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Burian A, Gruber-Dorninger M, Schweichart J, Yasindi A, Bulling M, Jirsa F, Winter C, Muia AW, Schagerl M. Drivers of microbial food-web structure along productivity gradients. Proc Biol Sci 2023; 290:20231531. [PMID: 37876193 PMCID: PMC10598424 DOI: 10.1098/rspb.2023.1531] [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: 08/29/2022] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
Ratios between viruses, heterotrophic prokaryotes and chlorophyll a are key indicators of microbial food structure and both virus-prokaryote and prokaryote-chlorophyll ratios have been proposed to decrease with system productivity. However, the mechanisms underlying these responses are still insufficiently resolved and their consistency across aquatic ecosystem types requires critical evaluation. We assessed microbial community ratios in highly productive African soda-lakes and used our data from naturally hypereutrophic systems which are largely underrepresented in literature, to complement earlier across-system meta-analyses. In contrast to marine and freshwater systems, prokaryote-chlorophyll ratios in African soda-lakes did not decrease along productivity gradients. High-resolution time series from two soda-lakes indicated that this lack of response could be driven by a weakened top-down control of heterotrophic prokaryotes. Our analysis of virus-prokaryote relationships, revealed a reduction of virus-prokaryote ratios by high suspended particle concentrations in soda-lakes. This effect, likely driven by the adsorption of free-living viruses, was also found in three out of four additionally analysed marine datasets. However, the decrease of virus-prokaryote ratios previously reported in highly productive marine systems, was neither detectable in soda-lakes nor freshwaters. Hence, our study demonstrates that system-specific analyses can reveal the diversity of mechanisms that structure microbial food-webs and shape their response to productivity increases.
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Affiliation(s)
- Alfred Burian
- Department of Computational Landscape Ecology, UFZ– Helmholtz Centre for Environmental Research, Leipzig, Germany
- Marine Ecology Department, Lurio University, Nampula, Mozambique
| | | | - Johannes Schweichart
- Biology Centre, University of South Bohemia in České, České Budějovice, Czech Republic
| | - Andrew Yasindi
- Department of Biological Sciences, Egerton University, Njoro, Kenya
| | - Mark Bulling
- Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Franz Jirsa
- Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
- Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Christian Winter
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | | | - Michael Schagerl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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Wang M, Sun X, Cao B, Chiariello NR, Docherty KM, Field CB, Gao Q, Gutknecht JLM, Guo X, He G, Hungate BA, Lei J, Niboyet A, Le Roux X, Shi Z, Shu W, Yuan M, Zhou J, Yang Y. Long-term elevated precipitation induces grassland soil carbon loss via microbe-plant-soil interplay. Glob Chang Biol 2023; 29:5429-5444. [PMID: 37317051 DOI: 10.1111/gcb.16811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 04/13/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023]
Abstract
Global climate models predict that the frequency and intensity of precipitation events will increase in many regions across the world. However, the biosphere-climate feedback to elevated precipitation (eP) remains elusive. Here, we report a study on one of the longest field experiments assessing the effects of eP, alone or in combination with other climate change drivers such as elevated CO2 (eCO2 ), warming and nitrogen deposition. Soil total carbon (C) decreased after a decade of eP treatment, while plant root production decreased after 2 years. To explain this asynchrony, we found that the relative abundances of fungal genes associated with chitin and protein degradation increased and were positively correlated with bacteriophage genes, suggesting a potential viral shunt in C degradation. In addition, eP increased the relative abundances of microbial stress tolerance genes, which are essential for coping with environmental stressors. Microbial responses to eP were phylogenetically conserved. The effects of eP on soil total C, root production, and microbes were interactively affected by eCO2 . Collectively, we demonstrate that long-term eP induces soil C loss, owing to changes in microbial community composition, functional traits, root production, and soil moisture. Our study unveils an important, previously unknown biosphere-climate feedback in Mediterranean-type water-limited ecosystems, namely how eP induces soil C loss via microbe-plant-soil interplay.
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Affiliation(s)
- Mengmeng Wang
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Xin Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Yale Institute for Biospheric Studies, Yale University, New Haven, Connecticut, USA
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, USA
| | - Baichuan Cao
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Nona R Chiariello
- Jasper Ridge Biological Preserve, Stanford University, Stanford, California, USA
| | - Kathryn M Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
| | - Christopher B Field
- Stanford Woods Institute for the Environment, Stanford University, Stanford, California, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Jessica L M Gutknecht
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, Minnesota, USA
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Genhe He
- School of Life Sciences, Key Laboratory of Agricultural Environmental Pollution Prevention and Control in Red Soil Hilly Region of Jiangxi Province, Jinggangshan University, Ji'an, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Audrey Niboyet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, CNRS, INRAE, IRD, Sorbonne Université, Université Paris Cité, UPEC, Paris, France
- AgroParisTech, Palaiseau, France
| | - Xavier Le Roux
- Laboratoire d'Ecologie Microbienne, INRAE, CNRS, VetAgroSup, UMR INRAE 1418, UMR CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Zhou Shi
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Wensheng Shu
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Mengting Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma, USA
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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Heffner T, Kaupper T, Heinrichs M, Lee HJ, Rüppel N, Horn MA, Ho A. Mitomycin C-induced effects on aerobic methanotrophs in a landfill cover soil; implications of a viral shunt? FEMS Microbiol Ecol 2023:7157097. [PMID: 37156510 DOI: 10.1093/femsec/fiad047] [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: 05/10/2023] Open
Abstract
A viral shunt can occur when phages going through a lytic cycle, including lysogenic phages triggered by inducing agents (e.g. mitomycin C), results in host lysis and the release of cell constituents and virions. The impact of a viral shunt on the carbon, including methane cycle in soil systems is poorly understood. Here, we determined the effects of mitomycin C on the aerobic methanotrophs in a landfill cover soil. To an extent, our results support a mitomycin C-induced viral shunt, as indicated by the significantly higher viral-like particle (VLP) counts relative to bacteria, elevated nutrient concentrations (ammonium, succinate), and initially impaired microbial activities (methane uptake and microbial respiration) after mitomycin C addition. The trend in microbial activities at <2 days largely corresponded to the expression of the pmoA and 16S rRNA genes. Thereafter (>11 days), the active bacterial community composition significantly diverged in the mitomycin C-supplemented incubations, suggesting the differential impact of mitomycin C on the bacterial community. Collectively, we provide insight on the effects of mitomycin C, and potentially a viral shunt, on the bacteria in the soil environment.
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Affiliation(s)
- Tanja Heffner
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Thomas Kaupper
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Mara Heinrichs
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany
| | - Hyo Jung Lee
- Department of Biology, Kunsan National University, 558 Daehak-ro, Gunsan 54150, Republic of Korea
| | - Nadine Rüppel
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Marcus A Horn
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Adrian Ho
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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Abstract
Viruses impact host cells and have indirect effects on ecosystem processes. Plankton such as ciliates can reduce the abundance of virions in water, but whether virus consumption translates into demographic consequences for the grazers is unknown. Here, we show that small protists not only can consume viruses they also can grow and divide given only viruses to eat. Moreover, the ciliate Halteria sp. foraging on chloroviruses displays dynamics and interaction parameters that are similar to other microbial trophic interactions. These results suggest that the effect of viruses on ecosystems extends beyond (and in contrast to) the viral shunt by redirecting energy up food chains.
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Malits A, Boras JA, Balagué V, Calvo E, Gasol JM, Marrasé C, Pelejero C, Pinhassi J, Sala MM, Vaqué D. Viral-Mediated Microbe Mortality Modulated by Ocean Acidification and Eutrophication: Consequences for the Carbon Fluxes Through the Microbial Food Web. Front Microbiol 2021; 12:635821. [PMID: 33935996 PMCID: PMC8079731 DOI: 10.3389/fmicb.2021.635821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Anthropogenic carbon emissions are causing changes in seawater carbonate chemistry including a decline in the pH of the oceans. While its aftermath for calcifying microbes has been widely studied, the effect of ocean acidification (OA) on marine viruses and their microbial hosts is controversial, and even more in combination with another anthropogenic stressor, i.e., human-induced nutrient loads. In this study, two mesocosm acidification experiments with Mediterranean waters from different seasons revealed distinct effects of OA on viruses and viral-mediated prokaryotic mortality depending on the trophic state and the successional stage of the plankton community. In the winter bloom situation, low fluorescence viruses, the most abundant virus-like particle (VLP) subpopulation comprising mostly bacteriophages, were negatively affected by lowered pH with nutrient addition, while the bacterial host abundance was stimulated. High fluorescence viruses, containing cyanophages, were stimulated by OA regardless of the nutrient conditions, while cyanobacteria of the genus Synechococcus were negatively affected by OA. Moreover, the abundance of very high fluorescence viruses infecting small haptophytes tended to be lower under acidification while their putative hosts' abundance was enhanced, suggesting a direct and negative effect of OA on viral-host interactions. In the oligotrophic summer situation, we found a stimulating effect of OA on total viral abundance and the viral populations, suggesting a cascading effect of the elevated pCO2 stimulating autotrophic and heterotrophic production. In winter, viral lysis accounted for 30 ± 16% of the loss of bacterial standing stock per day (VMMBSS) under increased pCO2 compared to 53 ± 35% in the control treatments, without effects of nutrient additions while in summer, OA had no significant effects on VMMBSS (35 ± 20% and 38 ± 5% per day in the OA and control treatments, respectively). We found that phage production and resulting organic carbon release rates significantly reduced under OA in the nutrient replete winter situation, but it was also observed that high nutrient loads lowered the negative effect of OA on viral lysis, suggesting an antagonistic interplay between these two major global ocean stressors in the Anthropocene. In summer, however, viral-mediated carbon release rates were lower and not affected by lowered pH. Eutrophication consistently stimulated viral production regardless of the season or initial conditions. Given the relevant role of viruses for marine carbon cycling and the biological carbon pump, these two anthropogenic stressors may modulate carbon fluxes through their effect on viruses at the base of the pelagic food web in a future global change scenario.
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Affiliation(s)
- Andrea Malits
- Biological Oceanography Laboratory, Austral Center for Scientific Research (CONICET), Ushuaia, Argentina
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Julia A. Boras
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Vanessa Balagué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Eva Calvo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Josep M. Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
- Center for Marine Ecosystems Research, School of Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Cèlia Marrasé
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Carles Pelejero
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Maria Montserrat Sala
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
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Evans C, Brandsma J, Meredith MP, Thomas DN, Venables HJ, Pond DW, Brussaard CPD. Shift from Carbon Flow through the Microbial Loop to the Viral Shunt in Coastal Antarctic Waters during Austral Summer. Microorganisms 2021; 9:460. [PMID: 33672195 PMCID: PMC7927135 DOI: 10.3390/microorganisms9020460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 01/28/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/30/2022] Open
Abstract
The relative flow of carbon through the viral shunt and the microbial loop is a pivotal factor controlling the contribution of secondary production to the food web and to rates of nutrient remineralization and respiration. The current study examines the significance of these processes in the coastal waters of the Antarctic during the productive austral summer months. Throughout the study a general trend towards lower bacterioplankton and heterotrophic nanoflagellate (HNF) abundances was observed, whereas virioplankton concentration increased. A corresponding decline of HNF grazing rates and shift towards viral production, indicative of viral infection, was measured. Carbon flow mediated by HNF grazing decreased by more than half from 5.7 µg C L-1 day-1 on average in December and January to 2.4 µg C L-1 day-1 in February. Conversely, carbon flow through the viral shunt increased substantially over the study from on average 0.9 µg C L-1 day-1 in December to 7.6 µg C L-1 day-1 in February. This study shows that functioning of the coastal Antarctic microbial community varied considerably over the productive summer months. In early summer, the system favors transfer of matter and energy to higher trophic levels via the microbial loop, however towards the end of summer carbon flow is redirected towards the viral shunt, causing a switch towards more recycling and therefore increased respiration and regeneration.
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Affiliation(s)
- Claire Evans
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
- Ocean BioGeosciences, National Oceanography Centre, Southampton, European Way, Southampton SO14 3ZH, UK
| | - Joost Brandsma
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Michael P. Meredith
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
| | - David N. Thomas
- Ecosystems & Environment, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Hugh J. Venables
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
| | - David W. Pond
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
- Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Corina P. D. Brussaard
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
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Rassner SME, Anesio AM, Girdwood SE, Hell K, Gokul JK, Whitworth DE, Edwards A. Can the Bacterial Community of a High Arctic Glacier Surface Escape Viral Control? Front Microbiol 2016; 7:956. [PMID: 27446002 PMCID: PMC4914498 DOI: 10.3389/fmicb.2016.00956] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 04/23/2016] [Accepted: 06/02/2016] [Indexed: 02/05/2023] Open
Abstract
Glacial ice surfaces represent a seasonally evolving three-dimensional photic zone which accumulates microbial biomass and potentiates positive feedbacks in ice melt. Since viruses are abundant in glacial systems and may exert controls on supraglacial bacterial production, we examined whether changes in resource availability would promote changes in the bacterial community and the dynamics between viruses and bacteria of meltwater from the photic zone of a Svalbard glacier. Our results indicated that, under ambient nutrient conditions, low estimated viral decay rates account for a strong viral control of bacterial productivity, incurring a potent viral shunt of a third of bacterial carbon in the supraglacial microbial loop. Moreover, it appears that virus particles are very stable in supraglacial meltwater, raising the prospect that viruses liberated in melt are viable downstream. However, manipulating resource availability as dissolved organic carbon, nitrogen, and phosphorous in experimental microcosms demonstrates that the photic zone bacterial communities can escape viral control. This is evidenced by a marked decline in virus-to-bacterium ratio (VBR) concomitant with increased bacterial productivity and number. Pyrosequencing shows a few bacterial taxa, principally Janthinobacterium sp., dominate both the source meltwater and microcosm communities. Combined, our results suggest that viruses maintain high VBR to promote contact with low-density hosts, by the manufacture of robust particles, but that this necessitates a trade-off which limits viral production. Consequently, dominant bacterial taxa appear to access resources to evade viral control. We propose that a delicate interplay of bacterial and viral strategies affects biogeochemical cycling upon glaciers and, ultimately, downstream ecosystems.
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Affiliation(s)
- Sara M E Rassner
- Institute of Biological, Rural and Environmental Sciences, Aberystwyth UniversityAberystwyth, UK; Department of Geography and Earth Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Alexandre M Anesio
- School of Geographical Sciences, Bristol Glaciology Centre, University of Bristol Bristol, UK
| | - Susan E Girdwood
- Institute of Biological, Rural and Environmental Sciences, Aberystwyth University Aberystwyth, UK
| | - Katherina Hell
- Institute of Ecology, University of Innsbruck Innsbruck, Austria
| | - Jarishma K Gokul
- Institute of Biological, Rural and Environmental Sciences, Aberystwyth University Aberystwyth, UK
| | - David E Whitworth
- Institute of Biological, Rural and Environmental Sciences, Aberystwyth University Aberystwyth, UK
| | - Arwyn Edwards
- Institute of Biological, Rural and Environmental Sciences, Aberystwyth University Aberystwyth, UK
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