metadata. Specifically, we modeled taxon responses to soil pH at the OTU level using hierarchical logistic regression (HOF) models, to provide information on both the shape of landscape scale pH-abundance responses, and pH optima (pH at which OTU abundance is maximal). We identify that most of the soil OTUs examined exhibited a non-flat relationship with soil pH. Further, the pH optima could not be generalized by broad taxonomy, highlighting the need for tools and databases synthesizing ecological traits at finer taxonomic resolution. We further demonstrate the utility of the database by testing against geographically dispersed query 16S datasets; evaluating efficacy by quantifying matches, and accuracy in predicting pH responses of query sequences from a separate large soil survey. We found that the CS database provided good coverage of dominant taxa; and that the taxa indicating soil pH in a query dataset corresponded with the pH classifications of top matches in the CS database. Furthermore we were able to predict query dataset community structure, using predicted abundances of dominant taxa based on query soil pH data and the HOF models of matched CS database taxa. The database with associated HOF model outputs is released as an online portal for querying single sequences of interest (https://shiny-apps.ceh.ac.uk/ID-TaxER/), and flat files are made available for use in bioinformatic pipelines. The further development of advanced informatics infrastructures incorporating modeled ecological attributes along with new functional genomic information will likely facilitate large scale exploration and prediction of soil microbial functional biodiversity under current and future environmental change scenarios.
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Affiliation(s)
- Briony Jones
- UK Centre for Ecology and Hydrology, Bangor, United Kingdom.,School of Environment, Natural Resources and Geography, Bangor University, Bangor, United Kingdom
| | - Tim Goodall
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Paul B L George
- UK Centre for Ecology and Hydrology, Bangor, United Kingdom.,School of Environment, Natural Resources and Geography, Bangor University, Bangor, United Kingdom
| | - Hyun S Gweon
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Jeremy Puissant
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Daniel S Read
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | | | | | - Davey L Jones
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
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8
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Broadbent AAD, Snell HSK, Michas A, Pritchard WJ, Newbold L, Cordero I, Goodall T, Schallhart N, Kaufmann R, Griffiths RI, Schloter M, Bahn M, Bardgett RD. Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt. ISME J 2021; 15:2264-2275. [PMID: 33619353 DOI: 10.1038/s41396-021-00922-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 12/30/2022]
Abstract
Soil microbial communities regulate global biogeochemical cycles and respond rapidly to changing environmental conditions. However, understanding how soil microbial communities respond to climate change, and how this influences biogeochemical cycles, remains a major challenge. This is especially pertinent in alpine regions where climate change is taking place at double the rate of the global average, with large reductions in snow cover and earlier spring snowmelt expected as a consequence. Here, we show that spring snowmelt triggers an abrupt transition in the composition of soil microbial communities of alpine grassland that is closely linked to shifts in soil microbial functioning and biogeochemical pools and fluxes. Further, by experimentally manipulating snow cover we show that this abrupt seasonal transition in wide-ranging microbial and biogeochemical soil properties is advanced by earlier snowmelt. Preceding winter conditions did not change the processes that take place during snowmelt. Our findings emphasise the importance of seasonal dynamics for soil microbial communities and the biogeochemical cycles that they regulate. Moreover, our findings suggest that earlier spring snowmelt due to climate change will have far reaching consequences for microbial communities and nutrient cycling in these globally widespread alpine ecosystems.
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Affiliation(s)
- Arthur A D Broadbent
- Department of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Helen S K Snell
- Department of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Antonios Michas
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Chair for Soil Science, Technical University of Munich, Emil-Ramann-Str 2, 85354, Freising, Germany
| | - William J Pritchard
- Department of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Lindsay Newbold
- UK Centre for Ecology & Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Irene Cordero
- Department of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Tim Goodall
- UK Centre for Ecology & Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Nikolaus Schallhart
- Faculty of Biology, University of Innsbruck, Sternwartestr. 15, Innsbruck, Austria
| | - Ruediger Kaufmann
- Department of Ecology, University of Innsbruck, Technikerstr. 25, Innsbruck, Austria
| | - Robert I Griffiths
- UK Centre for Ecology & Hydrology, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Chair for Soil Science, Technical University of Munich, Emil-Ramann-Str 2, 85354, Freising, Germany
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Sternwartestr. 15, Innsbruck, Austria
| | - Richard D Bardgett
- Department of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
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9
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Swart E, Goodall T, Kille P, Spurgeon DJ, Svendsen C. The earthworm microbiome is resilient to exposure to biocidal metal nanoparticles. Environ Pollut 2020; 267:115633. [PMID: 33254656 DOI: 10.1016/j.envpol.2020.115633] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 06/12/2023]
Abstract
Environmental pollution can disrupt the interactions between animals and their symbiotic bacteria, which can lead to adverse effects on the host even in the absence of direct chemical toxicity. It is therefore crucial to understand how environmental pollutants affect animal microbiomes, especially for those chemicals that are designed to target microbes. Here, we study the effects of two biocidal nanoparticles (NPs) (Ag and CuO) on the soil bacterial community and the resident gut microbiome of the earthworm Eisenia fetida over a 28-day period using metabarcoding techniques. Exposures to NPs were conducted following OECD test guidelines and effects on earthworm reproduction and juvenile biomass were additionally recorded in order to compare effects on the host to effects on microbiomes. By employing a full concentration series, we were able to link pollutants to microbiome effects in high resolution. Multivariate analysis, differential abundance analysis and species sensitivity distribution analysis showed that Ag-NPs are more toxic to soil bacteria than CuO-NPs. In contrast to the strong effects of CuO-NPs and Ag-NPs on the soil bacterial community, the earthworm gut microbiome is largely resilient to exposure to biocidal NPs. Despite this buffering effect, CuO-NPs did negatively affect the relative abundance of some earthworm symbionts, including 'Candidatus Lumbricincola'. Changes in the soil bacterial community and the earthworm microbiome occur at total copper concentrations often found or modelled to occur in agricultural fields, demonstrating that soil bacterial communities and individual taxa in the earthworm microbiome may be at risk from environmental copper exposure including in nanomaterial form.
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Affiliation(s)
- Elmer Swart
- UK Centre for Ecology and Hydrology, Maclean Building Benson Lane, Wallingford, OX10 8BB, United Kingdom.
| | - Tim Goodall
- UK Centre for Ecology and Hydrology, Maclean Building Benson Lane, Wallingford, OX10 8BB, United Kingdom
| | - Peter Kille
- School of Biosciences, Cardiff University, Sir Martin Evans Building Museum Avenue, Cardiff, CF10 3AX, United Kingdom
| | - David J Spurgeon
- UK Centre for Ecology and Hydrology, Maclean Building Benson Lane, Wallingford, OX10 8BB, United Kingdom
| | - Claus Svendsen
- UK Centre for Ecology and Hydrology, Maclean Building Benson Lane, Wallingford, OX10 8BB, United Kingdom.
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Swart E, Dvorak J, Hernádi S, Goodall T, Kille P, Spurgeon D, Svendsen C, Prochazkova P. The Effects of In Vivo Exposure to Copper Oxide Nanoparticles on the Gut Microbiome, Host Immunity, and Susceptibility to a Bacterial Infection in Earthworms. Nanomaterials (Basel) 2020; 10:E1337. [PMID: 32659907 PMCID: PMC7408611 DOI: 10.3390/nano10071337] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023]
Abstract
Nanomaterials (NMs) can interact with the innate immunity of organisms. It remains, however, unclear whether these interactions can compromise the immune functioning of the host when faced with a disease threat. Co-exposure with pathogens is thus a powerful approach to assess the immuno-safety of NMs. In this paper, we studied the impacts of in vivo exposure to a biocidal NM on the gut microbiome, host immune responses, and susceptibility of the host to a bacterial challenge in an earthworm. Eisenia fetida were exposed to CuO-nanoparticles in soil for 28 days, after which the earthworms were challenged with the soil bacterium Bacillus subtilis. Immune responses were monitored by measuring mRNA levels of known earthworm immune genes. Effects of treatments on the gut microbiome were also assessed to link microbiome changes to immune responses. Treatments caused a shift in the earthworm gut microbiome. Despite these effects, no impacts of treatment on the expression of earthworm immune markers were recorded. The methodological approach applied in this paper provides a useful framework for improved assessment of immuno-safety of NMs. In addition, we highlight the need to investigate time as a factor in earthworm immune responses to NM exposure.
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Affiliation(s)
- Elmer Swart
- UK Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Wallingford OX10 8BB, UK; (T.G.); (D.S.)
| | - Jiri Dvorak
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic; (J.D.); (P.P.)
| | - Szabolcs Hernádi
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK; (S.H.); (P.K.)
| | - Tim Goodall
- UK Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Wallingford OX10 8BB, UK; (T.G.); (D.S.)
| | - Peter Kille
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK; (S.H.); (P.K.)
| | - David Spurgeon
- UK Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Wallingford OX10 8BB, UK; (T.G.); (D.S.)
| | - Claus Svendsen
- UK Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Wallingford OX10 8BB, UK; (T.G.); (D.S.)
| | - Petra Prochazkova
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic; (J.D.); (P.P.)
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Malik AA, Puissant J, Buckeridge KM, Goodall T, Jehmlich N, Chowdhury S, Gweon HS, Peyton JM, Mason KE, van Agtmaal M, Blaud A, Clark IM, Whitaker J, Pywell RF, Ostle N, Gleixner G, Griffiths RI. Land use driven change in soil pH affects microbial carbon cycling processes. Nat Commun 2018; 9:3591. [PMID: 30181597 PMCID: PMC6123395 DOI: 10.1038/s41467-018-05980-1] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/06/2018] [Indexed: 01/28/2023] Open
Abstract
Soil microorganisms act as gatekeepers for soil–atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates. Land use intensification could modify microbial activity and thus ecosystem function. Here, Malik et al. sample microbes and carbon-related functions across a land use gradient, demonstrating that microbial biomass and carbon use efficiency are reduced in human-impacted near-neutral pH soils.
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Affiliation(s)
- Ashish A Malik
- Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK. .,Department of Ecology and Evolutionary Biology, University of California, Irvine, 92697, USA.
| | | | - Kate M Buckeridge
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Tim Goodall
- Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, 04318, Germany
| | - Somak Chowdhury
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, 07745, Germany
| | - Hyun Soon Gweon
- Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK.,School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK
| | - Jodey M Peyton
- Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK
| | - Kelly E Mason
- Centre for Ecology and Hydrology, Lancaster, LA1 4AP, UK
| | | | - Aimeric Blaud
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Ian M Clark
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | | | | | - Nick Ostle
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Gerd Gleixner
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, 07745, Germany
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Goodall T, Buffey JA, Rennie IG, Benson M, Parsons MA, Faulkner MK, MacNeil S. Effect of melanocyte stimulating hormone on human cultured choroidal melanocytes, uveal melanoma cells, and retinal epithelial cells. Invest Ophthalmol Vis Sci 1994; 35:826-37. [PMID: 8125745] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
PURPOSE To establish methodology for the culture of human choroidal melanocytes to compare their responsiveness to melanocyte stimulating hormone (MSH) with that of their transformed melanoma counterparts and with that of the retinal epithelial cell. METHODS Choroidal melanocytes from the choroid of eyes enucleated for the presence of malignant melanoma were cultured in MCDB 153 medium supplemented with insulin, transferrin, hydrocortisone, glutamine, nystatin, vitamin E, phorbol myristate acetate, bovine hypothalamic extract, cholera toxin, and chelexed fetal calf serum. RESULTS High yields of pure spindle-shaped bipolar melanocytes were obtained with a doubling time of 3 to 4 days in nine consecutive eyes. Cells continued to divide after 4 months in culture. In contrast, uveal malignant melanoma cells grew rapidly in a relatively simple medium of Ham's F12:DMEM (1:1) supplemented with fetal calf serum, insulin, transferrin and glutamine. This medium was unable to support choroidal melanocytes. Choroidal melanocytes were DOPA-positive with appreciable tyrosinase activity that significantly increased with treatment with MSH. MSH also significantly altered the size, local density, and distribution of primary and mature melanosomes of ocular melanocytes. In contrast, uveal melanoma cells had a low level of tyrosinase activity and failed to respond to MSH with either an increase in enzyme activity or melanosome size. Retinal epithelial cells failed to show significant tyrosinase activity under the conditions studied or any increase in melanosome size in response to MSH. CONCLUSION Ocular melanocytes show evidence of regulation by MSH and a range of mitogenic stimuli unlike the transformed melanoma cells, implying a loss of regulatory control in the latter.
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Affiliation(s)
- T Goodall
- Department of Medicine, University of Sheffield, United Kingdom
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Abstract
Following our recent finding that calmodulin antagonists can reduce cancer cell attachment to extracellular matrix proteins, we investigated the calmodulin antagonistic and anti-attachment properties of the non-steroidal anti-oestrogens tamoxifen and droloxifene. These drugs and four of their active metabolites were found to have calmodulin antagonist activity with IC50 values of 2-4 microM and to be capable of inhibiting attachment of murine B16 melanoma to extracellular matrix proteins in vitro. IC50 values for inhibition of attachment were 11 microM for tamoxifen and ranged from 5 to 40 microM for the other five compounds tested. (Poor reproducibility in drug potency between attachment experiments was almost certainly due to the low aqueous solubility of these drugs.) The effects of tamoxifen on cell/matrix adhesion were most evident between 15 min and 3 h of cell attachment. No effects of tamoxifen were evident in cells which had been allowed to attach for 6 h or more. Tamoxifen at concentrations between 0.1 and 30 microM was without effect on intracellular free calcium concentration. Tamoxifen also inhibited attachment of human ocular melanoma cells and human breast cancer (MCF7) cells to type I collagen. The concentration at which tamoxifen and its metabolites affect cell attachment in vitro (2-14 microM) is of the same order as the tissue concentrations of these drugs achieved clinically. The possibility exists that reduction of cell/matrix interactions may contribute to the clinical anti-metastatic efficacy of tamoxifen and some of its active metabolites.
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Affiliation(s)
- S Mac Neil
- University Department of Medicine, Northern General Hospital, Sheffield, UK
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