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Tiegs SD, Capps KA, Costello DM, Schmidt JP, Patrick CJ, Follstad Shah JJ, LeRoy CJ. Human activities shape global patterns of decomposition rates in rivers. Science 2024; 384:1191-1195. [PMID: 38815088 DOI: 10.1126/science.adn1262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/09/2024] [Indexed: 06/01/2024]
Abstract
Rivers and streams contribute to global carbon cycling by decomposing immense quantities of terrestrial plant matter. However, decomposition rates are highly variable and large-scale patterns and drivers of this process remain poorly understood. Using a cellulose-based assay to reflect the primary constituent of plant detritus, we generated a predictive model (81% variance explained) for cellulose decomposition rates across 514 globally distributed streams. A large number of variables were important for predicting decomposition, highlighting the complexity of this process at the global scale. Predicted cellulose decomposition rates, when combined with genus-level litter quality attributes, explain published leaf litter decomposition rates with high accuracy (70% variance explained). Our global map provides estimates of rates across vast understudied areas of Earth and reveals rapid decomposition across continental-scale areas dominated by human activities.
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Affiliation(s)
- S D Tiegs
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - K A Capps
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA
| | - D M Costello
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - J P Schmidt
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - C J Patrick
- Virginia Institute of Marine Science, Coastal Ocean Processes Section, William & Mary, Gloucester Point, VA 23062, USA
| | - J J Follstad Shah
- School of the Environment, Society, and Sustainability, University of Utah, Salt Lake City, UT 84112, USA
| | - C J LeRoy
- Environmental Studies Program, The Evergreen State College, Olympia, WA 98505, USA
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2
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Zhang M, Zou Y, Xiao S, Hou J. Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects. MARINE POLLUTION BULLETIN 2023; 194:115430. [PMID: 37647798 DOI: 10.1016/j.marpolbul.2023.115430] [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: 04/23/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
Marine and freshwater biodiversity is under threat from both natural and manmade causes. Biological monitoring is currently a top priority for biodiversity protection. Given present limitations, traditional biological monitoring methods may not achieve the proposed monitoring aims. Environmental DNA metabarcoding technology reflects species information by capturing and extracting DNA from environmental samples, using molecular biology techniques to sequence and analyze the DNA, and comparing the obtained information with existing reference libraries to obtain species identification. However, its practical application has highlighted several limitations. This paper summarizes the main steps in the environmental application of eDNA metabarcoding technology in aquatic ecosystems, including the discovery of unknown species, the detection of invasive species, and evaluations of biodiversity. At present, with the rapid development of big data and artificial intelligence, certain advanced technologies and devices can be combined with environmental DNA metabarcoding technology to promote further development of aquatic species monitoring and management.
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Affiliation(s)
- Miaolian Zhang
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yingtong Zou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Xiao
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Jing Hou
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
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3
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von Gönner J, Bowler DE, Gröning J, Klauer AK, Liess M, Neuer L, Bonn A. Citizen science for assessing pesticide impacts in agricultural streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159607. [PMID: 36273564 DOI: 10.1016/j.scitotenv.2022.159607] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
The majority of central European streams are in poor ecological condition. Pesticide inputs from terrestrial habitats present a key threat to sensitive insects in streams. Both standardized stream monitoring data and societal support are needed to conserve and restore freshwater habitats. Citizen science (CS) offers potential to complement international freshwater monitoring while it is often viewed critically due to concerns about data accuracy. Here, we developed a CS program based on the Water Framework Directive that enables citizen scientists to provide data on stream hydromorphology, physicochemical status and benthic macroinvertebrates to apply the trait-based bio-indicator SPEARpesticides for pesticide exposure. We compared CS monitoring data with professional data across 28 central German stream sites and could show that both CS and professional monitoring identified a similar average proportion of pesticide-sensitive macroinvertebrate taxa per stream site (20 %). CS data were highly correlated to the professional data for both stream hydromorphology and SPEARpesticides (r = 0.72 and 0.76). To assess the extent to which CS macroinvertebrate data can indicate pesticide exposure, we tested the relationship of CS generated SPEARpesticides values and measured pesticide concentrations at 21 stream sites, and found a fair correlation similar to professional results. We conclude that given appropriate training and support, citizen scientists can generate valid data on the ecological status and pesticide contamination of streams. By complementing official monitoring, data from well-managed CS programs can advance freshwater science and enhance the implementation of freshwater conservation goals.
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Affiliation(s)
- Julia von Gönner
- Helmholtz Centre for Environmental Research - UFZ, Department Ecosystem Services, Permoserstr. 15, 04318 Leipzig, Germany; Friedrich Schiller University Jena, Institute of Biodiversity, Dornburgerstr.159, 07743 Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany.
| | - Diana E Bowler
- Friedrich Schiller University Jena, Institute of Biodiversity, Dornburgerstr.159, 07743 Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany; UK Centre for Ecology & Hydrology, Benson Lane, Wallingford OX10 8BB, UK
| | - Jonas Gröning
- Helmholtz Centre for Environmental Research - UFZ, Department System-Ecotoxicology, Permoserstr. 15, 04318 Leipzig, Germany
| | - Anna-Katharina Klauer
- Saxony State Foundation for Nature and the Environment (LaNU), Riesaer Str. 7, 01129 Dresden, Germany
| | - Matthias Liess
- Helmholtz Centre for Environmental Research - UFZ, Department System-Ecotoxicology, Permoserstr. 15, 04318 Leipzig, Germany
| | - Lilian Neuer
- Friends of the Earth Germany e.V. (BUND), Kaiserin-Augusta-Allee 5, 10553 Berlin, Germany
| | - Aletta Bonn
- Helmholtz Centre for Environmental Research - UFZ, Department Ecosystem Services, Permoserstr. 15, 04318 Leipzig, Germany; Friedrich Schiller University Jena, Institute of Biodiversity, Dornburgerstr.159, 07743 Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany
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4
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Mancuso J, Messick E, Tiegs SD. Parsing spatial and temporal variation in stream ecosystem functioning. Ecosphere 2022. [DOI: 10.1002/ecs2.4202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Jasmine Mancuso
- Department of Biological Sciences Oakland University Rochester Michigan USA
| | - Emily Messick
- Department of Biological Sciences Oakland University Rochester Michigan USA
| | - Scott D. Tiegs
- Department of Biological Sciences Oakland University Rochester Michigan USA
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5
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Combining DNA and people power for healthy rivers: Implementing the STREAM community-based approach for global freshwater monitoring. Perspect Ecol Conserv 2021. [DOI: 10.1016/j.pecon.2021.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Jackson MC, Pawar S, Woodward G. The Temporal Dynamics of Multiple Stressor Effects: From Individuals to Ecosystems. Trends Ecol Evol 2021; 36:402-410. [DOI: 10.1016/j.tree.2021.01.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 12/30/2022]
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7
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Zhang Y, Leung JYS, Zhang Y, Cai Y, Zhang Z, Li K. Agricultural activities compromise ecosystem health and functioning of rivers: Insights from multivariate and multimetric analyses of macroinvertebrate assemblages. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 275:116655. [PMID: 33618216 DOI: 10.1016/j.envpol.2021.116655] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 01/26/2021] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Agricultural activities often lead to nutrient enrichment and habitat modification in rivers, possibly altering macroinvertebrate assemblages and hence ecosystem functioning. For the sake of environmental management and conservation, therefore, assessing the impacts of agricultural activities becomes indispensable, especially when these activities are predicted to be intensified in the future. In this study, the plain river network in the Lake Chaohu Basin was chosen to examine how agricultural activities influence the functioning of rivers by assessing land use, water quality, habitat condition and macroinvertebrate assemblages, followed by calculating the macroinvertebrate-based multimetric index (MMI) to indicate overall ecosystem health of the rivers. We found that agricultural activities lowered the diversity of macroinvertebrates (e.g. total number of taxa and Simpson index) primarily due to elevated ammonium concentrations in water and reduced microhabitat types, thereby impairing the habitat integrity and nutrient cycling of rivers. The macroinvertebrate-based MMI was positively correlated with increasing habitat quality but negatively with increasing nutrient concentrations, suggesting its high reliability for indicating the impacts of agricultural activities, which was further substantiated by classification and regression tree (CART) analysis. We recommend analyzing macroinvertebrate assemblages using both multivariate and multimetric approaches to offer a more comprehensive evaluation of the impacts of agricultural activities on ecosystem health. Some environmental (CODMn, NH4+-N and PO43--P) and biological parameters (total number of taxa), however, can be used as good proxies for MMI, when time and resources for gathering information to develop MMI are limited.
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Affiliation(s)
- You Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Jonathan Y S Leung
- Southern Seas Ecology Laboratories, The Environment Institute, School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Faculty of Materials and Energy, Southwest University, Chongqing, 400715, PR China
| | - Ying Zhang
- Water Resources Planning Bureau of Jiangsu Province, Nanjing, 210029, PR China
| | - Yongjiu Cai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Zhiming Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Kuanyi Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, PR China.
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8
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Abstract
Riparian zones form a boundary between aquatic and terrestrial ecosystems, with disproportionate influences on food web dynamics and ecosystem functioning in both habitats. However, riparian boundaries are frequently degraded by human activities, including urbanization, leading to direct impacts on terrestrial communities and indirect changes that are mediated through altered connectivity with adjacent aquatic ecosystems. We investigated how riparian habitat influences fish communities in an urban context. We electrofished nine urban site pairs with and without forested riparian buffers, alongside an additional 12 sites that were located throughout the river networks in the Oslo Fjord basin, Norway. Brown trout (Salmo trutta) were the dominant fish species. Riparian buffers had weak positive effects on fish densities at low to moderate levels of catchment urbanization, whereas fish were absent from highly polluted streams. Subtle shifts in fish size distributions suggested that riparian buffers play an important role in metapopulation dynamics. Stable isotopes in fish from buffered reaches indicated dietary shifts, pointing to the potential for a greater reliance on terrestrial-sourced carbon. Combining these results, we postulate that spatially-mediated ontogenetic diet shifts may be important for the persistence of brown trout in urban streams. Our results show that using a food web perspective is essential in understanding how riparian buffers can offset impacts in urban catchments.
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9
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Baker NJ, Pilotto F, Jourdan J, Beudert B, Haase P. Recovery from air pollution and subsequent acidification masks the effects of climate change on a freshwater macroinvertebrate community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143685. [PMID: 33288265 DOI: 10.1016/j.scitotenv.2020.143685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/30/2020] [Accepted: 11/07/2020] [Indexed: 06/12/2023]
Abstract
Freshwater ecosystems are dynamic, complex systems with a multitude of physical and ecological processes and stressors which drive fluctuations on the community-level. Disentangling the effects of different processes and stressors is challenging due to their interconnected nature. However, as protected areas (i.e. national parks) are less anthropogenically impacted, they are ideal for investigating single stressors. We focus on the Bavarian Forest National Park, a Long-Term Ecological Research (LTER) site in Germany, where the major stressors are climate warming, air pollution (i.e. acidification) and bark beetle infestations. We investigated the effects of these stressors on freshwater macroinvertebrates using comprehensive long-term (1983-2014) datasets comprising high-resolution macroinvertebrate and physico-chemical data from a near-natural stream. Macroinvertebrate communities have undergone substantial changes over the past 32 years, highlighted by increases in overall community abundance (+173%) and richness (+51.6%) as well as taxonomic restructuring driven by a disproportional increase of dipterans. Prior to the year 2000, regression analyses revealed a decline in sulphate deposition and subsequent recovery from historical acidification as potential drivers of the increases in abundance and richness rather than to increases in water temperature (1.5 °C overall increase). Post 2000, however, alterations to nutrient cycling caused by bark beetle infestations coupled with warming temperatures were correlated to taxonomic restructuring and disproportional increases of dipterans at the expense of sensitive taxa such as plecopterans and trichopterans. Our results highlight the challenges when investigating the effects of climate change within a multi-stressor context. Even in conservation areas, recovery from previous disturbance might mask the effects of ongoing disturbances like climate change. Overall, we observed strong community restructuring, demonstrating that stenothermal headwater communities face additional stress due to emerging competition with tolerant taxa. Conservation efforts should consider the temporal variability of communities and their recovery from disturbances to adequately identify species vulnerable to local or widespread extinction.
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Affiliation(s)
- Nathan Jay Baker
- Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.
| | - Francesca Pilotto
- Environmental Archaeology Lab, Department of Historical, Philosophical and Religious Studies, Umeå University, Umeå, Sweden
| | - Jonas Jourdan
- Department of Aquatic Ecotoxicology, Johann Wolfgang Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Burkhard Beudert
- Department of Conservation and Research, Bavarian Forest National Park, Grafenau, Germany
| | - Peter Haase
- Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany; Faculty of Biology, University of Duisburg-Essen, Essen, Germany
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10
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Organic Matter Decomposition and Ecosystem Metabolism as Tools to Assess the Functional Integrity of Streams and Rivers–A Systematic Review. WATER 2020. [DOI: 10.3390/w12123523] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Streams and rivers provide important services to humans, and therefore, their ecological integrity should be a societal goal. Although ecological integrity encompasses structural and functional integrity, stream bioassessment rarely considers ecosystem functioning. Organic matter decomposition and ecosystem metabolism are prime candidate indicators of stream functional integrity, and here we review each of these functions, the methods used for their determination, and their strengths and limitations for bioassessment. We also provide a systematic review of studies that have addressed organic matter decomposition (88 studies) and ecosystem metabolism (50 studies) for stream bioassessment since the year 2000. Most studies were conducted in temperate regions. Bioassessment based on organic matter decomposition mostly used leaf litter in coarse-mesh bags, but fine-mesh bags were also common, and cotton strips and wood were frequent in New Zealand. Ecosystem metabolism was most often based on the open-channel method and used a single-station approach. Organic matter decomposition and ecosystem metabolism performed well at detecting environmental change (≈75% studies), with performances varying between 50 and 100% depending on the type of environmental change; both functions were sensitive to restoration practices in 100% of the studies examined. Finally, we provide examples where functional tools are used to complement the assessments of stream ecological integrity. With this review, we hope to facilitate the widespread incorporation of ecosystem processes into bioassessment programs with the broader aim of more effectively managing stream and river ecosystems.
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11
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Rwenzori Score (RS): A Benthic Macroinvertebrate Index for Biomonitoring Rivers and Streams in the Rwenzori Region, Uganda. SUSTAINABILITY 2020. [DOI: 10.3390/su122410473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Rwenzori region in Uganda, a global biodiversity hotspot, is currently undergoing exponential economic and population growth, which puts continuous stress on its freshwater ecosystems. In Sub-Saharan Africa, biomonitoring campaigns using region-specific biotic indices is limited, particularly in Uganda. In this research, we present the Rwenzori Score (RS), a new macroinvertebrate-based biotic index developed to specifically assess the aquatic health of Rwenzori streams and rivers. We collected and measured both biological and physicochemical variables and identified 34,202 macroinvertebrates, belonging to 64 different taxa. The RS was developed in two steps. First, using canonical ordination, we identified chemical variables that correlated significantly with gradients in macroinvertebrate assemblage distribution and diversity. Second, based on selected variables and weighted averages, we determined specific family indicator values and assigned pollution tolerance values (varying from 1: tolerant; to 10: sensitive) to a family. Finally, we established four water quality classes: poor, fair, good, and excellent. The RS is highly correlated with the Average Score Per Taxon System (p < 0.05), a well-known and widely used biotic index. The RS has 5 unique taxa that are not included in other regional indices. In this regard, the development of the RS is a beneficial tool for tailor-made biomonitoring that can contribute to the sustainable development of the Rwenzori stream and river basins.
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12
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Martins FMS, Porto M, Feio MJ, Egeter B, Bonin A, Serra SRQ, Taberlet P, Beja P. Modelling technical and biological biases in macroinvertebrate community assessment from bulk preservative using multiple metabarcoding markers. Mol Ecol 2020; 30:3221-3238. [PMID: 32860303 PMCID: PMC8359330 DOI: 10.1111/mec.15620] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 01/05/2023]
Abstract
DNA metabarcoding from the ethanol used to store macroinvertebrate bulk samples is a convenient methodological option in molecular biodiversity assessment and biomonitoring of aquatic ecosystems, as it preserves specimens and reduces problems associated with sample sorting. However, this method may be affected by errors and biases, which need to be thoroughly quantified before it can be mainstreamed into biomonitoring programmes. Here, we used 80 unsorted macroinvertebrate samples collected in Portugal under a Water Framework Directive monitoring programme, to compare community diversity and taxonomic composition metrics estimated through morphotaxonomy versus metabarcoding from storage ethanol using three markers (COI‐M19BR2, 16S‐Inse01 and 18S‐Euka02) and a multimarker approach. A preliminary in silico analysis showed that the three markers were adequate for the target taxa, with detection failures related primarily to the lack of adequate barcodes in public databases. Metabarcoding of ethanol samples retrieved far less taxa per site (alpha diversity) than morphotaxonomy, albeit with smaller differences for COI‐M19BR2 and the multimarker approach, while estimates of taxa turnover (beta diversity) among sites were similar across methods. Using generalized linear mixed models, we found that after controlling for differences in read coverage across samples, the probability of detection of a taxon was positively related to its proportional abundance, and negatively so to the presence of heavily sclerotized exoskeleton (e.g., Coleoptera). Overall, using our experimental protocol with different template dilutions, the COI marker showed the best performance, but we recommend the use of a multimarker approach to detect a wider range of taxa in freshwater macroinvertebrate samples. Further methodological development and optimization efforts are needed to reduce biases associated with body armouring and rarity in some macroinvertebrate taxa.
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Affiliation(s)
- Filipa M S Martins
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, Portugal
| | - Miguel Porto
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, Portugal.,CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Maria J Feio
- Departamento de Ciência da Vida, Centro de Ciências do Mar e do Ambiente, MARE, Universidade de Coimbra, Coimbra, Portugal
| | - Bastian Egeter
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, Portugal
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes, Grenoble, France
| | - Sónia R Q Serra
- Departamento de Ciência da Vida, Centro de Ciências do Mar e do Ambiente, MARE, Universidade de Coimbra, Coimbra, Portugal
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes, Grenoble, France.,Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Pedro Beja
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, Portugal.,CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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13
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Macher JN, Drakou K, Papatheodoulou A, Hoorn BVD, Vasquez M. The mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus. METABARCODING AND METAGENOMICS 2020. [DOI: 10.3897/mbmg.4.58259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aquatic macroinvertebrates are often identified, based on morphology, but molecular approaches like DNA barcoding, metabarcoding and metagenomics are increasingly used for species identification. These approaches require the availability of DNA references deposited in public databases. Here we report the mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus, a European Union island country in the Mediterranean. Only three species could be provisionally assigned to a binomial species name, highlighting the current lack of molecular references for aquatic macroinvertebrates from Cyprus.
Graphical Abstract
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14
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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: 2.2] [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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15
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Mansfeldt C, Deiner K, Mächler E, Fenner K, Eggen RIL, Stamm C, Schönenberger U, Walser JC, Altermatt F. Microbial community shifts in streams receiving treated wastewater effluent. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 709:135727. [PMID: 31887504 DOI: 10.1016/j.scitotenv.2019.135727] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/22/2019] [Accepted: 11/22/2019] [Indexed: 05/17/2023]
Abstract
Wastewater treatment plant (WWTP) effluents release not only chemical constituents in watersheds, but also contain microorganisms. Thus, an understanding of what microorganisms are released and how they change microbial communities within natural streams is needed. To characterize the community shifts in streams receiving WWTP effluent, we sampled water-column microorganisms from upstream, downstream, and the effluent of WWTPs located on 23 headwater streams in which no other effluent was released upstream. We characterized the bacterial community by sequencing the V3-V4 region of the 16S rRNA gene. We hypothesized that the downstream community profile would be a hydraulic mixture between the two sources (i.e., upstream and effluent). In ordination analyses, the downstream bacterial community profile was a mixture between the upstream and effluent. For 14 of the sites, the main contribution (>50%) to the downstream community originated from bacteria in the WWTP effluent and significant shifts in relative abundance of specific sequence variants were detected. These shifts in sequence variants may serve as general bioindicators of wastewater-effluent influenced streams, with a human-gut related Ruminococcus genus displaying the highest shift (30-fold higher abundances downstream). However, not all taxa composition changes were predicted based on hydraulic mixing alone. Specifically, the decrease of Cyanobacteria/Chloroplast reads was not adequately described by hydraulic mixing. The potential alteration of stream microbial communities via a high inflow of human-gut related bacteria and a decrease in autotrophic functional groups resulting from WWTP effluent creates the potential for general shifts in stream ecosystem function.
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Affiliation(s)
- Cresten Mansfeldt
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Kristy Deiner
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Natural History Museum London, London, UK.
| | - Elvira Mächler
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Kathrin Fenner
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Department of Environmental Systems Science, ETH, Zürich, Switzerland; Chemistry Department, University of Zürich, Zürich, Switzerland
| | - Rik I L Eggen
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Department of Environmental Systems Science, ETH, Zürich, Switzerland
| | - Christian Stamm
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Urs Schönenberger
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | | | - Florian Altermatt
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
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16
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Altermatt F, Little CJ, Mächler E, Wang S, Zhang X, Blackman RC. Uncovering the complete biodiversity structure in spatial networks: the example of riverine systems. OIKOS 2020. [DOI: 10.1111/oik.06806] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Florian Altermatt
- Eawag, Swiss Federal Inst. of Aquatic Science and Technology, Dept of Aquatic Ecology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
| | - Chelsea J. Little
- Eawag, Swiss Federal Inst. of Aquatic Science and Technology, Dept of Aquatic Ecology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
| | - Elvira Mächler
- Eawag, Swiss Federal Inst. of Aquatic Science and Technology, Dept of Aquatic Ecology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
| | - Shaopeng Wang
- Inst. of Ecology, College of Urban and Environmental Science, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking Univ. Beijing PR China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing Univ. Nanjing PR China
| | - Rosetta C. Blackman
- Eawag, Swiss Federal Inst. of Aquatic Science and Technology, Dept of Aquatic Ecology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
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17
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Simons AL, Mazor R, Theroux S. Using co-occurrence network topology in assessing ecological stress in benthic macroinvertebrate communities. Ecol Evol 2019; 9:12789-12801. [PMID: 31788214 PMCID: PMC6875672 DOI: 10.1002/ece3.5751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 11/10/2022] Open
Abstract
Ecological monitoring of streams has often focused on assessing the biotic integrity of individual benthic macroinvertebrate (BMI) communities through local measures of diversity, such as taxonomic or functional richness. However, as individual BMI communities are frequently linked by a variety of ecological processes at a regional scale, there is a need to assess biotic integrity of groups of communities at the scale of watersheds. Using 4,619 sampled communities of streambed BMIs, we investigate this question using co-occurrence networks generated from groups of communities selected within California watersheds under different levels of stress due to upstream land use. Building on a number of arguments in theoretical ecology and network theory, we propose a framework for the assessment of the biotic integrity of watershed-scale groupings of BMI communities using measures of their co-occurrence network topology. We found significant correlations between stress, as described by a mean measure of upstream land use within a watershed, and topological measures of co-occurrence networks such as network size (r = -.81, p < 10-4), connectance (r = .31, p < 10-4), mean co-occurrence strength (r = .25, p < 10-4), degree heterogeneity (r = -.10, p < 10-4), and modularity (r = .11, p < 10-4). Using these five topological measures, we constructed a linear model of biotic integrity, here a composite of taxonomic and functional diversity known as the California Stream Condition Index, of groups of BMI communities within a watershed. This model can account for 66% of among-watershed variation in the mean biotic integrity of communities. These observations imply a role for co-occurrence networks in assessing the current status of biotic integrity for BMI communities, as well as their potential use in assessing other ecological communities.
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Affiliation(s)
- Ariel Levi Simons
- Dornsife College of Letters, Arts and SciencesUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Raphael Mazor
- Southern California Coastal Water Research ProjectCosta MesaCalifornia
| | - Susanna Theroux
- Southern California Coastal Water Research ProjectCosta MesaCalifornia
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18
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Giakoumis T, Voulvoulis N. Water Framework Directive programmes of measures: Lessons from the 1st planning cycle of a catchment in England. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 668:903-916. [PMID: 30870756 DOI: 10.1016/j.scitotenv.2019.01.405] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
The European Union's Water Framework Directive (WFD) required Member States to establish programmes of measures to achieve good water status formally by 2015, but on postponing the deadline by two six-year periods, by 2027 at the latest. With many Member States facing problems with developing such measures in the first planning cycle, and limited change in ecological status since the first river basin management plans were reported, we look at the implementation of the Directive in England, where only 17% of the surface water bodies were found at good status in 2015, a reduction of 4% since 2009. Using as a case study the Broadland Rivers catchment, we examine the measures taken for Cycle 1 and changes in the classifications of water body status, to investigate whether the way the measures were developed could have limited their potential to deliver WFD objectives. While the WFD was adopted to succeed and replace management practices targeting individually non-compliant element, findings indicate that little had changed in the way measures were developed. Although considerable progress has been made on the implementation of these measures, the limited progress in improving classifications demonstrates the limits of this approach and further makes the case for what the WFD was introduced for: the harmonised transposition of the Integrated River Basin Management paradigm, as the key for delivering good ecological status.
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Affiliation(s)
- T Giakoumis
- Centre for Environmental Policy, Imperial College London, London SW7 2AZ, United Kingdom
| | - N Voulvoulis
- Centre for Environmental Policy, Imperial College London, London SW7 2AZ, United Kingdom.
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19
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Simons AL, Mazor R, Stein ED, Nuzhdin S. Using alpha, beta, and zeta diversity in describing the health of stream-based benthic macroinvertebrate communities. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01896. [PMID: 31051052 DOI: 10.1002/eap.1896] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/08/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Ecological monitoring of streams has frequently focused on measures describing the taxonomic, and sometimes functional, α diversity of benthic macroinvertebrates (BMIs) within a single sampled community. However, as many ecological processes effectively link BMI stream communities there is a need to describe groups of communities using measures of regional diversity. Here we demonstrate a role for incorporating both a traditional pairwise measure of community turnover, β diversity, in assessing community health as well as ζ diversity, a more generalized framework for describing similarity between multiple communities. Using 4,395 samples of BMI stream communities in California, we constructed a model using measures of α, β, and ζ diversity, which accounted for 71.7% of among-watershed variation in the mean health of communities, as described by the California Streams Condition Index (CSCI). We also investigated the use of ζ diversity in assessing models of stochastic vs. niche assembly across communities of BMIs within watersheds, with the niche assembly model found to be the likelier of the two.
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Affiliation(s)
- Ariel Levi Simons
- Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, 90089-2910, USA
| | - Raphael Mazor
- Southern California Coastal Water Research Project, 3535 Harbor Blvd., Suite 110, Costa Mesa, California, 92626, USA
| | - Eric D Stein
- Southern California Coastal Water Research Project, 3535 Harbor Blvd., Suite 110, Costa Mesa, California, 92626, USA
| | - Sergey Nuzhdin
- Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, 90089-2910, USA
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20
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Tiegs SD, Costello DM, Isken MW, Woodward G, McIntyre PB, Gessner MO, Chauvet E, Griffiths NA, Flecker AS, Acuña V, Albariño R, Allen DC, Alonso C, Andino P, Arango C, Aroviita J, Barbosa MVM, Barmuta LA, Baxter CV, Bell TDC, Bellinger B, Boyero L, Brown LE, Bruder A, Bruesewitz DA, Burdon FJ, Callisto M, Canhoto C, Capps KA, Castillo MM, Clapcott J, Colas F, Colón-Gaud C, Cornut J, Crespo-Pérez V, Cross WF, Culp JM, Danger M, Dangles O, de Eyto E, Derry AM, Villanueva VD, Douglas MM, Elosegi A, Encalada AC, Entrekin S, Espinosa R, Ethaiya D, Ferreira V, Ferriol C, Flanagan KM, Fleituch T, Follstad Shah JJ, Frainer Barbosa A, Friberg N, Frost PC, Garcia EA, García Lago L, García Soto PE, Ghate S, Giling DP, Gilmer A, Gonçalves JF, Gonzales RK, Graça MAS, Grace M, Grossart HP, Guérold F, Gulis V, Hepp LU, Higgins S, Hishi T, Huddart J, Hudson J, Imberger S, Iñiguez-Armijos C, Iwata T, Janetski DJ, Jennings E, Kirkwood AE, Koning AA, Kosten S, Kuehn KA, Laudon H, Leavitt PR, Lemes da Silva AL, Leroux SJ, LeRoy CJ, Lisi PJ, MacKenzie R, Marcarelli AM, Masese FO, McKie BG, Oliveira Medeiros A, Meissner K, Miliša M, Mishra S, Miyake Y, Moerke A, Mombrikotb S, Mooney R, Moulton T, Muotka T, Negishi JN, Neres-Lima V, Nieminen ML, Nimptsch J, Ondruch J, Paavola R, Pardo I, Patrick CJ, Peeters ETHM, Pozo J, Pringle C, Prussian A, Quenta E, Quesada A, Reid B, Richardson JS, Rigosi A, Rincón J, Rîşnoveanu G, Robinson CT, Rodríguez-Gallego L, Royer TV, Rusak JA, Santamans AC, Selmeczy GB, Simiyu G, Skuja A, Smykla J, Sridhar KR, Sponseller R, Stoler A, Swan CM, Szlag D, Teixeira-de Mello F, Tonkin JD, Uusheimo S, Veach AM, Vilbaste S, Vought LBM, Wang CP, Webster JR, Wilson PB, Woelfl S, Xenopoulos MA, Yates AG, Yoshimura C, Yule CM, Zhang YX, Zwart JA. Global patterns and drivers of ecosystem functioning in rivers and riparian zones. SCIENCE ADVANCES 2019; 5:eaav0486. [PMID: 30662951 PMCID: PMC6326750 DOI: 10.1126/sciadv.aav0486] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/29/2018] [Indexed: 05/17/2023]
Abstract
River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.
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21
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Reid AJ, Carlson AK, Creed IF, Eliason EJ, Gell PA, Johnson PTJ, Kidd KA, MacCormack TJ, Olden JD, Ormerod SJ, Smol JP, Taylor WW, Tockner K, Vermaire JC, Dudgeon D, Cooke SJ. Emerging threats and persistent conservation challenges for freshwater biodiversity. Biol Rev Camb Philos Soc 2018; 94:849-873. [PMID: 30467930 DOI: 10.1111/brv.12480] [Citation(s) in RCA: 825] [Impact Index Per Article: 117.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 12/19/2022]
Abstract
In the 12 years since Dudgeon et al. (2006) reviewed major pressures on freshwater ecosystems, the biodiversity crisis in the world's lakes, reservoirs, rivers, streams and wetlands has deepened. While lakes, reservoirs and rivers cover only 2.3% of the Earth's surface, these ecosystems host at least 9.5% of the Earth's described animal species. Furthermore, using the World Wide Fund for Nature's Living Planet Index, freshwater population declines (83% between 1970 and 2014) continue to outpace contemporaneous declines in marine or terrestrial systems. The Anthropocene has brought multiple new and varied threats that disproportionately impact freshwater systems. We document 12 emerging threats to freshwater biodiversity that are either entirely new since 2006 or have since intensified: (i) changing climates; (ii) e-commerce and invasions; (iii) infectious diseases; (iv) harmful algal blooms; (v) expanding hydropower; (vi) emerging contaminants; (vii) engineered nanomaterials; (viii) microplastic pollution; (ix) light and noise; (x) freshwater salinisation; (xi) declining calcium; and (xii) cumulative stressors. Effects are evidenced for amphibians, fishes, invertebrates, microbes, plants, turtles and waterbirds, with potential for ecosystem-level changes through bottom-up and top-down processes. In our highly uncertain future, the net effects of these threats raise serious concerns for freshwater ecosystems. However, we also highlight opportunities for conservation gains as a result of novel management tools (e.g. environmental flows, environmental DNA) and specific conservation-oriented actions (e.g. dam removal, habitat protection policies, managed relocation of species) that have been met with varying levels of success. Moving forward, we advocate hybrid approaches that manage fresh waters as crucial ecosystems for human life support as well as essential hotspots of biodiversity and ecological function. Efforts to reverse global trends in freshwater degradation now depend on bridging an immense gap between the aspirations of conservation biologists and the accelerating rate of species endangerment.
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Affiliation(s)
- Andrea J Reid
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, K1S 5B6, Canada
| | - Andrew K Carlson
- Center for Systems Integration and Sustainability, Department of Fisheries and Wildlife and Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Irena F Creed
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, S7N 5C8, Canada
| | - Erika J Eliason
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93117, U.S.A
| | - Peter A Gell
- School of Life and Health Sciences, University Drive, Federation University Australia, Mount Helen, 3350, Australia
| | - Pieter T J Johnson
- Ecology & Evolutionary Biology, University of Colorado, Boulder, CO 80309, U.S.A
| | - Karen A Kidd
- Department of Biology and School of Geography and Earth Sciences, McMaster University, Hamilton, L8S 4K1, Canada
| | - Tyson J MacCormack
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, E4L 1G8, Canada
| | - Julian D Olden
- School of Aquatic and Fishery Science, University of Washington, Seattle, WA 98195-5020, U.S.A
| | - Steve J Ormerod
- Water Research Institute & School of Biosciences, Cardiff University, Cardiff, CF10 3AX, U.K
| | - John P Smol
- Paleoecological Environmental Assessment and Research Lab (PEARL), Department of Biology, Queen's University, Kingston, K7L 3N6, Canada
| | - William W Taylor
- Center for Systems Integration and Sustainability, Department of Fisheries and Wildlife and Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Klement Tockner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, 12587, Germany
| | - Jesse C Vermaire
- Institute of Environmental Science, Carleton University, Ottawa, K1S 5B6, Canada
| | - David Dudgeon
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, K1S 5B6, Canada.,Institute of Environmental Science, Carleton University, Ottawa, K1S 5B6, Canada
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22
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Angelopoulos NV, Harvey JP, Bolland JD, Nunn AD, Noble RAA, Smith MA, Taylor MJ, Masters JEG, Moxon J, Cowx IG. Overcoming the dichotomy of implementing societal flood risk management while conserving instream fish habitat - A long-term study from a highly modified urban river. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 224:69-76. [PMID: 30031920 DOI: 10.1016/j.jenvman.2018.07.030] [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: 05/18/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 06/08/2023]
Abstract
Flood Risk Management (FRM) is often essential to reduce the risk of flooding to properties and infrastructure in urban landscapes, but typically degrades the habitats required by many aquatic animals for foraging, refuge and reproduction. This conflict between flood risk management and biodiversity is driven by conflicting directives, such as the EU Floods and Water Framework Directives, and has led to a requirement for synergistic solutions for FRM that integrate river restoration actions. Unfortunately, ecological monitoring and appraisal of combined FRM and river restoration works is inadequate. This paper uses a case study from the River Don in Northern England to evaluate the effects of the FRM and subsequent river restoration works on instream habitat and the associated fish assemblage over an 8-year period. Flood risk management created a homogeneous channel but did not negatively affect fish species composition or densities, specifically brown trout. Densities of adult brown trout were comparable pre and post-FRM, while densities of juvenile bullhead and brown trout increased dramatically post FRM. River restoration works created a heterogeneous channel but did not significantly improve species composition or brown trout density. Species composition post-river restoration works returned to that similar to pre-FRM over a short-term period, but with improved numbers of juvenile bullhead. Although habitat complexity increased after river restoration works, long-term changes in species composition and densities were marginal, probably because the river reset habitat complexity within the time framework of the study.
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Affiliation(s)
- N V Angelopoulos
- Hull International Fisheries Institute, School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK.
| | - J P Harvey
- Hull International Fisheries Institute, School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - J D Bolland
- Hull International Fisheries Institute, School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - A D Nunn
- Hull International Fisheries Institute, School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - R A A Noble
- Hull International Fisheries Institute, School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - M A Smith
- Hull International Fisheries Institute, School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - M J Taylor
- Hull International Fisheries Institute, School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - J E G Masters
- Environment Agency, Fisheries, Biodiversity and Geomorphology, Yorkshire Area. Lateral, 8 City Walk. Leeds LS11 9AT, UK
| | - J Moxon
- Environment Agency, Fisheries, Biodiversity and Geomorphology, Yorkshire Area. Lateral, 8 City Walk. Leeds LS11 9AT, UK
| | - I G Cowx
- Hull International Fisheries Institute, School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
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23
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Pawlowski J, Kelly-Quinn M, Altermatt F, Apothéloz-Perret-Gentil L, Beja P, Boggero A, Borja A, Bouchez A, Cordier T, Domaizon I, Feio MJ, Filipe AF, Fornaroli R, Graf W, Herder J, van der Hoorn B, Iwan Jones J, Sagova-Mareckova M, Moritz C, Barquín J, Piggott JJ, Pinna M, Rimet F, Rinkevich B, Sousa-Santos C, Specchia V, Trobajo R, Vasselon V, Vitecek S, Zimmerman J, Weigand A, Leese F, Kahlert M. The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1295-1310. [PMID: 29801222 DOI: 10.1016/j.scitotenv.2018.05.002] [Citation(s) in RCA: 211] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/11/2018] [Accepted: 05/01/2018] [Indexed: 05/05/2023]
Abstract
The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.
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Affiliation(s)
- Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, CH-1211 Geneva, Switzerland.
| | - Mary Kelly-Quinn
- School of Biology & Environmental Science, University College Dublin, Ireland
| | - Florian Altermatt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland(;) Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | | | - Pedro Beja
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-601 Vairão, Portugal; CEABN/InBIO-Centro de Estudos Ambientais 'Prof. Baeta Neves', Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Angela Boggero
- LifeWatch, Italy and CNR-Institute of Ecosystem Study (CNR-ISE), Largo Tonolli 50, 28922 Verbania Pallanza, Italy
| | - Angel Borja
- AZTI, Marine Research Division, Herrera Kaia, Portualdea s/n, 20110 Pasaia, Spain
| | - Agnès Bouchez
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, CH-1211 Geneva, Switzerland
| | - Isabelle Domaizon
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Maria Joao Feio
- Marine and Environmental Sciences Centre, Faculty of Sciences and Technology, Department of Life Sciences, University of Coimbra, Portugal
| | - Ana Filipa Filipe
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-601 Vairão, Portugal; CEABN/InBIO-Centro de Estudos Ambientais 'Prof. Baeta Neves', Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Riccardo Fornaroli
- University of Milano Bicocca, Department of Earth and Environmental Sciences(DISAT), Piazza della Scienza 1,20126 Milano, Italy
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), 1180 Vienna, Austria
| | - Jelger Herder
- RAVON, Postbus 1413, Nijmegen 6501 BK, The Netherlands
| | | | - J Iwan Jones
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Marketa Sagova-Mareckova
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovska 507, 16106 Praha 6, Czechia
| | - Christian Moritz
- ARGE Limnologie GesmbH, Hunoldstraße 14, 6020 Innsbruck, Austria
| | - Jose Barquín
- Environmental Hydraulics Institute "IHCantabria", Universidad de Cantabria, C/ Isabel Torres n°15, Parque Científico y Tecnológico de Cantabria, 39011 Santander, Spain
| | - Jeremy J Piggott
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, the University of Dublin, College Green, Dublin 2, Ireland; Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand
| | - Maurizio Pinna
- Department of Biological and Environmental Sciences and Technologies, University of Salento, S.P. Lecce-Monteroni, 73100 Lecce, Italy
| | - Frederic Rimet
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Buki Rinkevich
- Israel Oceanographic and Limnological Research, Tel- Shikmona, Haifa 31080, Israel
| | - Carla Sousa-Santos
- MARE - Marine and Environmental Sciences Centre, ISPA - Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Valeria Specchia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, S.P. Lecce-Monteroni, 73100 Lecce, Italy
| | - Rosa Trobajo
- IRTA, Institute of Agriculture and Food Research and Technology, Marine and Continental Waters Program, Carretera Poble Nou Km 5.5, E-43540 St. Carles de la Ràpita, Catalonia, Spain
| | - Valentin Vasselon
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Simon Vitecek
- Department of Limnology and Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Jonas Zimmerman
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany
| | - Alexander Weigand
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitaetsstrasse 5, 45141 Essen, Germany; Musée National d'Histoire Naturelle, 25 Rue Münster, 2160 Luxembourg, Luxembourg
| | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitaetsstrasse 5, 45141 Essen, Germany
| | - Maria Kahlert
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE - 750 07 Uppsala, Sweden
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Tydecks L, Jeschke JM, Wolf M, Singer G, Tockner K. Spatial and topical imbalances in biodiversity research. PLoS One 2018; 13:e0199327. [PMID: 29975719 PMCID: PMC6033392 DOI: 10.1371/journal.pone.0199327] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 06/05/2018] [Indexed: 11/18/2022] Open
Abstract
The rapid erosion of biodiversity is among the biggest challenges human society is facing. Concurrently, major efforts are in place to quantify changes in biodiversity, to understand the consequences for ecosystem functioning and human wellbeing, and to develop sustainable management strategies. Based on comprehensive bibliometric analyses covering 134,321 publications, we report systematic spatial biases in biodiversity-related research. Research is dominated by wealthy countries, while major research deficits occur in regions with disproportionately high biodiversity as well as a high share of threatened species. Similarly, core scientists, who were assessed through their publication impact, work primarily in North America and Europe. Though they mainly exchange and collaborate across locations of these two continents, the connectivity among them has increased with time. Finally, biodiversity-related research has primarily focused on terrestrial systems, plants, and the species level, and is frequently conducted in Europe and Asia by researchers affiliated with European and North American institutions. The distinct spatial imbalances in biodiversity research, as demonstrated here, must be filled, research capacity built, particularly in the Global South, and spatially-explicit biodiversity data bases improved, curated and shared.
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Affiliation(s)
- Laura Tydecks
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Institute of Biology—Freie Universität Berlin, Berlin, Germany
| | - Jonathan M. Jeschke
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Institute of Biology—Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Max Wolf
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Gabriel Singer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Klement Tockner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Institute of Biology—Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
- Der Wissenschaftsfond (FWF), Vienna, Austria
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Colin N, Villéger S, Wilkes M, de Sostoa A, Maceda-Veiga A. Functional diversity measures revealed impacts of non-native species and habitat degradation on species-poor freshwater fish assemblages. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 625:861-871. [PMID: 29306829 DOI: 10.1016/j.scitotenv.2017.12.316] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/27/2017] [Accepted: 12/27/2017] [Indexed: 06/07/2023]
Abstract
Trait-based ecology has been developed for decades to infer ecosystem responses to stressors based on the functional structure of communities, yet its value in species-poor systems is largely unknown. Here, we used an extensive dataset in a Spanish region highly prone to non-native fish invasions (15 catchments, N=389 sites) to assess for the first time how species-poor communities respond to large-scale environmental gradients using a taxonomic and functional trait-based approach in riverine fish. We examined total species richness and three functional trait-based indices available when many sites have ≤3 species (specialization, FSpe; originality, FOri and entropy, FEnt). We assessed the responses of these taxonomic and functional indices along gradients of altitude, water pollution, physical habitat degradation and non-native fish biomass. Whilst species richness was relatively sensitive to spatial effects, functional diversity indices were responsive across natural and anthropogenic gradients. All four diversity measures declined with altitude but this decline was modulated by physical habitat degradation (richness, FSpe and FEnt) and the non-native:total fish biomass ratio (FSpe and FOri) in ways that varied between indices. Furthermore, FSpe and FOri were significantly correlated with Total Nitrogen. Non-native fish were a major component of the taxonomic and functional structure of fish communities, raising concerns about potential misdiagnosis between invaded and environmentally-degraded river reaches. Such misdiagnosis was evident in a regional fish index widely used in official monitoring programs. We recommend the application of FSpe and FOri to extensive datasets from monitoring programs in order to generate valuable cross-system information about the impacts of non-native species and habitat degradation, even in species-poor systems. Scoring non-native species apart from habitat degradation in the indices used to determine ecosystem health is essential to develop better management strategies.
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Affiliation(s)
- Nicole Colin
- Department of Evolutionary Biology, Ecology & Environmental Sciences-Institute of Research in Biodiversity (IRBio-UB), University of Barcelona, 08028 Barcelona, Spain; Center for Research on Biodiversity and Sustainable Environments (CIBAS), Universidad Católica de la Santísima Concepción, Concepción, Chile.
| | - Sébastien Villéger
- Biodiversité marine et ses usages (UMR 9190 MARBEC), CNRS, Université de Montpellier, Place Eugène Bataillon, CP 34095, Montpellier Cedex 5, France
| | - Martin Wilkes
- Centre for Agroecology, Water and Resilience, Coventry University, Ryton Organic Gardens, Wolston Lane, Ryton-On-Dunsmore, CV8 3LG, UK
| | - Adolfo de Sostoa
- Department of Evolutionary Biology, Ecology & Environmental Sciences-Institute of Research in Biodiversity (IRBio-UB), University of Barcelona, 08028 Barcelona, Spain
| | - Alberto Maceda-Veiga
- Department of Evolutionary Biology, Ecology & Environmental Sciences-Institute of Research in Biodiversity (IRBio-UB), University of Barcelona, 08028 Barcelona, Spain; Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), 41092, Sevilla, Spain
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Redeker KR, Cai LL, Dumbrell AJ, Bardill A, Chong JP, Helgason T. Noninvasive Analysis of the Soil Microbiome: Biomonitoring Strategies Using the Volatilome, Community Analysis, and Environmental Data. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2018.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2018.01.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Paskuliakova A, McGowan T, Tonry S, Touzet N. Phycoremediation of landfill leachate with the chlorophyte Chlamydomonas sp. SW15aRL and evaluation of toxicity pre and post treatment. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 147:622-630. [PMID: 28926816 DOI: 10.1016/j.ecoenv.2017.09.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 09/03/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
Landfill leachate treatment is an ongoing challenge in the wastewater management of existing sanitary landfill sites due to the complex nature of leachates and their heavy pollutant load. There is a continuous interest in treatment biotechnologies with expected added benefits for resource recovery; microalgal bioremediation is seen as promising in this regard. Toxicity reduction of landfill leachate subsequent to phycoremediation was investigated in this study. The treatment eventuated from the growth of the ammonia tolerant microalgal strain Chlamydomonas sp. SW15aRL using a N:P ratio adjustment in diluted leachate for facilitating the process. Toxicity tests ranging over a number of trophic levels were applied, including bacterial-yeast (MARA), protistean (microalgae growth inhibition test), crustacean (daphnia, rotifer) and higher plant (monocot, dicot) assays. Ammonia nitrogen in the diluted landfill leachate containing up to 158mgl-1 NH4+-N (60% dilution of the original) was reduced by 83% during the microalgal treatment. Testing prior to remediation indicated the highest toxicity in the crustacean assays Daphnia magna and Brachionus calyciflorus with EC50s at 24h of ~ 35% and 40% leachate dilution, respectively. A major reduction in toxicity was achieved with both bioassays post microalgal treatment with effects well below the EC20s. The microalgae inhibition test on the other hand indicated increased stimulation of growth after treatment as a result of toxicity reduction but also the presence of residual nutrients. Several concurrent processes of both biotic and abiotic natures contributed to pollutant reduction during the treatment. Modifying phosphate dosage especially seems to require further attention. As a by-product of the remediation process, up to 1.2gl-1 of microalgal biomass was obtained with ~ 18% DW lipid content.
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Affiliation(s)
- Andrea Paskuliakova
- Centre for Environmental Research Innovation and Sustainability (CERIS), Institute of Technology Sligo, Ash Lane, Sligo, Ireland.
| | - Ted McGowan
- School of Science, Department of Life Science, Institute of Technology Sligo, Ash Lane, Sligo, Ireland
| | - Steve Tonry
- Centre for Environmental Research Innovation and Sustainability (CERIS), Institute of Technology Sligo, Ash Lane, Sligo, Ireland
| | - Nicolas Touzet
- Centre for Environmental Research Innovation and Sustainability (CERIS), Institute of Technology Sligo, Ash Lane, Sligo, Ireland
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Kamenova S, Bartley T, Bohan D, Boutain J, Colautti R, Domaizon I, Fontaine C, Lemainque A, Le Viol I, Mollot G, Perga ME, Ravigné V, Massol F. Invasions Toolkit. ADV ECOL RES 2017. [DOI: 10.1016/bs.aecr.2016.10.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Friberg N, Angelopoulos N, Buijse A, Cowx I, Kail J, Moe T, Moir H, O’Hare M, Verdonschot P, Wolter C. Effective River Restoration in the 21st Century. ADV ECOL RES 2016. [DOI: 10.1016/bs.aecr.2016.08.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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31
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Litter Decomposition as an Indicator of Stream Ecosystem Functioning at Local-to-Continental Scales. ADV ECOL RES 2016. [DOI: 10.1016/bs.aecr.2016.08.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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