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O'Gorman EJ, Zhao L, Kordas RL, Dudgeon S, Woodward G. Warming indirectly simplifies food webs through effects on apex predators. Nat Ecol Evol 2023; 7:1983-1992. [PMID: 37798434 PMCID: PMC10697836 DOI: 10.1038/s41559-023-02216-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023]
Abstract
Warming alters ecosystems through direct physiological effects on organisms and indirect effects via biotic interactions, but their relative impacts in the wild are unknown due to the difficulty in warming natural environments. Here we bridge this gap by embedding manipulative field experiments within a natural stream temperature gradient to test whether warming and apex fish predators have interactive effects on freshwater ecosystems. Fish exerted cascading effects on algal production and microbial decomposition via both green and brown pathways in the food web, but only under warming. Neither temperature nor the presence of fish altered food web structure alone, but connectance and mean trophic level declined as consumer species were lost when both drivers acted together. A mechanistic model indicates that this temperature-induced trophic cascade is determined primarily by altered interactions, which cautions against extrapolating the impacts of warming from reductionist approaches that do not consider the wider food web.
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Affiliation(s)
- Eoin J O'Gorman
- School of Life Sciences, University of Essex, Colchester, UK.
| | - Lei Zhao
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.
| | - Rebecca L Kordas
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
| | - Steve Dudgeon
- Department of Biology, California State University, Northridge, CA, USA
| | - Guy Woodward
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK.
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2
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Patonai K, Jordán F, Castaldelli G, Congiu L, Gavioli A. Spatial variability of the Po River food web and its comparison with the Danube River food web. PLoS One 2023; 18:e0288652. [PMID: 37450464 PMCID: PMC10348563 DOI: 10.1371/journal.pone.0288652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023] Open
Abstract
Freshwater ecosystems are experiencing unprecedented pressure globally. To address environmental challenges, systematic and comparative studies on ecosystems are needed, though mostly lacking, especially for rivers. Here, we describe the food web of the Po River (as integrated from the white literature and monitoring data), describe the three river sections using network analysis, and compare our results with the previously compiled Danube River food web. The Po River food web was taxonomically aggregated in five consecutive steps (T1-T5) and it was also analyzed using the regular equivalence (REGE) algorithm to identify structurally similar nodes in the most aggregated T5 model. In total, the two river food webs shared 30 nodes. Two network metrics (normalized degree centrality [nDC]) and normalized betweenness centrality [nBC]) were compared using Mann-Whitney tests in the two rivers. On average, the Po River nodes have larger nDC values than in the Danube, meaning that neighboring connections are better mapped. Regarding nBC, there were no significant differences between the two rivers. Finally, based on both centrality indices, Carassius auratus is the most important node in the Po River food web, whereas phytoplankton and detritus are most important in the Danube River. Using network analysis and comparative methods, it is possible to draw attention to important trophic groups and knowledge gaps, which can guide future research. These simple models for the Po River food web can pave the way for more advanced models, supporting quantitative and predictive-as well as more functional-descriptions of ecosystems.
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Affiliation(s)
- Katalin Patonai
- Department of Environmental and Prevention Sciences, University of Ferrara, Ferrara, Italy
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Budapest, Hungary
| | - Ferenc Jordán
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giuseppe Castaldelli
- Department of Environmental and Prevention Sciences, University of Ferrara, Ferrara, Italy
| | | | - Anna Gavioli
- Department of Environmental and Prevention Sciences, University of Ferrara, Ferrara, Italy
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3
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Lu Q, Cheng C, Xiao L, Li J, Li X, Zhao X, Lu Z, Zhao J, Yao M. Food webs reveal coexistence mechanisms and community organization in carnivores. Curr Biol 2023; 33:647-659.e5. [PMID: 36669497 DOI: 10.1016/j.cub.2022.12.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/11/2022] [Accepted: 12/20/2022] [Indexed: 01/20/2023]
Abstract
Globally, massive carnivore guild extirpations have led to trophic downgrading and compromised ecosystem services. However, the complexity of multi-carnivore food webs complicates accurate identification of species interactions and community organization. Here, we used fecal DNA metabarcoding to investigate three communities that together encompass eight large- and meso-carnivore species and their 44 prey taxa of the Qinghai-Tibet Plateau (QTP), one of the last places on Earth that still harbors intact carnivore assemblages. Quantitative food-web analyses revealed pronounced interspecific variations in the carnivores' prey compositions and dietary partitioning both between and within guilds. Additionally, body masses of the carnivores and their prey exhibited consistent hump-shaped correlations across communities. Overall, differences in prey diversity, size category, and proportional utilization among the carnivore species result in trophic niche segregation that likely promotes carnivore coexistence in the harsh QTP environment. Network structure analyses detected significant modularity in all food webs but nestedness in only one. Furthermore, network characterization identified pikas (Ochotona spp.), bharal (Pseudois nayaur), and domestic yak (Bos grunniens) as potential keystone prey across the areas. Our results paint a holistic and detailed picture of the QTP carnivore assemblages' trophic networks and demonstrate that the combined use of the molecular dietary approach and network analysis can generate structural insights into carnivore coexistence and can identify functionally important species in complex communities. Such knowledge can help safeguard carnivore guild integrity and enhance community resilience to environmental perturbations in the sensitive QTP ecosystems.
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Affiliation(s)
- Qi Lu
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Chen Cheng
- Center for Nature and Society, School of Life Sciences, Peking University, Beijing 100871, China; Shan Shui Conservation Center, Beijing 100871, China
| | - Lingyun Xiao
- School of Life Sciences, Peking University, Beijing 100871, China; Department of Health and Environmental Sciences, Xi'an Jiaotong Liverpool University, Suzhou, Jiangsu 215123, China
| | - Juan Li
- School of Life Sciences, Peking University, Beijing 100871, China; Department of Health and Environmental Sciences, Xi'an Jiaotong Liverpool University, Suzhou, Jiangsu 215123, China
| | - Xueyang Li
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiang Zhao
- Shan Shui Conservation Center, Beijing 100871, China
| | - Zhi Lu
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China; Center for Nature and Society, School of Life Sciences, Peking University, Beijing 100871, China; Shan Shui Conservation Center, Beijing 100871, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
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4
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Iriart V, Baucom RS, Ashman TL. Interspecific variation in resistance and tolerance to herbicide drift reveals potential consequences for plant community co-flowering interactions and structure at the agro-eco interface. ANNALS OF BOTANY 2022; 130:1015-1028. [PMID: 36415945 PMCID: PMC9851304 DOI: 10.1093/aob/mcac137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS When plant communities are exposed to herbicide 'drift', wherein particles containing the active ingredient travel off-target, interspecific variation in resistance or tolerance may scale up to affect community dynamics. In turn, these alterations could threaten the diversity and stability of agro-ecosystems. We investigated the effects of herbicide drift on the growth and reproduction of 25 wild plant species to make predictions about the consequences of drift exposure on plant-plant interactions and the broader ecological community. METHODS We exposed potted plants from species that commonly occur in agricultural areas to a drift-level dose of the widely used herbicide dicamba or a control solution in the glasshouse. We evaluated species-level variation in resistance and tolerance for vegetative and floral traits. We assessed community-level impacts of drift by comparing the species evenness and flowering networks of glasshouse synthetic communities comprised of drift-exposed and control plants. KEY RESULTS Species varied significantly in resistance and tolerance to dicamba drift: some were negatively impacted while others showed overcompensatory responses. Species also differed in the way they deployed flowers over time following drift exposure. While drift had negligible effects on community evenness based on vegetative biomass, it caused salient differences in the structure of co-flowering networks within communities. Drift reduced the degree and intensity of flowering overlap among species, altered the composition of groups of species that were more likely to co-flower with each other than with others and shifted species roles (e.g. from dominant to inferior floral producers, and vice versa). CONCLUSIONS These results demonstrate that even low levels of herbicide exposure can significantly alter plant growth and reproduction, particularly flowering phenology. If field-grown plants respond similarly, then these changes would probably impact plant-plant competitive dynamics and potentially plant-pollinator interactions occurring within plant communities at the agro-ecological interface.
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Affiliation(s)
- Veronica Iriart
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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5
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Zhang J, Xu J, Tan X, Zhang Q. Nitrogen loadings affect trophic structure in stream food webs on the Tibetan Plateau, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:157018. [PMID: 35772539 DOI: 10.1016/j.scitotenv.2022.157018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Anthropogenic activities, such as agricultural and industrial development, have increased nutrient inputs into waterways, which affect trophic interactions and the flow of energy through food webs in the aquatic ecosystems. However, the responses of food web structure and function to specific anthropogenic stressors in the alpine stream systems remain unclear. Here, we studied the stream food webs in the Lhasa River on the Tibetan Plateau, China. We measured the isotopic ratios (δ13C and δ15N) of macroinvertebrate and fish functional feeding groups (FFGs) and their basal resources in the streams. Dietary contributions of basal resources to consumers and food web metrics including trophic length, diversity, and redundancy were used to quantify changes in stream food webs in response to anthropogenic disturbance. Dietary analysis showed that allochthonous resources contributed more than autochthonous resources to macroinvertebrate primary consumers regardless of the disturbance intensity in the adjacent land areas. Anthropogenic activities increased the δ15N values in epilithic algae and isotopic variation in basal resources and fish but reduced the trophic length and redundancy (i.e., fewer species or taxon at each trophic level) in food webs. Additionally, the total nitrogen concentration in waters was the most important environmental variable affecting trophic diversity and redundancy. Therefore, the reduction of nitrogen inputs into streams is critical for sustainable river management and biodiversity conservation in the streams on the Tibetan Plateau.
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Affiliation(s)
- Jian Zhang
- Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa 850000, Tibet, China; College of Science, Tibet University, Lhasa 850000, Tibet, China; Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan, Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jilei Xu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan, Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiang Tan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan, Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Quanfa Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan, Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
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6
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O'Gorman EJ. Machine learning ecological networks. Science 2022; 377:918-919. [PMID: 36007050 DOI: 10.1126/science.add7563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Deep-learning tools can help to construct historical, modern-day, and future food webs.
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Affiliation(s)
- Eoin J O'Gorman
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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7
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Garrison JA, Nordström MC, Albertsson J, Nascimento FJA. Temporal and spatial changes in benthic invertebrate trophic networks along a taxonomic richness gradient. Ecol Evol 2022; 12:e8975. [PMID: 35784047 PMCID: PMC9168554 DOI: 10.1002/ece3.8975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/31/2022] [Accepted: 05/10/2022] [Indexed: 11/23/2022] Open
Abstract
Species interactions underlie most ecosystem functions and are important for understanding ecosystem changes. Representing one type of species interaction, trophic networks were constructed from biodiversity monitoring data and known trophic links to assess how ecosystems have changed over time. The Baltic Sea is subject to many anthropogenic pressures, and low species diversity makes it an ideal candidate for determining how pressures change food webs. In this study, we used benthic monitoring data for 20 years (1980–1989 and 2010–2019) from the Swedish coast of the Baltic Sea and Skagerrak to investigate changes in benthic invertebrate trophic interactions. We constructed food webs and calculated fundamental food web metrics evaluating network horizontal and vertical diversity, as well as stability that were compared over space and time. Our results show that the west coast of Sweden (Skagerrak) suffered a reduction in benthic invertebrate biodiversity by 32% between the 1980s and 2010s, and that the number of links, generality of predators, and vulnerability of prey have been significantly reduced. The other basins (Bothnian Sea, Baltic Proper, and Bornholm Basin) do not show any significant changes in species richness or consistent significant trends in any food web metrics investigated, demonstrating resilience at a lower species diversity. The decreased complexity of the Skagerrak food webs indicates vulnerability to further perturbations and pressures should be limited as much as possible to ensure continued ecosystem functions.
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Affiliation(s)
- Julie A. Garrison
- Department of Ecology, Environment and Plant Sciences Stockholm University Stockholm Sweden
| | | | - Jan Albertsson
- Umeå Marine Sciences Centre Umeå University Hörnefors Sweden
| | - Francisco J. A. Nascimento
- Department of Ecology, Environment and Plant Sciences Stockholm University Stockholm Sweden
- Baltic Sea Centre Stockholm University Stockholm Sweden
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8
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Rappaport DI, Swain A, Fagan WF, Dubayah R, Morton DC. Animal soundscapes reveal key markers of Amazon forest degradation from fire and logging. Proc Natl Acad Sci U S A 2022; 119:e2102878119. [PMID: 35471905 PMCID: PMC9170030 DOI: 10.1073/pnas.2102878119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 02/24/2022] [Indexed: 11/18/2022] Open
Abstract
Safeguarding tropical forest biodiversity requires solutions for monitoring ecosystem structure over time. In the Amazon, logging and fire reduce forest carbon stocks and alter habitat, but the long-term consequences for wildlife remain unclear, especially for lesser-known taxa. Here, we combined multiday acoustic surveys, airborne lidar, and satellite time series covering logged and burned forests (n = 39) in the southern Brazilian Amazon to identify acoustic markers of forest degradation. Our findings contradict expectations from the Acoustic Niche Hypothesis that animal communities in more degraded habitats occupy fewer “acoustic niches” defined by time and frequency. Instead, we found that aboveground biomass was not a consistent proxy for acoustic biodiversity due to the divergent patterns of “acoustic space occupancy” between logged and burned forests. Ecosystem soundscapes highlighted a stark, and sustained reorganization in acoustic community assembly after multiple fires; animal communication networks were quieter, more homogenous, and less acoustically integrated in forests burned multiple times than in logged or once-burned forests. These findings demonstrate strong biodiversity cobenefits from protecting burned Amazon forests from recurrent fire. By contrast, soundscape changes after logging were subtle and more consistent with acoustic community recovery than reassembly. In both logged and burned forests, insects were the dominant acoustic markers of degradation, particularly during midday and nighttime hours, which are not typically sampled by traditional biodiversity field surveys. The acoustic fingerprints of degradation history were conserved across replicate recording locations, indicating that soundscapes may offer a robust, taxonomically inclusive solution for digitally tracking changes in acoustic community composition over time.
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Affiliation(s)
| | - Anshuman Swain
- Department of Biological Sciences, University of Maryland, College Park, MD 20742
| | - William F. Fagan
- Department of Biological Sciences, University of Maryland, College Park, MD 20742
| | - Ralph Dubayah
- Department of Geographical Sciences, University of Maryland, College Park, MD 20742
| | - Douglas C. Morton
- Department of Geographical Sciences, University of Maryland, College Park, MD 20742
- Biospheric Sciences Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD 20771
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9
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Food web rewiring drives long-term compositional differences and late-disturbance interactions at the community level. Proc Natl Acad Sci U S A 2022; 119:e2117364119. [PMID: 35439049 PMCID: PMC9173581 DOI: 10.1073/pnas.2117364119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Multiple anthropogenic disturbances affect the structure and functioning of communities. Recent evidence highlighted that, after pulse disturbance, the functioning a community performs may be recovered fast due to functional redundancy, whereas community multivariate composition needs a longer time. Yet, the mechanisms that drive the different community recovery times have not been quantified empirically. We use quantitative food-web analysis to assess the influence of species interactions on community recovery. We found species-interactions strength to be the main mechanism driving differences between structural and functional recovery. Additionally, we show that interactions between multiple disturbances appear in the long term only when both species-interaction strength and food-web architecture change significantly. Ecological communities are constantly exposed to multiple natural and anthropogenic disturbances. Multivariate composition (if recovered) has been found to need significantly more time to be regained after pulsed disturbance compared to univariate diversity metrics and functional endpoints. However, the mechanisms driving the different recovery times of communities to single and multiple disturbances remain unexplored. Here, we apply quantitative ecological network analyses to try to elucidate the mechanisms driving long-term community-composition dissimilarity and late-stage disturbance interactions at the community level. For this, we evaluate the effects of two pesticides, nutrient enrichment, and their interactions in outdoor mesocosms containing a complex freshwater community. We found changes in interactions strength to be strongly related to compositional changes and identified postdisturbance interaction-strength rewiring to be responsible for most of the observed compositional changes. Additionally, we found pesticide interactions to be significant in the long term only when both interaction strength and food-web architecture are reshaped by the disturbances. We suggest that quantitative network analysis has the potential to unveil ecological processes that prevent long-term community recovery.
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10
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Bani A, Randall KC, Clark DR, Gregson BH, Henderson DK, Losty EC, Ferguson RM. Mind the gaps: What do we know about how multiple chemical stressors impact freshwater aquatic microbiomes? ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Woodward G, Morris O, Barquín J, Belgrano A, Bull C, de Eyto E, Friberg N, Guðbergsson G, Layer-Dobra K, Lauridsen RB, Lewis HM, McGinnity P, Pawar S, Rosindell J, O’Gorman EJ. Using Food Webs and Metabolic Theory to Monitor, Model, and Manage Atlantic Salmon—A Keystone Species Under Threat. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.675261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Populations of Atlantic salmon are crashing across most of its natural range: understanding the underlying causes and predicting these collapses in time to intervene effectively are urgent ecological and socioeconomic priorities. Current management techniques rely on phenomenological analyses of demographic population time-series and thus lack a mechanistic understanding of how and why populations may be declining. New multidisciplinary approaches are thus needed to capitalize on the long-term, large-scale population data that are currently scattered across various repositories in multiple countries, as well as marshaling additional data to understand the constraints on the life cycle and how salmon operate within the wider food web. Here, we explore how we might combine data and theory to develop the mechanistic models that we need to predict and manage responses to future change. Although we focus on Atlantic salmon—given the huge data resources that already exist for this species—the general principles developed here could be applied and extended to many other species and ecosystems.
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12
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Pozsgai G, Ben Fekih I, Kohnen MV, Amrani S, Bérces S, Fülöp D, Jaber MYM, Meyling NV, Ruszkiewicz-Michalska M, Pfliegler WP, Sánchez-García FJ, Zhang J, Rensing C, Lövei GL, You M. Associations between carabid beetles and fungi in the light of 200 years of published literature. Sci Data 2021; 8:294. [PMID: 34737321 PMCID: PMC8569211 DOI: 10.1038/s41597-021-01072-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 10/08/2021] [Indexed: 12/01/2022] Open
Abstract
Describing and conserving ecological interactions woven into ecosystems is one of the great challenges of the 21st century. Here, we present a unique dataset compiling the biotic interactions between two ecologically and economically important taxa: ground beetles (Coleoptera: Carabidae) and fungi. The resulting dataset contains the carabid-fungus associations collected from 392 scientific publications, 129 countries, mostly from the Palearctic region, published over a period of 200 years. With an updated taxonomy to match the currently accepted nomenclature, 3,378 unique associations among 5,564 records were identified between 1,776 carabid and 676 fungal taxa. Ectoparasitic Laboulbeniales were the most frequent fungal group associated with carabids, especially with Trechinae. The proportion of entomopathogens was low. Three different formats of the data have been provided along with an interactive data digest platform for analytical purposes. Our database summarizes the current knowledge on biotic interactions between insects and fungi, while offering a valuable resource to test large-scale hypotheses on those interactions. Measurement(s) | species associations | Technology Type(s) | digital curation | Factor Type(s) | associations between Carabidae and Fungi | Sample Characteristic - Organism | Carabidae • Fungi • Laboulbeniales | Sample Characteristic - Location | global |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.14602770
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Affiliation(s)
- Gábor Pozsgai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China. .,CE3C - Centre for Ecology, Evolution and Environmental Changes, Azorean Biodiversity Group and Universidade dos Açores, Angra do Heroísmo, 9700-042, Azores, Portugal.
| | - Ibtissem Ben Fekih
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Markus V Kohnen
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Said Amrani
- Laboratoire de Biologie et de Physiologie des Organismes, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediène, BP 32 El Alia, Alger, 16111, Algeria
| | - Sándor Bérces
- Duna-Ipoly National Park Directorate, Költő u. 21, H-1121, Budapest, Hungary.,Juhász-Nagy Pál Doctoral School, University of Debrecen, Egyetem tér 1, H-4032, Debrecen, Hungary
| | - Dávid Fülöp
- Department of Zoology, Plant Protection Institute, Centre for Agricultural Research, Nagykovácsi út 26-30, H-1029, Budapest, Hungary
| | - Mohammed Y M Jaber
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Nicolai Vitt Meyling
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Malgorzata Ruszkiewicz-Michalska
- Department of Algology and Mycology Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, PL-90-237, Łódź, Poland
| | - Walter P Pfliegler
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
| | - Francisco Javier Sánchez-García
- Fujian Provincial Key Laboratory of Insect Ecology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Área de Biología Animal, Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, 30100, Spain
| | - Jie Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Gábor L Lövei
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China.,Department of Agroecology, Aarhus University, Flakkebjerg Research Centre, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China.
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13
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Dash B, Rout SS, Lovaraju A, Charan Kumar B, Bharati A, Ganesh T, Satyanarayana B, Raman AV, Rakhesh M, Raut D. Macrobenthic community of a tropical bay system revisited: Historical changes in response to anthropogenic forcing. MARINE POLLUTION BULLETIN 2021; 171:112775. [PMID: 34375747 DOI: 10.1016/j.marpolbul.2021.112775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
The present study examines historical perspectives of the macrobenthic community in response to different phases of anthropogenic perturbations in Kakinada Bay, a tropical embayment on the east coast of India. Multivariate analysis of the snapshot data (1958-2017) revealed considerable changes in the Bay environment following a breakwater construction across the Bay mouth in 1997. Subsequently, port expansion activities, industrialization, urbanization, and geomorphic alterations in the Godavari delta brought deterrent changes in the Bay. The fluctuations over the years in hydrographical and sediment characteristics increased environmental heterogeneity and caused significant spatio-temporal shifts in the macrobenthic community between 1995-1996 and 2016-2017. The observed variabilities were suggestive of anthropogenic perturbations of the system with future repercussions on Bay ecosystem functioning. Overall, this study provides evidence on the long-term impact of anthropogenic activities on coastal marine communities and stresses the importance of macrobenthos as bioindicators of such changes in tropical systems.
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Affiliation(s)
- Bhagyashree Dash
- Marine Biology Laboratory, Department of Zoology, Andhra University, Visakhapatnam, India; Centre for Excellence in Environment & Public Health, Department of Zoology, Ravenshaw University, Cuttack, India
| | - Sonali Sanghamitra Rout
- Marine Biology Laboratory, Department of Zoology, Andhra University, Visakhapatnam, India; Centre for Excellence in Environment & Public Health, Department of Zoology, Ravenshaw University, Cuttack, India
| | - Avvari Lovaraju
- Marine Biology Laboratory, Department of Zoology, Andhra University, Visakhapatnam, India
| | - Basuri Charan Kumar
- Marine Biology Laboratory, Department of Zoology, Andhra University, Visakhapatnam, India; National Centre for Coastal Research, Ministry of Earth Sciences, Chennai, India
| | - Adapa Bharati
- Marine Biology Laboratory, Department of Zoology, Andhra University, Visakhapatnam, India
| | - Thiruchitrambalam Ganesh
- Department of Ocean Studies and Marine Biology, Pondicherry University, Port Blair, A & N Islands, India
| | - Behara Satyanarayana
- Mangrove Research Unit, Institute of Oceanography and Environment, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Akkur Vasudevan Raman
- Marine Biology Laboratory, Department of Zoology, Andhra University, Visakhapatnam, India
| | - Madhusoodhanan Rakhesh
- Ecosystem Based Management of Marine Resources Programme, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait.
| | - Dipti Raut
- Centre for Excellence in Environment & Public Health, Department of Zoology, Ravenshaw University, Cuttack, India.
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14
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Bloor JMG, Si-Moussi S, Taberlet P, Carrère P, Hedde M. Analysis of complex trophic networks reveals the signature of land-use intensification on soil communities in agroecosystems. Sci Rep 2021; 11:18260. [PMID: 34521879 PMCID: PMC8440573 DOI: 10.1038/s41598-021-97300-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/20/2021] [Indexed: 11/29/2022] Open
Abstract
Increasing evidence suggests that agricultural intensification is a threat to many groups of soil biota, but how the impacts of land-use intensity on soil organisms translate into changes in comprehensive soil interaction networks remains unclear. Here for the first time, we use environmental DNA to examine total soil multi-trophic diversity and food web structure for temperate agroecosystems along a gradient of land-use intensity. We tested for response patterns in key properties of the soil food webs in sixteen fields ranging from arable crops to grazed permanent grasslands as part of a long-term management experiment. We found that agricultural intensification drives reductions in trophic group diversity, although taxa richness remained unchanged. Intensification generally reduced the complexity and connectance of soil interaction networks and induced consistent changes in energy pathways, but the magnitude of management-induced changes depended on the variable considered. Average path length (an indicator of food web redundancy and resilience) did not respond to our management intensity gradient. Moreover, turnover of network structure showed little response to increasing management intensity. Our data demonstrates the importance of considering different facets of trophic networks for a clearer understanding of agriculture-biodiversity relationships, with implications for nature-based solutions and sustainable agriculture.
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Affiliation(s)
- Juliette M G Bloor
- Université Clermont Auvergne, INRAE, VetAgro-Sup, UREP, Clermont-Ferrand, France.
| | - Sara Si-Moussi
- Eco&Sols, Université Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.,Laboratoire d'Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes, Grenoble, France.,Laboratoire TIMC-IMAG, CNRS, Grenoble INP, Université Grenoble Alpes, Grenoble, France
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes, Grenoble, France.,UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | - Pascal Carrère
- Université Clermont Auvergne, INRAE, VetAgro-Sup, UREP, Clermont-Ferrand, France
| | - Mickaël Hedde
- Eco&Sols, Université Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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15
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Windsor FM, Tavella J, Rother DC, Raimundo RLG, Devoto M, Guimarães PR, Evans DM. Identifying plant mixes for multiple ecosystem service provision in agricultural systems using ecological networks. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Fredric M. Windsor
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Julia Tavella
- Facultad de Agronomía Universidad de Buenos Aires Buenos Aires Argentina
| | - Débora C. Rother
- Departamento de Ecologia Universidade de São Paulo São Paulo Brazil
| | - Rafael L. G. Raimundo
- Departamento de Engenharia e Meio Ambiente Universidade Federal da Paraíba Joao Pessoa Brazil
| | - Mariano Devoto
- Facultad de Agronomía Universidad de Buenos Aires Buenos Aires Argentina
| | | | - Darren M. Evans
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
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16
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Patonai K, Jordán F. Integrating trophic data from the literature: The Danube River food web. FOOD WEBS 2021. [DOI: 10.1016/j.fooweb.2021.e00203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Pocock MJO, Schmucki R, Bohan DA. Inferring species interactions from ecological survey data: A mechanistic approach to predict quantitative food webs of seed feeding by carabid beetles. Ecol Evol 2021; 11:12858-12871. [PMID: 34594544 PMCID: PMC8462163 DOI: 10.1002/ece3.8032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/30/2021] [Accepted: 07/24/2021] [Indexed: 11/05/2022] Open
Abstract
Ecological networks are valuable for ecosystem analysis but their use is often limited by a lack of data because many types of ecological interaction, for example, predation, are short-lived and difficult to observe or detect. While there are different methods for inferring the presence of interactions, they have rarely been used to predict the interaction strengths that are required to construct weighted, or quantitative, ecological networks.Here, we develop a trait-based approach suitable for inferring weighted networks, that is, with varying interaction strengths. We developed the method for seed-feeding carabid ground beetles (Coleoptera: Carabidae) although the principles can be applied to other species and types of interaction.Using existing literature data from experimental seed-feeding trials, we predicted a per-individual interaction cost index based on carabid and seed size. This was scaled up to the population level to create inferred weighted networks using the abundance of carabids and seeds from empirical samples and energetic intake rates of carabids from the literature. From these weighted networks, we also derived a novel measure of expected predation pressure per seed type per network.This method was applied to existing ecological survey data from 255 arable fields with carabid data from pitfall traps and plant seeds from seed rain traps. Analysis of these inferred networks led to testable hypotheses about how network structure and predation pressure varied among fields.Inferred networks are valuable because (a) they provide null models for the structuring of food webs to test against empirical species interaction data, for example, DNA analysis of carabid gut regurgitates and (b) they allow weighted networks to be constructed whenever we can estimate interactions between species and have ecological census data available. This permits ecological network analysis even at times and in places when interactions were not directly assessed.
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Affiliation(s)
| | - Reto Schmucki
- UK Centre for Ecology & HydrologyWallingford, OxfordshireUK
| | - David A. Bohan
- Agroécologie, AgroSup DijonINRAE, Université de Bourgogne Franche‐ComtéDijonFrance
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18
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Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
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19
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Sulliván SMP, Bohenek JR, Cáceres C, Pomeroy LW. Multiple urban stressors drive fish-based ecological networks in streams of Columbus, Ohio, USA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:141970. [PMID: 32920387 DOI: 10.1016/j.scitotenv.2020.141970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/11/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
Integrating a network perspective into multiple-stressor research can reveal indirect stressor effects and simultaneously estimate both taxonomic and functional community characteristics, thus representing a novel approach to stressor paradigms in rivers. Using six years of data from twelve streams of Columbus, Ohio, USA, the effects of nutrients (N:P), impervious surface (%IS), and sedimentation on network properties were quantified. Variability in the strength and distribution of trophic interactions was assessed by incorporating biomass into networks. All stressors impacted some properties of network topology - linkage density (average number of links per species), connectance (fraction of all possible links realized in a network), and compartmentalization (degree to which networks contain discrete sub-webs), including synergistic interactive effects between sedimentation and stream size. We also found support for antagonistic effects between (1) sedimentation and %IS and between %IS and N:P on the weighted index mean link weight, which represents the magnitude of trophic interactions among species in a network, and (2) %IS and stream size on strength standard deviation, a measure of the distribution of total magnitude of all trophic interactions per species in a network. Overall, our results point to the potential for urban stressors such as impervious surfaces and sedimentation - alone and as interactions - to decrease network complexity, compartmentalization, and stability, likely through homogenizing habitat and limiting food resources. The observation that larger streams often buffered the negative effects of these stressors suggests that restoration and other management approaches might be most beneficial in smaller headwater streams of urban catchments.
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Affiliation(s)
- S Mažeika Patricio Sulliván
- Olentangy River Wetland Research Park, School of Environment and Natural Resources, The Ohio State University, Columbus, OH 43202, USA.
| | - Jason R Bohenek
- Olentangy River Wetland Research Park, School of Environment and Natural Resources, The Ohio State University, Columbus, OH 43202, USA
| | - Carlos Cáceres
- Olentangy River Wetland Research Park, School of Environment and Natural Resources, The Ohio State University, Columbus, OH 43202, USA
| | - Laura W Pomeroy
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH 43210, USA; Translational Data Analytics Institute, Ohio State University, Columbus, OH 43210, USA
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20
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Gray C, Ma A, McLaughlin O, Petit S, Woodward G, Bohan DA. Ecological plasticity governs ecosystem services in multilayer networks. Commun Biol 2021; 4:75. [PMID: 33462363 PMCID: PMC7813848 DOI: 10.1038/s42003-020-01547-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/30/2020] [Indexed: 11/16/2022] Open
Abstract
Agriculture is under pressure to achieve sustainable development goals for biodiversity and ecosystem services. Services in agro-ecosystems are typically driven by key species, and changes in the community composition and species abundance can have multifaceted effects. Assessment of individual services overlooks co-variance between different, but related, services coupled by a common group of species. This partial view ignores how effects propagate through an ecosystem. We conduct an analysis of 374 agricultural multilayer networks of two related services of weed seed regulation and gastropod mollusc predation delivered by carabid beetles. We found that weed seed regulation increased with the herbivore predation interaction frequency, computed from the network of trophic links between carabids and weed seeds in the herbivore layer. Weed seed regulation and herbivore interaction frequencies declined as the interaction frequencies between carabids and molluscs in the carnivore layer increased. This suggests that carabids can switch to gastropod predation with community change, and that link turnover rewires the herbivore and carnivore network layers affecting seed regulation. Our study reveals that ecosystem services are governed by ecological plasticity in structurally complex, multi-layer networks. Sustainable management therefore needs to go beyond the autecological approaches to ecosystem services that predominate, particularly in agriculture.
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Affiliation(s)
- Clare Gray
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London, E1 4NS, UK
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, UK
| | - Athen Ma
- Queen Mary University of London, School of Electronic Engineering and Computer Science, Mile End Road, London, E1 4NS, UK
| | - Orla McLaughlin
- Agroécologie, AgroSup Dijon, INRAe, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Sandrine Petit
- Agroécologie, AgroSup Dijon, INRAe, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Guy Woodward
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, UK
| | - David A Bohan
- Agroécologie, AgroSup Dijon, INRAe, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France.
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21
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Rhodes OE, Bréchignac F, Bradshaw C, Hinton TG, Mothersill C, Arnone JA, Aubrey DP, Barnthouse LW, Beasley JC, Bonisoli-Alquati A, Boring LR, Bryan AL, Capps KA, Clément B, Coleman A, Condon C, Coutelot F, DeVol T, Dharmarajan G, Fletcher D, Flynn W, Gladfelder G, Glenn TC, Hendricks S, Ishida K, Jannik T, Kapustka L, Kautsky U, Kennamer R, Kuhne W, Lance S, Laptyev G, Love C, Manglass L, Martinez N, Mathews T, McKee A, McShea W, Mihok S, Mills G, Parrott B, Powell B, Pryakhin E, Rypstra A, Scott D, Seaman J, Seymour C, Shkvyria M, Ward A, White D, Wood MD, Zimmerman JK. Integration of ecosystem science into radioecology: A consensus perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 740:140031. [PMID: 32559536 DOI: 10.1016/j.scitotenv.2020.140031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
In the Fall of 2016 a workshop was held which brought together over 50 scientists from the ecological and radiological fields to discuss feasibility and challenges of reintegrating ecosystem science into radioecology. There is a growing desire to incorporate attributes of ecosystem science into radiological risk assessment and radioecological research more generally, fueled by recent advances in quantification of emergent ecosystem attributes and the desire to accurately reflect impacts of radiological stressors upon ecosystem function. This paper is a synthesis of the discussions and consensus of the workshop participant's responses to three primary questions, which were: 1) How can ecosystem science support radiological risk assessment? 2) What ecosystem level endpoints potentially could be used for radiological risk assessment? and 3) What inference strategies and associated methods would be most appropriate to assess the effects of radionuclides on ecosystem structure and function? The consensus of the participants was that ecosystem science can and should support radiological risk assessment through the incorporation of quantitative metrics that reflect ecosystem functions which are sensitive to radiological contaminants. The participants also agreed that many such endpoints exit or are thought to exit and while many are used in ecological risk assessment currently, additional data need to be collected that link the causal mechanisms of radiological exposure to these endpoints. Finally, the participants agreed that radiological risk assessments must be designed and informed by rigorous statistical frameworks capable of revealing the causal inference tying radiological exposure to the endpoints selected for measurement.
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Affiliation(s)
- Olin E Rhodes
- Savannah River Ecology Lab, Drawer E, Aiken, SC 29802, United States of America.
| | - Francois Bréchignac
- Institut de Radioprotection et de Sûreté Nucléaire, International Union of Radioecology, Center of Cadarache, Bldg 159, BP 1, 13115 St Paul-lez-Durance cedex, France
| | - Clare Bradshaw
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Thomas G Hinton
- Institute of Environmental Radioactivity, 1 Kanayagawa, Fukushima University, Fukushima 960-1296, Japan
| | | | - John A Arnone
- Division of Earth and Ecosystem Sciences Desert Research Institute, 2215 Raggio Parkway, Reno, NV 89512, United States of America
| | - Doug P Aubrey
- Savannah River Ecology Lab, Warnell School of Forestry and Natural Resources, Drawer E, Aiken, SC 29802, United States of America
| | - Lawrence W Barnthouse
- LWB Environmental Services, Inc., 1620 New London Rd., Hamilton, OH 45013, United States of America
| | - James C Beasley
- Savannah River Ecology Lab, Warnell School of Forestry and Natural Resources, Drawer E, Aiken, SC 29802, United States of America
| | - Andrea Bonisoli-Alquati
- Department of Biological Sciences, California State Polytechnic University, Pomona, Pomona, CA 91768, United States of America
| | - Lindsay R Boring
- Joseph W. Jones Ecological Research Center, #988 Jones Center Dr., Newton, GA 39870, United States of America
| | - Albert L Bryan
- Savannah River Ecology Lab, Drawer E, Aiken, SC 29802, United States of America
| | - Krista A Capps
- Savannah River Ecology Lab, Drawer E, Aiken, SC 29802, United States of America; Odum School of Ecology, University of Georgia, Athens, GA 30602, United States of America
| | - Bernard Clément
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, F-69518, rue Maurice Audin, Vaulx-en-Velin, France
| | - Austin Coleman
- Savannah River Ecology Lab, Drawer E, Aiken, SC 29802, United States of America
| | - Caitlin Condon
- School of Nuclear Science and Engineering, 100 Radiation Center, Oregon State University, Corvallis, OR 97331, United States of America
| | - Fanny Coutelot
- Environmental Engineering and Earth Sciences, 342 Computer Ct., Clemson University, Clemson, SC 29625, United States of America
| | - Timothy DeVol
- Environmental Engineering and Earth Sciences, 342 Computer Ct., Clemson University, Anderson, SC 29625-6510, United States of America
| | - Guha Dharmarajan
- Savannah River Ecology Lab, Drawer E, Aiken, SC 29802, United States of America
| | - Dean Fletcher
- Savannah River Ecology Lab, Drawer E, Aiken, SC 29802, United States of America
| | - Wes Flynn
- Department of Forestry and Natural Resources, Purdue University, 715 W State Street, West Lafayette, IN 47907, United States of America
| | - Garth Gladfelder
- School of Nuclear Science and Engineering, 100 Radiation Center, Oregon State University, Corvallis, OR 97331, United States of America
| | - Travis C Glenn
- Department of Environmental Health Science, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, United States of America
| | - Susan Hendricks
- Hancock Biological Station, 561 Emma Dr., Murray State University, Murray, KY 42071, United States of America
| | - Ken Ishida
- The University of Tokyo, Yokoze, 6632-12, Yokoze-town, Chichibu-gun, 368-0072, Japan
| | - Tim Jannik
- Savannah River National Laboratory, SRS Bldg. 999-W, Room 312, Aiken, SC 29808, United States of America
| | - Larry Kapustka
- LK Consultancy, P.O Box 373, 100 202 Blacklock Way SW, Turner Valley, Alberta T0L 2A0, Canada
| | - Ulrik Kautsky
- Svensk Kärnbränslehantering AB, PO Box 3091, SE-169 03 Solna, Sweden
| | - Robert Kennamer
- Savannah River Ecology Lab, Drawer E, Aiken, SC 29802, United States of America
| | - Wendy Kuhne
- Savannah River National Laboratory, 735-A, B-102, Aiken, SC 29808, United States of America
| | - Stacey Lance
- Savannah River Ecology Lab, Drawer E, Aiken, SC 29802, United States of America
| | - Gennadiy Laptyev
- Ukrainian HydroMeteorological Institute, 37 Prospekt Nauki, Kiev 02038, Ukraine
| | - Cara Love
- Savannah River Ecology Lab, Drawer E, Aiken, SC 29802, United States of America
| | - Lisa Manglass
- Environmental Engineering and Earth Sciences, 342 Computer Ct., Clemson University, Anderson, SC 29625-6510, United States of America
| | - Nicole Martinez
- Environmental Engineering and Earth Sciences, 342 Computer Ct., Clemson University, Anderson, SC 29625-6510, United States of America
| | - Teresa Mathews
- Oak Ridge National Laboratory, One Bethel Valley Rd., Oak Ridge, TN 37831, United States of America
| | - Arthur McKee
- Flathead Lake Biological Station, 32125 Bio Station Lane, Polson, MT 59860, United States of America
| | - William McShea
- Smithsonian's Conservation Biology Institute, 1500 Remount Rd., Front Royal, VA 22630, United States of America
| | - Steve Mihok
- Canadian Nuclear Safety Commission, P.O. Box 1046, Station B, 280 Slater St., Ottawa, Ontario K1P 5S9, Canada
| | - Gary Mills
- Savannah River Ecology Lab, Drawer E, Aiken, SC 29802, United States of America
| | - Ben Parrott
- Savannah River Ecology Lab, Drawer E, Aiken, SC 29802, United States of America
| | - Brian Powell
- Department of Environmental Engineering and Earth Sciences, 342 Computer Ct., Clemson University, Clemson, SC 29625, United States of America; Savannah River National Laboratory, Aiken, SC 29808, United States of America
| | - Evgeny Pryakhin
- Urals Research Center for Radiation Medicine, Vorovsky Str., 68a, Chelyabinsk 454141, Russia
| | - Ann Rypstra
- Ecology Research Center, Miami University, Oxford, OH 45056, United States of America
| | - David Scott
- Savannah River Ecology Lab, Drawer E, Aiken, SC 29802, United States of America
| | - John Seaman
- Savannah River Ecology Lab, Drawer E, Aiken, SC 29802, United States of America
| | - Colin Seymour
- Dept. of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Maryna Shkvyria
- Kyiv zoological park of national importance, prosp. Peremohy, 32, Kyiv 04116, Ukraine
| | - Amelia Ward
- Department of Biological Sciences, PO Box 870344, University of Alabama, Tuscaloosa, AL 35487, United States of America
| | - David White
- Hancock Biological Station, 561 Emma Dr., Murray State University, Murray, KY 42071, United States of America
| | - Michael D Wood
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT. United Kingdom
| | - Jess K Zimmerman
- University of Puerto Rico, #17 Ave Universidad, San Juan 00925, Puerto Rico
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22
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Pomeranz JPF, Wesner JS, Harding JS. Changes in stream food‐web structure across a gradient of acid mine drainage increase local community stability. Ecology 2020; 101:e03102. [DOI: 10.1002/ecy.3102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 03/09/2020] [Accepted: 04/14/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Justin P. F. Pomeranz
- School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch 8140 New Zealand
| | - Jeff S. Wesner
- Department of Biology University of South Dakota 414 E. Clark Street Vermillion South Dakota 57069 USA
| | - Jon S. Harding
- School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch 8140 New Zealand
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23
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Jackson MC, Fourie HE, Dalu T, Woodford DJ, Wasserman RJ, Zengeya TA, Ellender BR, Kimberg PK, Jordaan MS, Chimimba CT, Weyl OLF. Food web properties vary with climate and land use in South African streams. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13601] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Michelle C. Jackson
- Department of Zoology University of Oxford Oxford UK
- Imperial College London, Silwood Park Campus Ascot UK
- Centre for Invasion Biology (CIB), Department of Zoology and Entomology University of Pretoria Pretoria South Africa
| | - Hermina E. Fourie
- Centre for Invasion Biology (CIB), Department of Zoology and Entomology University of Pretoria Pretoria South Africa
| | - Tatenda Dalu
- Department of Ecology and Resource Management University of Venda Thohoyandou South Africa
- South African Institute for Aquatic Biodiversity (SAIAB) Makhanda South Africa
| | - Darragh J. Woodford
- South African Institute for Aquatic Biodiversity (SAIAB) Makhanda South Africa
- Centre for Invasion Biology (CIB), School of Animal, Plant and Environmental Sciences University of the Witwatersand Johannesburg South Africa
| | - Ryan J. Wasserman
- South African Institute for Aquatic Biodiversity (SAIAB) Makhanda South Africa
- Department of Zoology and Entomology Rhodes University Makhanda South Africa
| | - Tsungai A. Zengeya
- Centre for Invasion Biology (CIB), Department of Zoology and Entomology University of Pretoria Pretoria South Africa
- South African National Biodiversity Institute (SANBI) Kirstenbosch Research Centre Cape Town South Africa
| | - Bruce R. Ellender
- South African Institute for Aquatic Biodiversity (SAIAB) Makhanda South Africa
- Upper Zambezi Programme World Wide Fund For Nature Lusaka Zambia
| | | | - Martine S. Jordaan
- South African Institute for Aquatic Biodiversity (SAIAB) Makhanda South Africa
- CapeNature Biodiversity Capabilities Unit Stellenbosch South Africa
- Centre for Invasion Biology (CIB) University of Stellenbosch Stellenbosch South Africa
| | - Christian T. Chimimba
- Centre for Invasion Biology (CIB), Department of Zoology and Entomology University of Pretoria Pretoria South Africa
| | - Olaf L. F. Weyl
- DSI/NRF Research Chair in Inland Fisheries and Freshwater Ecology South African Institute for Aquatic Biodiversity (SAIAB) Makhanda South Africa
- Department of Ichthyology and Fisheries Science Rhodes University Makhanda South Africa
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24
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Terry JCD, Lewis OT. Finding missing links in interaction networks. Ecology 2020; 101:e03047. [PMID: 32219855 DOI: 10.1002/ecy.3047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 02/05/2020] [Accepted: 02/24/2020] [Indexed: 12/22/2022]
Abstract
Documenting which species interact within ecological communities is challenging and labor intensive. As a result, many interactions remain unrecorded, potentially distorting our understanding of network structure and dynamics. We test the utility of four structural models and a new coverage-deficit model for predicting missing links in both simulated and empirical bipartite networks. We find they can perform well, although the predictive power of structural models varies with the underlying network structure. The accuracy of predictions can be improved by ensembling multiple models. Augmenting observed networks with most-likely missing links improves estimates of qualitative network metrics. Tools to identify likely missing links can be simple to implement, allowing the prioritization of research effort and more robust assessment of network properties.
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Affiliation(s)
| | - Owen T Lewis
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
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25
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DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness. Proc Natl Acad Sci U S A 2020; 117:8539-8545. [PMID: 32217735 PMCID: PMC7165428 DOI: 10.1073/pnas.1918741117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The complexity and natural variability of ecosystems present a challenge for reliable detection of change due to anthropogenic influences. This issue is exacerbated by necessary trade-offs that reduce the quality and resolution of survey data for assessments at large scales. The Peace-Athabasca Delta (PAD) is a large inland wetland complex in northern Alberta, Canada. Despite its geographic isolation, the PAD is threatened by encroachment of oil sands mining in the Athabasca watershed and hydroelectric dams in the Peace watershed. Methods capable of reliably detecting changes in ecosystem health are needed to evaluate and manage risks. Between 2011 and 2016, aquatic macroinvertebrates were sampled across a gradient of wetland flood frequency, applying both microscope-based morphological identification and DNA metabarcoding. By using multispecies occupancy models, we demonstrate that DNA metabarcoding detected a much broader range of taxa and more taxa per sample compared to traditional morphological identification and was essential to identifying significant responses to flood and thermal regimes. We show that family-level occupancy masks high variation among genera and quantify the bias of barcoding primers on the probability of detection in a natural community. Interestingly, patterns of community assembly were nearly random, suggesting a strong role of stochasticity in the dynamics of the metacommunity. This variability seriously compromises effective monitoring at local scales but also reflects resilience to hydrological and thermal variability. Nevertheless, simulations showed the greater efficiency of metabarcoding, particularly at a finer taxonomic resolution, provided the statistical power needed to detect change at the landscape scale.
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26
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Compson ZG, Monk WA, Hayden B, Bush A, O'Malley Z, Hajibabaei M, Porter TM, Wright MTG, Baker CJO, Al Manir MS, Curry RA, Baird DJ. Network-Based Biomonitoring: Exploring Freshwater Food Webs With Stable Isotope Analysis and DNA Metabarcoding. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00395] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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27
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Zhang X. Environmental DNA Shaping a New Era of Ecotoxicological Research. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:5605-5612. [PMID: 31009204 DOI: 10.1021/acs.est.8b06631] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Aquatic ecosystems, such as rivers and lakes, are exposed to multiple stressors from anthropogenic activity and changes in climate, which have resulted in a general decrease in biodiversity, alteration of community structures, and can ultimately result in reduction of resources provided by natural ecosystems. Adverse outcomes caused by pollutants to ecosystems are determined not only by toxic properties but also ecological contexts of ecosystems, including indigenous biodiversity and community composition. It is therefore important to identify key factors, such as diversity of species and traits that determine the vulnerability of structures and functions of ecosystems in response to toxic substances. Detection and quantification of biodiversity and its activities using environmental DNA (eDNA) is arguably one of the most important technical advances in ecology in recent years. A huge opportunity has appeared to allow more relevant approaches for assessments of risks posed to ecosystems by toxic substances. eDNA approaches provide effective and efficient tools to evaluate the effects of chemical pollutants on (1) the occurrences and population of wildlife, (2) communities, and (3) the function of ecosystem in the field. Here a conceptual framework of adverse outcome pathways to relate molecular initiating events to apical ecosystem-level responses is proposed to connecting laboratory-based prediction to observations under field conditions. Particularly, future research opportunities on effects on biodiversity, community structure, and ecosystem function by toxic substances will be discussed.
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Affiliation(s)
- Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment , Nanjing University , Nanjing 210023 , China
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28
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Maloney EM. How do we take the pulse of an aquatic ecosystem? Current and historical approaches to measuring ecosystem integrity. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2019; 38:289-301. [PMID: 30387526 DOI: 10.1002/etc.4308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/23/2018] [Accepted: 10/31/2018] [Indexed: 06/08/2023]
Abstract
Global environmental monitoring has indicated that the structure and function of some aquatic ecosystems has been significantly altered by human activities. There are many potential causes for these changes; however, one major concern is the increasing release of anthropogenic contaminants into aquatic environments. Although toxicological responses of individual organisms are typically well characterized, few studies have focused on characterizing toxicity at the ecosystem level. In fact, because of their scale and complexity, changes in ecosystem integrity are rarely considered in assessments of risks to ecosystems. This work attempts to move the conversation forward by defining integrity of ecosystems, reviewing current and historical approaches to measuring ecosystem integrity status (e.g., structural and functional measurements), and highlighting methods that could significantly contribute to the field of ecosystem toxicology (e.g., keystone species, environmental energetics, ecotoxicological modeling, and adverse outcome pathways [AOPs]). Through a critical analysis of current and historical methodologies, the present study offers a comprehensive, conceptual framework for the assessment of risks of contaminant exposure for whole ecosystems and proposes steps to facilitate better diagnoses of the integrity of aquatic systems. Environ Toxicol Chem 2019;38:289-301. © 2018 SETAC.
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Affiliation(s)
- Erin M Maloney
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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29
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Pomeranz JPF, Thompson RM, Poisot T, Harding JS. Inferring predator–prey interactions in food webs. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13125] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Ross M. Thompson
- Institute for Applied Ecology University of Canberra Bruce ACT Australia
| | - Timothée Poisot
- Département de Sciences Biologiques Université de Montréal Montréal QC Canada
| | - Jon S. Harding
- School of Biological Sciences University of Canterbury Christchurch New Zealand
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30
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Redhead JW, Woodcock BA, Pocock MJ, Pywell RF, Vanbergen AJ, Oliver TH. Potential landscape-scale pollinator networks across Great Britain: structure, stability and influence of agricultural land cover. Ecol Lett 2018; 21:1821-1832. [DOI: 10.1111/ele.13157] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/12/2018] [Accepted: 08/08/2018] [Indexed: 01/25/2023]
Affiliation(s)
- John W. Redhead
- NERC Centre for Ecology and Hydrology; Maclean Building Wallingford Oxfordshire OX108BB UK
- School of Biological Sciences; University of Reading; Harborne Building Reading Berkshire RG6 6AS UK
| | - Ben A. Woodcock
- NERC Centre for Ecology and Hydrology; Maclean Building Wallingford Oxfordshire OX108BB UK
| | - Michael J.O. Pocock
- NERC Centre for Ecology and Hydrology; Maclean Building Wallingford Oxfordshire OX108BB UK
| | - Richard F. Pywell
- NERC Centre for Ecology and Hydrology; Maclean Building Wallingford Oxfordshire OX108BB UK
| | - Adam J. Vanbergen
- NERC Centre for Ecology and Hydrology; Bush Estate Penicuik Midlothian EH26 0QB UK
- Agroécologie, AgroSup Dijon, INRA; Univ. Bourgogne Franche-Comté; F-21000 Dijon France
| | - Tom H. Oliver
- NERC Centre for Ecology and Hydrology; Maclean Building Wallingford Oxfordshire OX108BB UK
- School of Biological Sciences; University of Reading; Harborne Building Reading Berkshire RG6 6AS UK
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31
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Hansen AG, Gardner JR, Connelly KA, Polacek M, Beauchamp DA. Trophic compression of lake food webs under hydrologic disturbance. Ecosphere 2018. [DOI: 10.1002/ecs2.2304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Adam G. Hansen
- Colorado Parks and Wildlife 317 West Prospect Road Fort Collins Colorado 80526 USA
| | - Jennifer R. Gardner
- Washington Cooperative Fish and Wildlife Research Unit School of Aquatic and Fishery Sciences University of Washington Box 355020 Seattle Washington 98195 USA
| | - Kristin A. Connelly
- Washington Cooperative Fish and Wildlife Research Unit School of Aquatic and Fishery Sciences University of Washington Box 355020 Seattle Washington 98195 USA
| | - Matt Polacek
- Washington Department of Fish and Wildlife 317 ½ North Pearl Street, Suite 7 Ellensburg Washington 98926 USA
| | - David A. Beauchamp
- US Geological Survey Western Fisheries Research Center 6505 Northeast 65th Street Seattle Washington 98115 USA
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32
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Biomonitoring for the 21st Century: Integrating Next-Generation Sequencing Into Ecological Network Analysis. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2017.12.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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33
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Linking DNA Metabarcoding and Text Mining to Create Network-Based Biomonitoring Tools: A Case Study on Boreal Wetland Macroinvertebrate Communities. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2018.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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34
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Ma A, Bohan DA, Canard E, Derocles SA, Gray C, Lu X, Macfadyen S, Romero GQ, Kratina P. A Replicated Network Approach to ‘Big Data’ in Ecology. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2018.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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35
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Pearson CE, Symondson WOC, Clare EL, Ormerod SJ, Iparraguirre Bolaños E, Vaughan IP. The effects of pastoral intensification on the feeding interactions of generalist predators in streams. Mol Ecol 2017; 27:590-602. [PMID: 29219224 PMCID: PMC5887918 DOI: 10.1111/mec.14459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 10/10/2017] [Accepted: 11/08/2017] [Indexed: 12/29/2022]
Abstract
Land‐use change can alter trophic interactions with wide‐ranging functional consequences, yet the consequences for aquatic food webs have been little studied. In part, this may reflect the challenges of resolving the diets of aquatic organisms using classical gut contents analysis, especially for soft‐bodied prey. We used next‐generation sequencing to resolve prey use in nearly 400 individuals of two predatory invertebrates (the Caddisfly, Rhyacophila dorsalis, and the Stonefly Dinocras cephalotes) in streams draining land with increasingly intensive livestock farming. Rhyacophila dorsalis occurred in all streams, whereas D. cephalotes was restricted to low intensities, allowing us to test whether: (i) apparent sensitivity to agriculture in the latter species reflects a more specialized diet and (ii) diet in R. dorsalis varied between sites with and without D. cephalotes. DNA was extracted from dissected gut contents, amplified without blocking probes and sequenced using Ion Torrent technology. Both predators were generalists, consuming 30 prey taxa with a preference for taxa that were abundant in all streams or that increased with intensification. Where both predators were present, their diets were nearly identical, and R. dorsalis's diet was virtually unchanged in the absence of D. cephalotes. The loss of D. cephalotes from more intensive sites was probably due to physicochemical stressors, such as sedimentation, rather than to dietary specialization, although wider biotic factors (e.g., competition with other predatory taxa) could not be excluded. This study provides a uniquely detailed description of predator diets along a land‐use intensity gradient, offering new insights into how anthropogenic stressors affect stream communities.
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Affiliation(s)
- C E Pearson
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - W O C Symondson
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - E L Clare
- School of Biological and Chemical Sciences, Queen Mary University, London, UK
| | - S J Ormerod
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - E Iparraguirre Bolaños
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK.,Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country, Bilbao, Spain
| | - I P Vaughan
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
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36
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Farnsworth KD, Albantakis L, Caruso T. Unifying concepts of biological function from molecules to ecosystems. OIKOS 2017. [DOI: 10.1111/oik.04171] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | | | - Tancredi Caruso
- Queen's Univ. Belfast, MBC; 97 Lisburn Road, Belfast, BT97BL UK
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37
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Pálinkás Z, Kiss J, Zalai M, Szénási Á, Dorner Z, North S, Woodward G, Balog A. Effects of genetically modified maize events expressing Cry34Ab1, Cry35Ab1, Cry1F, and CP4 EPSPS proteins on arthropod complex food webs. Ecol Evol 2017; 7:2286-2293. [PMID: 28405292 PMCID: PMC5383485 DOI: 10.1002/ece3.2848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/16/2017] [Accepted: 02/07/2017] [Indexed: 11/21/2022] Open
Abstract
Four genetically modified (GM) maize (Zea mays L.) hybrids (coleopteran resistant, coleopteran and lepidopteran resistant, lepidopteran resistant and herbicide tolerant, coleopteran and herbicide tolerant) and its non-GM control maize stands were tested to compare the functional diversity of arthropods and to determine whether genetic modifications alter the structure of arthropods food webs. A total number of 399,239 arthropod individuals were used for analyses. The trophic groups' number and the links between them indicated that neither the higher magnitude of Bt toxins (included resistance against insect, and against both insects and glyphosate) nor the extra glyphosate treatment changed the structure of food webs. However, differences in the average trophic links/trophic groups were detected between GM and non-GM food webs for herbivore groups and plants. Also, differences in characteristic path lengths between GM and non-GM food webs for herbivores were observed. Food webs parameterized based on 2-year in-field assessments, and their properties can be considered a useful and simple tool to evaluate the effects of Bt toxins on non-target organisms.
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Affiliation(s)
- Zoltán Pálinkás
- Institute of Plant ProtectionFaculty of Agriculture and Environmental SciencesSzent István UniversityGödöllőHungary
| | - József Kiss
- Institute of Plant ProtectionFaculty of Agriculture and Environmental SciencesSzent István UniversityGödöllőHungary
| | - Mihály Zalai
- Institute of Plant ProtectionFaculty of Agriculture and Environmental SciencesSzent István UniversityGödöllőHungary
| | - Ágnes Szénási
- Institute of Plant ProtectionFaculty of Agriculture and Environmental SciencesSzent István UniversityGödöllőHungary
| | - Zita Dorner
- Institute of Plant ProtectionFaculty of Agriculture and Environmental SciencesSzent István UniversityGödöllőHungary
| | - Samuel North
- Faculty of Natural SciencesDepartment of Life SciencesImperial College LondonLondonUnited Kingdom
| | - Guy Woodward
- Faculty of Natural SciencesDepartment of Life SciencesImperial College LondonLondonUnited Kingdom
| | - Adalbert Balog
- Department of HorticultureFaculty of Technical and Human ScienceSapientia Hungarian University of TransylvaniaCluj NapocaRomania
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38
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Naman SM, Greene CM, Rice CA, Chamberlin J, Conway-Cranos L, Cordell JR, Hall JE, Rhodes LD. Stable isotope-based trophic structure of pelagic fish and jellyfish across natural and anthropogenic landscape gradients in a fjord estuary. Ecol Evol 2016; 6:8159-8173. [PMID: 27878085 PMCID: PMC5108267 DOI: 10.1002/ece3.2450] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/08/2016] [Accepted: 08/12/2016] [Indexed: 11/23/2022] Open
Abstract
Identifying causes of structural ecosystem shifts often requires understanding trophic structure, an important determinant of energy flow in ecological communities. In coastal pelagic ecosystems worldwide, increasing jellyfish (Cnidaria and Ctenophora) at the expense of small fish has been linked to anthropogenic alteration of basal trophic pathways. However, this hypothesis remains untested in part because baseline description of fish–jellyfish trophic dynamics, and the environmental features that influence them are lacking. Using stable isotopes of carbon (δ13C) and nitrogen (δ15N), we examined spatiotemporal patterns of fish and jellyfish trophic structure in greater Puget Sound, an urbanizing fjord estuary in the NW United States. We quantified niche positions of constituent species, niche widths and trophic overlap between fish and jellyfish assemblages, and several community‐level trophic diversity metrics (resource diversity, trophic length, and niche widths) of fish and jellyfish combined. We then related assemblage‐ and community‐level measures to landscape gradients of terrestrial–marine connectivity and anthropogenic influence in adjacent catchments. Relative niche positions among species varied considerably and displayed no clear pattern except that fish generally had higher δ15N and lower δ13C relative to jellyfish, which resulted in low assemblage‐level trophic overlap. Fish assemblages had larger niche widths than jellyfish in most cases and, along with whole community trophic diversity, exhibited contrasting seasonal patterns across oceanographic basins, which was positively correlated to landscape variation in terrestrial connectivity. In contrast, jellyfish niche widths were unrelated to terrestrial connectivity, but weakly negatively correlated to urban land use in adjacent catchments. Our results indicate that fish–jellyfish trophic structure is highly heterogeneous and that disparate processes may underlie the trophic ecology of these taxa; consequently, they may respond divergently to environmental change. In addition, spatiotemporal variation in ecosystem connectivity, in this case through freshwater influence, may influence trophic structure across heterogeneous landscapes.
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Affiliation(s)
- Sean M Naman
- Department of Zoology University of British Columbia Vancouver BC Canada
| | | | - Casimir A Rice
- NOAA Fisheries Mukilteo Research Station Mukilteo WA USA
| | | | - Letitia Conway-Cranos
- NOAA Fisheries Northwest Fisheries Science Center Seattle WA USA; Present address: Washington Department of Fish and Wildlife Habitat Program Olympia WA USA
| | - Jeffery R Cordell
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - Jason E Hall
- NOAA Fisheries Northwest Fisheries Science Center Seattle WA USA
| | - Linda D Rhodes
- NOAA Fisheries Northwest Fisheries Science Center Seattle WA USA
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39
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Hajibabaei M, Baird DJ, Fahner NA, Beiko R, Golding GB. A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150330. [PMID: 27481782 PMCID: PMC4971182 DOI: 10.1098/rstb.2015.0330] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2016] [Indexed: 01/10/2023] Open
Abstract
Encompassing the breadth of biodiversity in biomonitoring programmes has been frustrated by an inability to simultaneously identify large numbers of species accurately and in a timely fashion. Biomonitoring infers the state of an ecosystem from samples collected and identified using the best available taxonomic knowledge. The advent of DNA barcoding has now given way to the extraction of bulk DNA from mixed samples of organisms in environmental samples through the development of high-throughput sequencing (HTS). This DNA metabarcoding approach allows an unprecedented view of the true breadth and depth of biodiversity, but its adoption poses two important challenges. First, bioinformatics techniques must simultaneously perform complex analyses of large datasets and translate the results of these analyses to a range of users. Second, the insights gained from HTS need to be amalgamated with concepts such as Linnaean taxonomy and indicator species, which are less comprehensive but more intuitive. It is clear that we are moving beyond proof-of-concept studies to address the challenge of implementation of this new approach for environmental monitoring and regulation. Interpreting Darwin's 'tangled bank' through a DNA lens is now a reality, but the question remains: how can this information be generated and used reliably, and how does it relate to accepted norms in ecosystem study?This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
- Mehrdad Hajibabaei
- Centre for Biodiversity Genomics @ Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Ontario, Canada N1G 2W1
| | - Donald J Baird
- Environment and Climate Change Canada @ Canadian Rivers Institute, University of New Brunswick, 10 Bailey Drive, PO Box 4400, Fredericton, New Brunswick, Canada E3B 5A3
| | - Nicole A Fahner
- Centre for Biodiversity Genomics @ Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Ontario, Canada N1G 2W1
| | - Robert Beiko
- Faculty of Computer Science, Dalhousie University, 6050 University Avenue, PO Box 15000, Halifax, Nova Scotia, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
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40
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Grechi L, Franco A, Palmeri L, Pivato A, Barausse A. An ecosystem model of the lower Po river for use in ecological risk assessment of xenobiotics. Ecol Modell 2016. [DOI: 10.1016/j.ecolmodel.2016.03.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Bongiorni L, Fiorentino F, Auriemma R, Aubry FB, Camatti E, Camin F, Nasi F, Pansera M, Ziller L, Grall J. Food web of a confined and anthropogenically affected coastal basin (the Mar Piccolo of Taranto) revealed by carbon and nitrogen stable isotopes analyses. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:12725-12738. [PMID: 26381790 DOI: 10.1007/s11356-015-5380-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/07/2015] [Indexed: 06/05/2023]
Abstract
Carbon and nitrogen stable isotope analysis was used to examine the food web of the Mar Piccolo of Taranto, a coastal basin experiencing several anthropogenic impacts. Main food sources (algal detritus, seaweeds, particulate organic matter (POM) and sediment organic matter (SOM)) and benthic and pelagic consumers were collected during two contrasting seasons (June and April), at four sites distributed over two inlets, and characterized by different level of confinements, anthropogenic inputs and the presence of mussels farming. δ(13)C values of organic sources revealed an important contribution of POM to both planktonic and benthic pathways, as well as the influence of terrigenous inputs within both inlets, probably due to high seasonal land runoff. Although δ(13)C of both sources and consumers varied little between sampling sites and dates, δ(15)N spatial variability was higher and clearly reflected the organic enrichment in the second inlet as well as the uptake of anthropogenically derived material by benthic consumers. On the other hand, within the first inlet, the isotopic composition of consumers did not change in response to chemical contamination. However, the impact of polluted sediments near the Navy Arsenal in the first inlet was detectable at the level of the macrobenthic trophic structure, showing high dominance of motile, upper level consumers capable to face transient conditions and the reduction of the more resident deposit feeders. We therefore underline the great potential of matching stable isotope analysis with quantitative studies of community structure to assess the effects of multiple anthropogenic stressors.
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Affiliation(s)
- Lucia Bongiorni
- Istituto di Scienze Marine - Consiglio Nazionale delle Ricerche (ISMAR - CNR), Arsenale - Tesa 104, Castello 2737/F, 30122, Venezia, Italy.
| | - Federica Fiorentino
- Istituto di Scienze Marine - Consiglio Nazionale delle Ricerche (ISMAR - CNR), Arsenale - Tesa 104, Castello 2737/F, 30122, Venezia, Italy
| | - Rocco Auriemma
- OGS (Istituto Nazionale di Oceanografia e Geofisica Sperimentale di Oceanografia), Sezione Oceanografia, Via A. Piccard 54, 34151, Trieste, Italy
| | - Fabrizio Bernardi Aubry
- Istituto di Scienze Marine - Consiglio Nazionale delle Ricerche (ISMAR - CNR), Arsenale - Tesa 104, Castello 2737/F, 30122, Venezia, Italy
| | - Elisa Camatti
- Istituto di Scienze Marine - Consiglio Nazionale delle Ricerche (ISMAR - CNR), Arsenale - Tesa 104, Castello 2737/F, 30122, Venezia, Italy
| | - Federica Camin
- Piattaforma Isotopi Stabili e Tracciabilità, Dipartimento Qualità Alimentare e Nutrizione, Fondazione E. Mach - Istituto Agrario di San Michele all'Adige, Via Mach 1, 38010 San Michele all'Adige, Trento, Italy
| | - Federica Nasi
- OGS (Istituto Nazionale di Oceanografia e Geofisica Sperimentale di Oceanografia), Sezione Oceanografia, Via A. Piccard 54, 34151, Trieste, Italy
| | - Marco Pansera
- Istituto di Scienze Marine - Consiglio Nazionale delle Ricerche (ISMAR - CNR), Arsenale - Tesa 104, Castello 2737/F, 30122, Venezia, Italy
| | - Luca Ziller
- Piattaforma Isotopi Stabili e Tracciabilità, Dipartimento Qualità Alimentare e Nutrizione, Fondazione E. Mach - Istituto Agrario di San Michele all'Adige, Via Mach 1, 38010 San Michele all'Adige, Trento, Italy
| | - Jacques Grall
- Observatoire, Séries Faune-Flore, UMS 3113 CNRS, Institut Universitaire Européen de la Mer, rue Dumont d'Urville, 29280, Plouzané, France
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McMeans BC, McCann KS, Tunney TD, Fisk AT, Muir AM, Lester N, Shuter B, Rooney N. The adaptive capacity of lake food webs: from individuals to ecosystems. ECOL MONOGR 2016. [DOI: 10.1890/15-0288.1] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Bailey C. McMeans
- Department of Integrative Biology; University of Guelph; Guelph Ontario N1G 2W1 Canada
| | - Kevin S. McCann
- Department of Integrative Biology; University of Guelph; Guelph Ontario N1G 2W1 Canada
| | - Tyler D. Tunney
- Center for Limnology; University of Wisconsin-Madison; Madison Wisconsin 53706 USA
| | - Aaron T. Fisk
- Great Lakes Institute for Environmental Research; University of Windsor; Windsor Ontario N9B 3P4 Canada
| | - Andrew M. Muir
- Great Lakes Fisheries Commission; Ann Arbor Michigan 48105 USA
| | - Nigel Lester
- Harkness Laboratory of Fisheries Research; Aquatic Research and Monitoring Section; Ontario Ministry of Natural Resources; Peterborough Ontario K9J 7B8 Canada
| | - Brian Shuter
- Harkness Laboratory of Fisheries Research; Aquatic Research and Monitoring Section; Ontario Ministry of Natural Resources; Peterborough Ontario K9J 7B8 Canada
| | - Neil Rooney
- School of Environmental Sciences; University of Guelph; Guelph Ontario N1G 2W1 Canada
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Gray C, Hildrew A, Lu X, Ma A, McElroy D, Monteith D, O’Gorman E, Shilland E, Woodward G. Recovery and Nonrecovery of Freshwater Food Webs from the Effects of Acidification. ADV ECOL RES 2016. [DOI: 10.1016/bs.aecr.2016.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Pocock MJ, Evans DM, Fontaine C, Harvey M, Julliard R, McLaughlin Ó, Silvertown J, Tamaddoni-Nezhad A, White PC, Bohan DA. The Visualisation of Ecological Networks, and Their Use as a Tool for Engagement, Advocacy and Management. ADV ECOL RES 2016. [DOI: 10.1016/bs.aecr.2015.10.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Schuwirth N, Dietzel A, Reichert P. The importance of biotic interactions for the prediction of macroinvertebrate communities under multiple stressors. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12605] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nele Schuwirth
- Eawag: Swiss Federal Institute of Aquatic Science and Technology Ueberlandstrasse 133, P.O.Box 611 CH‐8600 Dübendorf Switzerland
| | - Anne Dietzel
- Eawag: Swiss Federal Institute of Aquatic Science and Technology Ueberlandstrasse 133, P.O.Box 611 CH‐8600 Dübendorf Switzerland
| | - Peter Reichert
- Eawag: Swiss Federal Institute of Aquatic Science and Technology Ueberlandstrasse 133, P.O.Box 611 CH‐8600 Dübendorf Switzerland
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Lindenmayer D, Pierson J, Barton P, Beger M, Branquinho C, Calhoun A, Caro T, Greig H, Gross J, Heino J, Hunter M, Lane P, Longo C, Martin K, McDowell WH, Mellin C, Salo H, Tulloch A, Westgate M. A new framework for selecting environmental surrogates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 538:1029-1038. [PMID: 26298409 DOI: 10.1016/j.scitotenv.2015.08.056] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/11/2015] [Accepted: 08/11/2015] [Indexed: 06/04/2023]
Abstract
Surrogate concepts are used in all sub-disciplines of environmental science. However, controversy remains regarding the extent to which surrogates are useful for resolving environmental problems. Here, we argue that conflicts about the utility of surrogates (and the related concepts of indicators and proxies) often reflect context-specific differences in trade-offs between measurement accuracy and practical constraints. By examining different approaches for selecting and applying surrogates, we identify five trade-offs that correspond to key points of contention in the application of surrogates. We then present an 8-step Adaptive Surrogacy Framework that incorporates cross-disciplinary perspectives from a wide spectrum of the environmental sciences, aiming to unify surrogate concepts across disciplines and applications. Our synthesis of the science of surrogates is intended as a first step towards fully leveraging knowledge accumulated across disciplines, thus consolidating lessons learned so that they may be accessible to all those operating in different fields, yet facing similar hurdles.
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Affiliation(s)
- David Lindenmayer
- Fenner School of Environment and Society, The Australian National University, 141 Linnaeus Way, Acton, ACT 2601, Australia.
| | - Jennifer Pierson
- Fenner School of Environment and Society, The Australian National University, 141 Linnaeus Way, Acton, ACT 2601, Australia
| | - Philip Barton
- Fenner School of Environment and Society, The Australian National University, 141 Linnaeus Way, Acton, ACT 2601, Australia
| | - Maria Beger
- Centre for Biodiversity and Conservation Science, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Cristina Branquinho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Bloco C2, 1749-016 Lisboa, Portugal
| | - Aram Calhoun
- Department of Wildlife, Fisheries, and Conservation Biology, University of Maine, Orono, ME, USA
| | - Tim Caro
- Department of Wildlife, Fish and Conservation Biology, University of California, Davis, CA 95616, USA
| | - Hamish Greig
- School of Biology and Ecology, University of Maine, Orono, ME, USA
| | - John Gross
- Climate Change Response Program, United States National Park Service, 1201 Oakridge Drive, Fort Collins, CO 80525, USA
| | - Jani Heino
- Finnish Environment Institute, Natural Environment Centre, Biodiversity, P.O. Box 413, FI-90014 Oulu, Finland
| | - Malcolm Hunter
- Department of Wildlife, Fisheries, and Conservation Biology, University of Maine, Orono, ME, USA
| | - Peter Lane
- Fenner School of Environment and Society, The Australian National University, 141 Linnaeus Way, Acton, ACT 2601, Australia
| | - Catherine Longo
- National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, CA, USA
| | - Kathy Martin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - William H McDowell
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA
| | - Camille Mellin
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Hanna Salo
- Department of Geography and Geology, University of Turku, Turku Finland
| | - Ayesha Tulloch
- Fenner School of Environment and Society, The Australian National University, 141 Linnaeus Way, Acton, ACT 2601, Australia
| | - Martin Westgate
- Fenner School of Environment and Society, The Australian National University, 141 Linnaeus Way, Acton, ACT 2601, Australia
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Joining the dots: An automated method for constructing food webs from compendia of published interactions. FOOD WEBS 2015. [DOI: 10.1016/j.fooweb.2015.09.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Gibson JF, Shokralla S, Curry C, Baird DJ, Monk WA, King I, Hajibabaei M. Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing. PLoS One 2015; 10:e0138432. [PMID: 26488407 PMCID: PMC4619546 DOI: 10.1371/journal.pone.0138432] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 08/29/2015] [Indexed: 01/18/2023] Open
Abstract
Biodiversity metrics are critical for assessment and monitoring of ecosystems threatened by anthropogenic stressors. Existing sorting and identification methods are too expensive and labour-intensive to be scaled up to meet management needs. Alternately, a high-throughput DNA sequencing approach could be used to determine biodiversity metrics from bulk environmental samples collected as part of a large-scale biomonitoring program. Here we show that both morphological and DNA sequence-based analyses are suitable for recovery of individual taxonomic richness, estimation of proportional abundance, and calculation of biodiversity metrics using a set of 24 benthic samples collected in the Peace-Athabasca Delta region of Canada. The high-throughput sequencing approach was able to recover all metrics with a higher degree of taxonomic resolution than morphological analysis. The reduced cost and increased capacity of DNA sequence-based approaches will finally allow environmental monitoring programs to operate at the geographical and temporal scale required by industrial and regulatory end-users.
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Affiliation(s)
- Joel F Gibson
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada; Environment Canada, Canada Centre for Inland Waters, Burlington, Ontario, Canada
| | - Shadi Shokralla
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Colin Curry
- Environment Canada, Canadian Rivers Institute, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Donald J Baird
- Environment Canada, Canadian Rivers Institute, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Wendy A Monk
- Canadian Rivers Institute, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Ian King
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Mehrdad Hajibabaei
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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