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Liu Z, Wang P, Li J, Luo X, Zhang Y, Huang X, Zhang X, Li W, Qin Q. Comparative metagenomic analysis of microbial community compositions and functions in cage aquaculture and its nearby non-aquaculture environments. Front Microbiol 2024; 15:1398005. [PMID: 38841063 PMCID: PMC11150647 DOI: 10.3389/fmicb.2024.1398005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 06/07/2024] Open
Abstract
In the context of burgeoning global aquaculture, its environmental repercussions, particularly in marine ecosystems, have gained significant attentions. Cage aquaculture, a prominent method, has been observed to significantly influence marine environments by discharging substantial amounts of organic materials and pollutants. It is also one of the important reasons for water eutrophication. This study investigated the impacts of cage aquaculture on microbial diversity and functional potential using metagenomics. Specifically, a comparison was made of the physicochemical indicators and microbial diversity between three grouper aquaculture cage nets in Lingshui Xincun Port and three nearby non-aquaculture area surface waters. We found that compared to non-aquaculture areas, the eutrophication indicators in aquaculture environments significantly increased, and the abundances of Vibrio and Pseudoalteromonas in aquaculture environments significantly rose. Additionally, microbial functional genes related to carbon, nitrogen, and sulfur metabolisms were also found to be significantly affected by aquaculture activities. The correlation analysis between microbial populations and environmental factors revealed that the abundances of most microbial taxa showed positive correlations with dissolved inorganic nitrogen, soluble reactive phosphorus, NH4+, and negative correlations with dissolved oxygen. Overall, this study elucidated the significant impacts of aquaculture-induced eutrophication on the diversity and functions of planktonic bacterial communities.
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Affiliation(s)
- Zetian Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jialing Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaoqing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ya Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xiaohong Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xin Zhang
- School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan, China
| | - Wenjun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
| | - Qiwei Qin
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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2
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Bell KL, Campos M, Hoffmann BD, Encinas-Viso F, Hunter GC, Webber BL. Environmental DNA methods for biosecurity and invasion biology in terrestrial ecosystems: Progress, pitfalls, and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171810. [PMID: 38513869 DOI: 10.1016/j.scitotenv.2024.171810] [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: 12/21/2023] [Revised: 03/13/2024] [Accepted: 03/16/2024] [Indexed: 03/23/2024]
Abstract
Analysis of environmental DNA (eDNA) enables indirect detection of species without the need to directly observe and sample them. For biosecurity and invasion biology, eDNA-based methods are useful to address biological invasions at all phases, from detecting arrivals to confirming eradication of past invasions. We conducted a systematic review of the literature and found that in biosecurity and invasion biology, eDNA has primarily been used to detect new incursions and monitor spread in marine and freshwater ecosystems, with much slower uptake in terrestrial ecosystems, reflecting a broader trend common to the usage of eDNA tools. In terrestrial ecosystems, eDNA research has mostly focussed on the use of eDNA metabarcoding to characterise biodiversity, rather than targeting biosecurity threats or non-native populations. We discuss how eDNA-based methods are being applied to terrestrial ecosystems for biosecurity and managing non-native populations at each phase of the invasion continuum: transport, introduction, establishment, and spread; across different management options: containment, control, and eradication; and for detecting the impact of non-native organisms. Finally, we address some of the current technical issues and caveats of eDNA-based methods, particularly for terrestrial ecosystems, and how these might be solved. As eDNA-based methods improve, they will play an increasingly important role in the early detection and adaptive management of biological invasions, and the implementation of effective biosecurity controls.
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Affiliation(s)
- Karen L Bell
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| | - Mariana Campos
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; Harry Butler Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
| | | | - Francisco Encinas-Viso
- CSIRO Centre of Australian National Biodiversity Research, Black Mountain, Australian Capital Territory 2601, Australia
| | - Gavin C Hunter
- CSIRO Health & Biosecurity, Black Mountain, Australian Capital Territory 2601, Australia
| | - Bruce L Webber
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
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3
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Brauge T, Mougin J, Ells T, Midelet G. Sources and contamination routes of seafood with human pathogenic Vibrio spp.: A Farm-to-Fork approach. Compr Rev Food Sci Food Saf 2024; 23:e13283. [PMID: 38284576 DOI: 10.1111/1541-4337.13283] [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: 07/17/2023] [Revised: 11/03/2023] [Accepted: 11/29/2023] [Indexed: 01/30/2024]
Abstract
Vibrio spp., known human foodborne pathogens, thrive in freshwater, estuaries, and marine settings, causing vibriosis upon ingestion. The rising global vibriosis cases due to climate change necessitate a deeper understanding of Vibrio epidemiology and human transmission. This review delves into Vibrio contamination in seafood, scrutinizing its sources and pathways. We comprehensively assess the contamination of human-pathogenic Vibrio in the seafood chain, covering raw materials to processed products. A "Farm-to-Fork" approach, aligned with the One Health concept, is essential for grasping the complex nature of Vibrio contamination. Vibrio's widespread presence in natural and farmed aquatic environments establishes them as potential entry points into the seafood chain. Environmental factors, including climate, human activities, and wildlife, influence contamination sources and routes, underscoring the need to understand the origin and transmission of pathogens in raw seafood. Once within the seafood chain, the formation of protective biofilms on various surfaces in production and processing poses significant food safety risks, necessitating proper cleaning and disinfection to prevent microbial residue. In addition, inadequate seafood handling, from inappropriate processing procedures to cross-contamination via pests or seafood handlers, significantly contributes to Vibrio food contamination, thus warranting attention to reduce risks. Information presented here support the imperative for proactive measures, robust research, and interdisciplinary collaboration in order to effectively mitigate the risks posed by human pathogenic Vibrio contamination, safeguarding public health and global food security. This review serves as a crucial resource for researchers, industrials, and policymakers, equipping them with the knowledge to develop biosecurity measures associated with Vibrio-contaminated seafood.
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Affiliation(s)
- Thomas Brauge
- ANSES, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Boulogne sur Mer, France
| | - Julia Mougin
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Timothy Ells
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, Nova Scotia, Canada
| | - Graziella Midelet
- ANSES, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Boulogne sur Mer, France
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4
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Johnson LA, Dufour SC, Smith DDN, Manning AJ, Ahmed B, Binette S, Hamoutene D. Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 268:115683. [PMID: 37976931 DOI: 10.1016/j.ecoenv.2023.115683] [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: 08/09/2023] [Revised: 10/24/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
In marine sediments surrounding salmon aquaculture sites, organic matter (OM) enrichment has been shown to influence resident bacterial community composition; however, additional effects on these communities due to combined use of the sea-lice therapeutant emamectin benzoate (EMB) and the widely used antibiotic oxytetracycline (OTC) are unknown. Here, we use sediment microcosms to assess the influence of OM, EMB, and OTC on benthic bacterial communities. Microcosms consisted of mud or sand sediments enriched with OM (fish and feed wastes) and spiked with EMB and OTC at environmentally-relevant concentrations. Samples were collected from initial matrices at the initiation of the trial and after 110 days for 16 S rRNA gene sequencing of the V3-V4 region and microbiome profiling. The addition of OM in both mud and sand sediments reduced alpha diversities; for example, an average of 1106 amplicon sequence variants (ASVs) were detected in mud with no OM addition, while only 729 and 596 ASVs were detected in mud with low OM and high OM, respectively. Sediments enriched with OM had higher relative abundances of Spirochaetota, Firmicutes, and Bacteroidota. For instance, Spirochaetota were detected in sediments with no OM with a relative abundance range of 0.01-1.2%, while in sediments enriched with OM relative abundance varied from 0.16% to 26.1%. In contrast, the addition of EMB (60 ng/g) or OTC (150 ng/g) did not result in distinct taxonomic shifts in the bacterial communities compared to un-spiked sediments during the timeline of this experiment. EMB and OTC concentrations may have been below effective inhibitor concentrations for taxa in these communities; further work should explore gene content and the presence of antibiotic resistance genes (ARGs) in sediment-dwelling bacteria.
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Affiliation(s)
- Lisa A Johnson
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada
| | - Suzanne C Dufour
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada
| | - Derek D N Smith
- Environment and Climate Change Canada, 335 River Road, Ottawa, ON K1V 1C7, Canada
| | - Anthony J Manning
- Research & Productivity Council (RPC), Fredericton, NB E3B 6Z9, Canada
| | - Bulbul Ahmed
- Research & Productivity Council (RPC), Fredericton, NB E3B 6Z9, Canada
| | - Sherry Binette
- Research & Productivity Council (RPC), Fredericton, NB E3B 6Z9, Canada
| | - Dounia Hamoutene
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada.
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5
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Leontidou K, Rubel V, Stoeck T. Comparing quantile regression spline analyses and supervised machine learning for environmental quality assessment at coastal marine aquaculture installations. PeerJ 2023; 11:e15425. [PMID: 37334127 PMCID: PMC10274583 DOI: 10.7717/peerj.15425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/25/2023] [Indexed: 06/20/2023] Open
Abstract
Organic enrichment associated with marine finfish aquaculture is a local stressor of marine coastal ecosystems. To maintain ecosystem services, the implementation of biomonitoring programs focusing on benthic diversity is required. Traditionally, impact-indices are determined by extracting and identifying benthic macroinvertebrates from samples. However, this is a time-consuming and expensive method with low upscaling potential. A more rapid, inexpensive, and robust method to infer the environmental quality of marine environments is eDNA metabarcoding of bacterial communities. To infer the environmental quality of coastal habitats from metabarcoding data, two taxonomy-free approaches have been successfully applied for different geographical regions and monitoring goals, namely quantile regression splines (QRS) and supervised machine learning (SML). However, their comparative performance remains untested for monitoring the impact of organic enrichment introduced by aquaculture on marine coastal environments. We compared the performance of QRS and SML using bacterial metabarcoding data to infer the environmental quality of 230 aquaculture samples collected from seven farms in Norway and seven farms in Scotland along an organic enrichment gradient. As a measure of environmental quality, we used the Infaunal Quality Index (IQI) calculated from benthic macrofauna data (reference index). The QRS analysis plotted the abundance of amplicon sequence variants (ASVs) as a function to the IQI from which the ASVs with a defined abundance peak were assigned to eco-groups and a molecular IQI was subsequently calculated. In contrast, the SML approach built a random forest model to directly predict the macrofauna-based IQI. Our results show that both QRS and SML perform well in inferring the environmental quality with 89% and 90% accuracy, respectively. For both geographic regions, there was high correspondence between the reference IQI and both the inferred molecular IQIs (p < 0.001), with the SML model showing a higher coefficient of determination compared to QRS. Among the 20 most important ASVs identified by the SML approach, 15 were congruent with the good quality spline ASV indicators identified via QRS for both Norwegian and Scottish salmon farms. More research on the response of the ASVs to organic enrichment and the co-influence of other environmental parameters is necessary to eventually select the most powerful stressor-specific indicators. Even though both approaches are promising to infer environmental quality based on metabarcoding data, SML showed to be more powerful in handling the natural variability. For the improvement of the SML model, addition of new samples is still required, as background noise introduced by high spatio-temporal variability can be reduced. Overall, we recommend the development of a powerful SML approach that will be onwards applied for monitoring the impact of aquaculture on marine ecosystems based on eDNA metabarcoding data.
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Guajardo-Leiva S, Mendez KN, Meneses C, Díez B, Castro-Nallar E. A First Insight into the Microbial and Viral Communities of Comau Fjord—A Unique Human-Impacted Ecosystem in Patagonia (42∘ S). Microorganisms 2023; 11:microorganisms11040904. [PMID: 37110327 PMCID: PMC10143455 DOI: 10.3390/microorganisms11040904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
While progress has been made in surveying the oceans to understand microbial and viral communities, the coastal ocean and, specifically, estuarine waters, where the effects of anthropogenic activity are greatest, remain partially understudied. The coastal waters of Northern Patagonia are of interest since this region experiences high-density salmon farming as well as other disturbances such as maritime transport of humans and cargo. Here, we hypothesized that viral and microbial communities from the Comau Fjord would be distinct from those collected in global surveys yet would have the distinctive features of microbes from coastal and temperate regions. We further hypothesized that microbial communities will be functionally enriched in antibiotic resistance genes (ARGs) in general and in those related to salmon farming in particular. Here, the analysis of metagenomes and viromes obtained for three surface water sites showed that the structure of the microbial communities was distinct in comparison to global surveys such as the Tara Ocean, though their composition converges with that of cosmopolitan marine microbes belonging to Proteobacteria, Bacteroidetes, and Actinobacteria. Similarly, viral communities were also divergent in structure and composition but matched known viral members from North America and the southern oceans. Microbial communities were functionally enriched in ARGs dominated by beta-lactams and tetracyclines, bacitracin, and the group macrolide–lincosamide–streptogramin (MLS) but were not different from other communities from the South Atlantic, South Pacific, and Southern Oceans. Similarly, viral communities were characterized by exhibiting protein clusters similar to those described globally (Tara Oceans Virome); however, Comau Fjord viromes displayed up to 50% uniqueness in their protein content. Altogether, our results indicate that microbial and viral communities from the Comau Fjord are a reservoir of untapped diversity and that, given the increasing anthropogenic impacts in the region, they warrant further study, specifically regarding resilience and resistance against antimicrobials and hydrocarbons.
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Affiliation(s)
- Sergio Guajardo-Leiva
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
- Centro de Ecología Integrativa, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
| | - Katterinne N. Mendez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
| | - Claudio Meneses
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- ANID—Millennium Science Initiative Program—Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8370186, Chile
| | - Beatriz Díez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Center for Climate and Resilience Research (CR)2, Santiago 8370449, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago 7800003, Chile
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
- Centro de Ecología Integrativa, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
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7
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Littlefair JE, Rennie MD, Cristescu ME. Environmental nucleic acids: A field-based comparison for monitoring freshwater habitats using eDNA and eRNA. Mol Ecol Resour 2022; 22:2928-2940. [PMID: 35730338 PMCID: PMC9796649 DOI: 10.1111/1755-0998.13671] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 01/01/2023]
Abstract
Nucleic acids released by organisms and isolated from environmental substrates are increasingly being used for molecular biomonitoring. While environmental DNA (eDNA) has received much attention, the potential of environmental RNA as a biomonitoring tool remains under-explored. Several recent studies using paired DNA and RNA metabarcoding of bulk samples suggest that RNA might better reflect "metabolically active" parts of the community. However, such studies mainly capture organismal eDNA and eRNA. For larger eukaryotes, isolation of extra-organismal RNA will be important, but viability needs to be examined in a field-based setting. In this study we evaluate (a) whether extra-organismal eRNA release from macroeukaryotes can be detected given its supposedly rapid degradation, and (b) if the same field collection methods for eDNA can be applied to eRNA. We collected eDNA and eRNA from water in lakes where fish community composition is well documented, enabling a comparison between the two nucleic acids in two different seasons with monitoring using conventional methods. We found that eRNA is released from macroeukaryotes and can be filtered from water and metabarcoded in a similar manner as eDNA to reliably provide species composition information. eRNA had a small but significantly greater true positive rate than eDNA, indicating that it correctly detects more species known to exist in the lakes. Given relatively small differences between the two molecules in describing fish community composition, we conclude that if eRNA provides significant advantages in terms of lability, it is a strong candidate to add to the suite of molecular monitoring tools.
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Affiliation(s)
- Joanne E. Littlefair
- Department of BiologyMcGill UniversityMontréalQuebecCanada,Queen Mary University of LondonLondonUK
| | - Michael D. Rennie
- IISD Experimental Lakes AreaWinnipegManitobaCanada,Department of BiologyLakehead UniversityThunder BayOntarioCanada
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8
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Da Silva RRP, White CA, Bowman JP, Ross DJ. Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture. MARINE POLLUTION BULLETIN 2022; 182:113957. [PMID: 35872476 DOI: 10.1016/j.marpolbul.2022.113957] [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: 05/04/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Finfish aquaculture is a fast-growing primary industry and is increasingly common in coastal ecosystems. Bacterioplankton is ubiquitous in marine environment and respond rapidly to environmental changes. Changes in bacterioplankton community are not well understood in semi-enclosed stratified embayments. This study aims to examine aquaculture effects in the composition and functional profiles of the bacterioplankton community using amplicon sequencing along a distance gradient from two finfish leases in a marine embayment. Results revealed natural stratification in bacterioplankton associated to NOx, conductivity, salinity, temperature and PO4. Among the differentially abundant bacteria in leases, we found members associated with nutrient enrichment and aquaculture activities. Abundant predicted functions near leases were assigned to organic matter degradation, fermentation, and antibiotic resistance. This study provides a first effort to describe changes in the bacterioplankton community composition and function due to finfish aquaculture in a semi-enclosed and highly stratified embayment with a significant freshwater input.
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Affiliation(s)
- R R P Da Silva
- Institute for Marine and Antarctic Studies (IMAS), Nubeena Crescent, Taroona, Tasmania 7053, Australia.
| | - C A White
- Institute for Marine and Antarctic Studies (IMAS), Nubeena Crescent, Taroona, Tasmania 7053, Australia
| | - J P Bowman
- Tasmanian Institute of Agriculture (TIA), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - D J Ross
- Institute for Marine and Antarctic Studies (IMAS), Nubeena Crescent, Taroona, Tasmania 7053, Australia
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9
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Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell'Anno A, Duarte S, Eisendle U, Ferrari BJD, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151783. [PMID: 34801504 DOI: 10.1016/j.scitotenv.2021.151783] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/06/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
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Affiliation(s)
- J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - K Bruce
- NatureMetrics Ltd, CABI Site, Bakeham Lane, Egham TW20 9TY, UK
| | - K Panksep
- Institute of Technology, University of Tartu, Tartu 50411, Estonia; Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Estonia
| | - F I Aguirre
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - S Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - L Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Baussant
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Bouchez
- INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - L Carugati
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - K Cermakova
- ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | - C Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - F O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - R Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - A Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - S Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - U Eisendle
- University of Salzburg, Dept. of Biosciences, 5020 Salzburg, Austria
| | - B J D Ferrari
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - F Frontalini
- Department of Pure and Applied Sciences, Urbino University, Urbino, Italy
| | - L Frühe
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - A Haegerbaeumer
- Bielefeld University, Animal Ecology, 33615 Bielefeld, Germany
| | - V Kisand
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - A Krolicka
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - F Leese
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Germany
| | - F Lejzerowicz
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - E Lyautey
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - I Maček
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - M Sagova-Marečková
- Czech University of Life Sciences, Dept. of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - J K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - X Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Warkworth 0941, New Zealand
| | - T Stoeck
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - R Vivien
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - A Weigand
- National Museum of Natural History Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Luxembourg
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy.
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10
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Qin M, Xu H, Zhao D, Zeng J, Wu QL. Aquaculture drives distinct patterns of planktonic and sedimentary bacterial communities: insights into co-occurrence pattern and assembly processes. Environ Microbiol 2022; 24:4079-4093. [PMID: 35099108 DOI: 10.1111/1462-2920.15922] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/13/2021] [Accepted: 01/19/2022] [Indexed: 11/03/2022]
Abstract
Aquaculture would change the environmental condition in the lake ecosystem, affecting the structure and function of the aquatic ecosystem. However, little is known about the underlying mechanisms controlling the distribution patterns of bacterial community respond to aquaculture in water column and sediment. Here, we investigated the composition, co-occurrence patterns, and assembly processes of planktonic and sedimentary bacterial communities (PBC vs. SBC) from an aquaculture-influenced zone of the Eastern Lake Taihu, China. We found that aquaculture activity greatly influenced the diversity and composition of SBC by inducing excess nitrogen into the sediments. Meanwhile, network analysis revealed that aquaculture activity strengthened species interactions within the SBC network but weakened the species interactions within the PBC network. Aquaculture activity also increased the importance of deterministic processes governing the assembly of SBC by heightening the importance of environmental filtering, whereas it decreased the relative importance of deterministic processes within the assembly of PBC. In addition, ecological restoration with macrophytes increased the diversity of PBC and formed a more stable PBC network by increasing the number of network keystones. Overall, our results indicated that aquaculture drove distinct co-occurrence patterns and assembly mechanisms of PBC and SBC. This study has fundamental implications in the lake ecosystem for evaluating the microbially mediated ecological consequences of aquaculture.
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Affiliation(s)
- Mengyu Qin
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Huimin Xu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, 100039, China
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11
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Dully V, Rech G, Wilding TA, Lanzén A, MacKichan K, Berrill I, Stoeck T. Comparing sediment preservation methods for genomic biomonitoring of coastal marine ecosystems. MARINE POLLUTION BULLETIN 2021; 173:113129. [PMID: 34784523 DOI: 10.1016/j.marpolbul.2021.113129] [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: 10/07/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
To avoid loss of genetic information in environmental DNA (eDNA) field samples, the preservation of nucleic acids during field sampling is a critical step. In the development of standard operating procedures (SOPs) for eDNA-based compliance monitoring, the effect of different routinely used sediment preservations on biological community structures serving as bioindicators has gone untested. We compared eDNA metabarcoding results of marine bacterial communities from sample aliquots that were treated with a nucleic acid preservation solution (treated samples) and aliquots that were frozen without further treatment (non-treated samples). Sediment samples were obtained from coastal locations subjected to different stressors (aquaculture, urbanization, industry). DNA extraction efficiency, bacterial community profiles, and measures of alpha- and beta-diversity were highly congruent between treated and non-treated samples. As both preservation methods provide the same relevant information to environmental managers and regulators, we recommend the inclusion of both methods into SOPs for biomonitoring in marine coastal environments.
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Affiliation(s)
- Verena Dully
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany
| | - Giulia Rech
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany
| | - Thomas A Wilding
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Scotland, United Kingdom
| | - Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | | - Iain Berrill
- Scottish Salmon Producers Organization, Edinburgh, Scotland, United Kingdom
| | - Thorsten Stoeck
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany.
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12
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Pearman JK, Biessy L, Howarth JD, Vandergoes MJ, Rees A, Wood SA. Deciphering the molecular signal from past and alive bacterial communities in aquatic sedimentary archives. Mol Ecol Resour 2021; 22:877-890. [PMID: 34562066 DOI: 10.1111/1755-0998.13515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/01/2021] [Accepted: 09/22/2021] [Indexed: 01/04/2023]
Abstract
Lake sediments accumulate information on biological communities thus acting as natural archives. Traditionally paleolimnology has focussed on fossilized remains of organisms, however, many organisms do not leave fossil evidence, meaning major ecosystem components are missing from environmental reconstructions. Many paleolimnology studies now incorporate molecular methods, including investigating microbial communities using environmental DNA (eDNA), but there is uncertainty about the contribution of living organisms to molecular inventories. In the present study, we obtained DNA and RNA inventories from sediment spanning 700 years to investigate the contribution of past and active communities to the molecular signal from sedimentary archives. Additionally, a droplet digital PCR (ddPCR) targeting the 16S ribosomal RNA (16S rRNA) gene of the photosynthetic cyanobacterial genera Microcystis was used to explore if RNA signals were from legacy RNA. We posit that the RNA signal is a mixture of legacy RNA, dormant cells, living bacteria and modern-day trace level contaminants that were introduced during sampling and preferentially amplified. The presence of legacy RNA was confirmed by the detection of Microcystis in sediments aged to ~200 years ago. Recent comparisons between 16S rRNA gene metabarcoding and traditional paleo proxies showed that past changes in bacterial communities can be reconstructed from sedimentary archives. The recovery of RNA in the present study has provided new insights into the origin of these signals. However, caution is required during analysis and interpretation of 16S rRNA gene metabarcoding data especially in recent sediments were there are potentially active bacteria.
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Affiliation(s)
- John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Laura Biessy
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | | | - Andrew Rees
- University of Victoria, Wellington, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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13
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Zhou A, Xie S, Zhang Y, Chuan J, Tang H, Li X, Zhang L, Xu G, Zou J. Interaction of environmental eukaryotic microorganisms and fungi in the pond-cultured carps: new insights into the potential pathogenic fungi in the freshwater aquaculture. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:38839-38854. [PMID: 33745047 DOI: 10.1007/s11356-021-13231-y] [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: 11/26/2020] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
The quality and safety of the aquatic products have gradually become the focus of global attention. In this study, the environmental eukaryotic and fungi communities in pond-cultured grass carp (Ctenopharyngodon idellus) and the koi carp (Cyprinus carpio L.) were investigated. For comparative analysis, the alpha diversity shows that the environmental microbial abundance in the koi carp groups were higher than that in the grass carp groups, while beta diversity reveals that the differences of the microbial community composition and structures in the grass carp groups were significantly higher than those in the koi carp groups. Meanwhile, the environmental microbial diversity of grass carp groups was higher than that of koi carp groups at phylum level, but showed no significant difference at genus level. Additionally, the dominant total phyla were Opisthokonta, Stramenopiles plusAlveolates plusRhizaria, Archaeplastida, Cryptophyceae, and Centrohelida for the 18S rRNA gene and Ciliophora, Chlorophyta, and Ascomycota for the ITS2 rRNA gene in both of the two carp groups. Additionally, annotation analysis showed that the biomarkers in the grass carp groups are significantly higher than those of the koi carp groups. Furthermore, the functional prediction of Funguild showed significant difference in outputs, while similarity in trophic modes and guild types between the two carp groups. Meanwhile, the total relative abundances of animal pathogen, fungal parasite, and plant pathogen were extremely similar between the two carp groups. Surprisingly, one pathogenic fungus of genus Fusarium was identified in both the environments of two carp groups based on filtered operational taxonomic unit tables. Overall, this is the first robust report to understand the characteristics of environmental eukaryotic microorganisms and fungi in the edible and ornamental carps. Our results also provide the basic data for the prevention of fungal diseases and the healthy culture of the carps.
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Affiliation(s)
- Aiguo Zhou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5 T1, Canada
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Shaolin Xie
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Yue Zhang
- Departments of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Jiacheng Chuan
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5 T1, Canada
| | - Huijuan Tang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Xiang Li
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5 T1, Canada
| | - Li Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Guohuan Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Jixing Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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14
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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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15
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Frühe L, Dully V, Forster D, Keeley NB, Laroche O, Pochon X, Robinson S, Wilding TA, Stoeck T. Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms. Front Microbiol 2021; 12:637811. [PMID: 33995296 PMCID: PMC8116884 DOI: 10.3389/fmicb.2021.637811] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3-V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.
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Affiliation(s)
- Larissa Frühe
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Verena Dully
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Dominik Forster
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Nigel B Keeley
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Research, Bergen, Norway
| | - Olivier Laroche
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Shawn Robinson
- St. Andrews Biological Station, Department of Fisheries and Oceans, St. Andrews, NB, Canada
| | | | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
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16
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Aylagas E, Atalah J, Sánchez-Jerez P, Pearman JK, Casado N, Asensi J, Toledo-Guedes K, Carvalho S. A step towards the validation of bacteria biotic indices using DNA metabarcoding for benthic monitoring. Mol Ecol Resour 2021; 21:1889-1903. [PMID: 33825307 DOI: 10.1111/1755-0998.13395] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/16/2021] [Accepted: 03/15/2021] [Indexed: 12/20/2022]
Abstract
Environmental genomics is a promising field for monitoring biodiversity in a timely fashion. Efforts have increasingly been dedicated to the use of bacteria DNA derived data to develop biotic indices for benthic monitoring. However, a substantial debate exists about whether bacteria-derived data using DNA metabarcoding should follow, for example, a taxonomy-based or a taxonomy-free approach to marine bioassessments. Here, we showcase the value of DNA-based monitoring using the impact of fish farming as an example of anthropogenic disturbances in coastal areas and compare the performance of taxonomy-based and taxonomy-free approaches in detecting environmental alterations. We analysed samples collected near to the farm cages and along distance gradients from two aquaculture installations, and at control sites, to evaluate the effect of this activity on bacterial assemblages. Using the putative response of bacterial taxa to stress we calculated the taxonomy-based biotic index microgAMBI. The distribution of individual amplicon sequence variants (ASVs), as a function of a gradient in sediment acid volatile sulphides, was then used to derive a taxonomy-free bacterial biotic index specific for this data set using a de novo approach based on quantile regression splines. Our results show that microgAMBI revealed a organically enriched environment along the gradient. However, the de novo biotic index outperformed microgAMBI by providing a higher discriminatory power in detecting changes in abiotic factors directly related to fish production, whilst allowing the identification of new ASVs bioindicators. The de novo strategy applied here represents a robust method to define new bioindicators in regions or habitats where no previous information about the response of bacteria to environmental stressors exists.
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Affiliation(s)
- Eva Aylagas
- Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Javier Atalah
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Pablo Sánchez-Jerez
- Department of Marine Science and Applied Biology, University of Alicante, Alicante, Spain
| | - John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Nuria Casado
- Department of Marine Science and Applied Biology, University of Alicante, Alicante, Spain
| | - Jorge Asensi
- Department of Marine Science and Applied Biology, University of Alicante, Alicante, Spain
| | - Kilian Toledo-Guedes
- Department of Marine Science and Applied Biology, University of Alicante, Alicante, Spain
| | - Susana Carvalho
- Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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17
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Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance. WATER 2021. [DOI: 10.3390/w13081113] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The field of eDNA is growing exponentially in response to the need for detecting rare and invasive species for management and conservation decisions. Developing technologies and standard protocols within the biosecurity sector must address myriad challenges associated with marine environments, including salinity, temperature, advective and deposition processes, hydrochemistry and pH, and contaminating agents. These approaches must also provide a robust framework that meets the need for biosecurity management decisions regarding threats to human health, environmental resources, and economic interests, especially in areas with limited clean-laboratory resources and experienced personnel. This contribution aims to facilitate dialogue and innovation within this sector by reviewing current approaches for sample collection, post-sampling capture and concentration of eDNA, preservation, and extraction, all through a biosecurity monitoring lens.
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18
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Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats. PLoS One 2020; 15:e0244682. [PMID: 33378355 PMCID: PMC7773206 DOI: 10.1371/journal.pone.0244682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022] Open
Abstract
In recent years, metabarcoding has become a key tool to describe microbial communities from natural and artificial environments. Thanks to its high throughput nature, metabarcoding efficiently explores microbial biodiversity under different conditions. It can be performed on environmental (e)DNA to describe so-called total microbial community, or from environmental (e)RNA to describe active microbial community. As opposed to total microbial communities, active ones exclude dead or dormant organisms. For what concerns Fungi, which are mostly filamentous microorganisms, the relationship between DNA-based (total) and RNA-based (active) communities is unclear. In the present study, we evaluated the consequences of performing metabarcoding on both soil and wood-extracted eDNA and eRNA to delineate molecular operational taxonomic units (MOTUs) and differentiate fungal communities according to the environment they originate from. DNA and RNA-based communities differed not only in their taxonomic composition, but also in the relative abundances of several functional guilds. From a taxonomic perspective, we showed that several higher taxa are globally more represented in either “active” or “total” microbial communities. We also observed that delineation of MOTUs based on their co-occurrence among DNA and RNA sequences highlighted differences between the studied habitats that were overlooked when all MOTUs were considered, including those identified exclusively by eDNA sequences. We conclude that metabarcoding on eRNA provides original functional information on the specific roles of several taxonomic or functional groups that would not have been revealed using eDNA alone.
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19
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Clark DE, Pilditch CA, Pearman JK, Ellis JI, Zaiko A. Environmental DNA metabarcoding reveals estuarine benthic community response to nutrient enrichment - Evidence from an in-situ experiment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 267:115472. [PMID: 32891048 DOI: 10.1016/j.envpol.2020.115472] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/27/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Nutrient loading is a major threat to estuaries and coastal environments worldwide, therefore, it is critical that we have good monitoring tools to detect early signs of degradation in these ecologically important and vulnerable ecosystems. Traditionally, bottom-dwelling macroinvertebrates have been used for ecological health assessment but recent advances in environmental genomics mean we can now characterize less visible forms of biodiversity, offering a more holistic view of the ecosystem and potentially providing early warning signals of disturbance. We carried out a manipulative nutrient enrichment experiment (0, 150 and 600 g N fertilizer m-2) in two estuaries in New Zealand to assess the effects of nutrient loading on benthic communities. After seven months of enrichment, environmental DNA (eDNA) metabarcoding was used to examine the response of eukaryotic (18S rRNA), diatom only (rbcL) and bacterial (16S rRNA) communities. Multivariate analyses demonstrated changes in eukaryotic, diatom and bacterial communities in response to nutrient enrichment at both sites, despite differing environmental conditions. These patterns aligned with changes in macrofaunal communities identified using traditional morphological techniques, confirming concordance between disturbance indicators detected by eDNA and current monitoring approaches. Clear shifts in eukaryotic and bacterial indicator taxa were seen in response to nutrient loading while changes in diatom only communities were more subtle. Community changes were discernible between 0 and 150 g N m-2 treatments, suggesting that estuary health assessment tools could be developed to detect early signs of degradation. Increasing variation in community structure associated with nutrient loading could also be used as an indicator of stress or approaching tipping points. This work represents a first step towards the development of molecular-based estuary monitoring tools, which could provide a more holistic and standardized approach to ecosystem health assessment with faster turn-around times and lower costs.
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Affiliation(s)
- D E Clark
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand; University of Waikato, Gate 1, Knighton Rd, Hamilton, 3240, New Zealand.
| | - C A Pilditch
- University of Waikato, Gate 1, Knighton Rd, Hamilton, 3240, New Zealand
| | - J K Pearman
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - J I Ellis
- University of Waikato, Private Bag 3105, Tauranga, 3110, New Zealand
| | - A Zaiko
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth, 0941, New Zealand
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20
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Xu W, Gong L, Yang S, Gao Y, Ma X, Xu L, Chen H, Luo Z. Spatiotemporal Dynamics of Vibrio Communities and Abundance in Dongshan Bay, South of China. Front Microbiol 2020; 11:575287. [PMID: 33324364 PMCID: PMC7726330 DOI: 10.3389/fmicb.2020.575287] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
The Vibrio genus inhabit estuarine and marine ecosystem throughout the world and can cause severe infections in humans and animals. Previous studies have demonstrated the dynamics of Vibrio at both community and population levels and assessed the close relationship between environmental factors and Vibrio diversity and abundance, such as temperature, salinity, and dissolved oxygen. It is also generally believed that aquaculture is the fastest-growing food sector, which is also applying great environmental impacts on microbial communities in aquatic ecosystems. However, our understanding of the spatiotemporal quantification of Vibrio throughout the four seasons in the aquaculture zone and response to environmental factors remains poor. To explore the spatiotemporal distribution and abundance of the Vibrio community with their related environmental factors and detect the relationships among them, we collected 10 seawater sites spanning four seasons across the whole year in Dongshan Bay for investigating the Vibrio community dynamics. Marked differences in diversity and abundance of the Vibrio community were observed between seasons, which were mainly driven by temperature, dissolved oxygen, nitrate, and nitrite. qPCR analysis showed that Vibrio abundance was most abundant in the summer (5.37 × 106 copies/L), compared with the autumn (4.58 × 106 copies/L), spring (1.18 × 106 copies/L), and winter (1.55 × 104 copies/L). A total of 22 Vibrio operational taxonomic units (OTUs) and 28 species were identified by universal bacteria 16S rRNA gene and cultivation methods, with Vibrio fortis the dominant in these aquaculture areas. To summarize, our present study is one of the few studies to research the occurrence of Vibrio in marine aquaculture of South China, and the results indicate that Vibrio are widely distributed in aquaculture environment and that a further risk assessment is needed to be conducted.
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Affiliation(s)
- Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - LinFeng Gong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Shuai Yang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yuanhao Gao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xiaowan Ma
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Limei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Haisheng Chen
- Fishery Technology Promotion Station of Dongshan, Zhangzhou, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China.,School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing, China
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21
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Aylagas E, Borja A, Pochon X, Zaiko A, Keeley N, Bruce K, Hong P, Ruiz GM, Stein ED, Theroux S, Geraldi N, Ortega A, Gajdzik L, Coker DJ, Katan Y, Hikmawan T, Saleem A, Alamer S, Jones BH, Duarte CM, Pearman J, Carvalho S. Translational Molecular Ecology in practice: Linking DNA-based methods to actionable marine environmental management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140780. [PMID: 32693276 DOI: 10.1016/j.scitotenv.2020.140780] [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: 04/28/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Molecular-based approaches can provide timely biodiversity assessments, showing an immense potential to facilitate decision-making in marine environmental management. However, the uptake of molecular data into environmental policy remains minimal. Here, we showcase a selection of local to global scale studies applying molecular-based methodologies for environmental management at various stages of implementation. Drawing upon lessons learned from these case-studies, we provide a roadmap to facilitate applications of DNA-based methods to marine policies and to overcome the existing challenges. The main impediment identified is the need for standardized protocols to guarantee data comparison across spatial and temporal scales. Adoption of Translational Molecular Ecology - the sustained collaboration between molecular ecologists and stakeholders, will enhance consensus with regards to the objectives, methods, and outcomes of environmental management projects. Establishing a sustained dialogue among stakeholders is key to accelerating the adoption of molecular-based approaches for marine monitoring and assessment.
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Affiliation(s)
- Eva Aylagas
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Angel Borja
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia, Portualdea s/n, 20110 Pasaia, Spain
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Nigel Keeley
- Benthic Resources and Processors Group, Institute of Marine Research, Postboks 6606 Langnes, 9296 Tromsø, Norway
| | - Kat Bruce
- Nature Metrics Ltd, CABI site, Bakeham Lane, Egham TW20 9TY, United Kingdom
| | - Peiying Hong
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gregory M Ruiz
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, MD 21037, USA; Aquatic Bioinvasion Research and Policy Institute, Environmental Science and Management, Portland State University, Portland, OR 97201, USA
| | - Eric D Stein
- Southern California Coastal Water Research Project, 3535 Harbor Blvd., Suite 110, Costa Mesa, CA 92626-1437, USA
| | - Susanna Theroux
- Southern California Coastal Water Research Project, 3535 Harbor Blvd., Suite 110, Costa Mesa, CA 92626-1437, USA
| | - Nathan Geraldi
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alejandra Ortega
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Laura Gajdzik
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Darren J Coker
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Yasser Katan
- Environmental Protection Department, Saudi Aramco, Dhahran 3131, Saudi Arabia
| | - Tyas Hikmawan
- Environmental Protection Department, Saudi Aramco, Dhahran 3131, Saudi Arabia
| | - Ammar Saleem
- The General Authority of Meteorology and Environmental Protection, The Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Sultan Alamer
- The General Authority of Meteorology and Environmental Protection, The Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Burton H Jones
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - John Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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22
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Pearman JK, Keeley NB, Wood SA, Laroche O, Zaiko A, Thomson-Laing G, Biessy L, Atalah J, Pochon X. Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture. PeerJ 2020; 8:e10231. [PMID: 33194417 PMCID: PMC7597629 DOI: 10.7717/peerj.10231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/02/2020] [Indexed: 12/21/2022] Open
Abstract
Marine sediments contain a high diversity of micro- and macro-organisms which are important in the functioning of biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently been advocated as a rapid and cost-effective approach to measuring ecological impacts and efforts are underway to incorporate eDNA tools into monitoring. Before these methods can replace or complement existing methods, robustness and repeatability of each analytical step has to be demonstrated. One area that requires further investigation is the selection of sediment DNA extraction method. Environmental DNA sediment samples were obtained along a disturbance gradient adjacent to a Chinook (Oncorhynchus tshawytscha) salmon farm in Otanerau Bay, New Zealand. DNA was extracted using four extraction kits (Qiagen DNeasy PowerSoil, Qiagen DNeasy PowerSoil Pro, Qiagen RNeasy PowerSoil Total RNA/DNA extraction/elution and Favorgen FavorPrep Soil DNA Isolation Midi Kit) and three sediment volumes (0.25, 2, and 5 g). Prokaryotic and eukaryotic communities were amplified using primers targeting the 16S and 18S ribosomal RNA genes, respectively, and were sequenced on an Illumina MiSeq. Diversity and community composition estimates were obtained from each extraction kit, as well as their relative performance in established metabarcoding biotic indices. Differences were observed in the quality and quantity of the extracted DNA amongst kits with the two Qiagen DNeasy PowerSoil kits performing best. Significant differences were observed in both prokaryotes and eukaryotes (p < 0.001) richness among kits. A small proportion of amplicon sequence variants (ASVs) were shared amongst the kits (~3%) although these shared ASVs accounted for the majority of sequence reads (prokaryotes: 59.9%, eukaryotes: 67.2%). Differences were observed in the richness and relative abundance of taxonomic classes revealed with each kit. Multivariate analysis showed that there was a significant interaction between "distance" from the farm and "kit" in explaining the composition of the communities, with the distance from the farm being a stronger determinant of community composition. Comparison of the kits against the bacterial and eukaryotic metabarcoding biotic index suggested that all kits showed similar patterns along the environmental gradient. Overall, we advocate for the use of Qiagen DNeasy PowerSoil kits for use when characterizing prokaryotic and eukaryotic eDNA from marine farm sediments. We base this conclusion on the higher DNA quality values and richness achieved with these kits compared to the other kits/amounts investigated in this study. The additional advantage of the PowerSoil Kits is that DNA extractions can be performed using an extractor robot, offering additional standardization and reproducibility of results.
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Affiliation(s)
- John K. Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | | | - Laura Biessy
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Javier Atalah
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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23
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Lanzén A, Mendibil I, Borja Á, Alonso-Sáez L. A microbial mandala for environmental monitoring: Predicting multiple impacts on estuarine prokaryote communities of the Bay of Biscay. Mol Ecol 2020; 30:2969-2987. [PMID: 32479653 DOI: 10.1111/mec.15489] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/08/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023]
Abstract
Routine monitoring of benthic biodiversity is critical for managing and understanding the anthropogenic impacts on marine, transitional and freshwater ecosystems. However, traditional reliance on morphological identification generally makes it cost-prohibitive to increase the scale of monitoring programmes. Metabarcoding of environmental DNA has clear potential to overcome many of the problems associated with traditional monitoring, with prokaryotes and other microorganisms showing particular promise as bioindicators. However, due to the limited knowledge regarding the ecological roles and responses of environmental microorganisms to different types of pressure, the use of de novo approaches is necessary. Here, we use two such approaches for the prediction of multiple impacts present in estuaries and coastal areas of the Bay of Biscay based on microbial communities. The first (Random Forests) is a machine learning method while the second (Threshold Indicator Taxa Analysis and quantile regression splines) is based on de novo identification of bioindicators. Our results show that both methods overlap considerably in the indicator taxa identified, but less for sequence variants. Both methods also perform well in spite of the complexity of the studied ecosystem, providing predictive models with strong correlation to reference values and fair to good agreement with ecological status groups. The ability to predict several specific types of pressure is especially appealing. The cross-validated models and biotic indices developed can be directly applied to predict the environmental status of estuaries in the same geographical region, although more work is needed to evaluate and improve them for use in new regions or habitats.
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Affiliation(s)
- Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - Iñaki Mendibil
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain
| | - Ángel Borja
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain
| | - Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain
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24
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Frühe L, Cordier T, Dully V, Breiner HW, Lentendu G, Pawlowski J, Martins C, Wilding TA, Stoeck T. Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes. Mol Ecol 2020; 30:2988-3006. [PMID: 32285497 DOI: 10.1111/mec.15434] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 01/02/2023]
Abstract
Increasing anthropogenic impact and global change effects on natural ecosystems has prompted the development of less expensive and more efficient bioassessments methodologies. One promising approach is the integration of DNA metabarcoding in environmental monitoring. A critical step in this process is the inference of ecological quality (EQ) status from identified molecular bioindicator signatures that mirror environmental classification based on standard macroinvertebrate surveys. The most promising approaches to infer EQ from biotic indices (BI) are supervised machine learning (SML) and the calculation of indicator values (IndVal). In this study we compared the performance of both approaches using DNA metabarcodes of bacteria and ciliates as bioindicators obtained from 152 samples collected from seven Norwegian salmon farms. Results from standard macroinvertebrate-monitoring of the same samples were used as reference to compare the accuracy of both approaches. First, SML outperformed the IndVal approach to infer EQ from eDNA metabarcodes. The Random Forest (RF) algorithm appeared to be less sensitive to noisy data (a typical feature of massive environmental sequence data sets) and uneven data coverage across EQ classes (a typical feature of environmental compliance monitoring scheme) compared to a widely used method to infer IndVals for the calculation of a BI. Second, bacteria allowed for a more accurate EQ assessment than ciliate eDNA metabarcodes. For the implementation of DNA metabarcoding into routine monitoring programmes to assess EQ around salmon aquaculture cages, we therefore recommend bacterial DNA metabarcodes in combination with SML to classify EQ categories based on molecular signatures.
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Affiliation(s)
- Larissa Frühe
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Verena Dully
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Hans-Werner Breiner
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Guillaume Lentendu
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene Ecodiagnostics Ltd, Geneva, Switzerland.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | | | - Thomas A Wilding
- Scottish Marine Institute, Scottish Association for Marine Science, Oban, Scotland
| | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
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25
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Palmer R, Fleming GTA, Glaeser S, Semmler T, Flamm A, Ewers C, Kämpfer P, Budich O, Berrow S, O'Brien J, Siebert U, Collins E, Ruttledge M, Eisenberg T. Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon. DISEASES OF AQUATIC ORGANISMS 2020; 139:161-174. [PMID: 32406871 DOI: 10.3354/dao03478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.
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Affiliation(s)
- Roy Palmer
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway H91TK33, Ireland
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26
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Wood SA, Biessy L, Latchford JL, Zaiko A, von Ammon U, Audrezet F, Cristescu ME, Pochon X. Release and degradation of environmental DNA and RNA in a marine system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135314. [PMID: 31780169 DOI: 10.1016/j.scitotenv.2019.135314] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/27/2019] [Accepted: 10/29/2019] [Indexed: 05/21/2023]
Abstract
Over the last decade, there has been growing interest in the analysis of environmental DNA (eDNA) to infer the presence of organisms in aquatic environments. The efficacy of eDNA/eRNA based tools are highly depend on the turnover rate of the molecule (their release and degradation). Environmental DNA has been shown to persist for days, weeks or years in environmental samples. Environmental RNA (eRNA) is thought to degrade faster than eDNA, however to our knowledge, no experimental studies have explored this. Here we present an aquarium study to investigate eDNA and eRNA shedding rates and degradation for two sessile marine invertebrates. The copy numbers for eDNA and eRNA were assessed using droplet digital PCR targeting the mitochondrial Cytochrome c Oxidase subunit 1 (COI) gene. Environmental RNA persisted after organism removal for much longer than expected with detections for up to 13 h. In contrast, eDNA was detected is samples collected up to 94 h after organism removal. There was no evidence that the decay rates constants for eDNA and eRNA were different (p = 0.6, Kruskal-Wallis tests). Both eDNA and eRNA was detected in biofilms collected at the end of the experiment (day 21). This suggests binding with organic or inorganic compounds or stabilization of these molecules in the biofilm matrix. The finding of the prolonged persistence of eRNA may provide new opportunities for improved biodiversity surveys through reducing false positives caused by legacy DNA and could also facilitate new research on environmental transcriptomics.
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Affiliation(s)
- Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.
| | - Laura Biessy
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Janie L Latchford
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Ulla von Ammon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - François Audrezet
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand
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27
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Keeley N, Valdemarsen T, Strohmeier T, Pochon X, Dahlgren T, Bannister R. Mixed-habitat assimilation of organic waste in coastal environments - It's all about synergy! THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 699:134281. [PMID: 31671307 DOI: 10.1016/j.scitotenv.2019.134281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Fish farms are increasingly situated in strong current sites above or near to mixed-bottom habitats that include organisms not normally considered in the context of organic enrichment. This study takes a holistic view of the benthic enrichment process by combining different survey techniques on complimentary spatial scales: conventional macrofaunal cores, larger-scale visual quantification of epibiota and environmental-DNA metabarcoding of microbial communities. A large tube forming polychaete (Arenicola marina), normally found intertidally and living too deep for conventional sampling, was observed occupying an opportunistic niche in areas of high deposition and in very close association with Capitellid worm complexes. The surface-dwelling brittlestar, Ophiocomina nigra, was abundant at distances of 250-1000 m from Farm-B, suggesting a positive response to enrichment, but was displaced where sedimentation exceed 5 g m2 d-1. A corresponding gradient was evident within the sediment microbial communities, supporting established theories about ecosystem engineering and multi-species synergies for organic waste assimilation. Many of the bacteria present in the near-farm sediments were linked to the farmed fish and fish health issues suggesting one or two-way inoculation pressures. These functionally different benthic organisms are intrinsically linked and the resulting synergy has the potential to assimilate significant quantities of anthropogenically produced organic waste contributing to environmental sustainability.
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Affiliation(s)
| | - Thomas Valdemarsen
- University of Southern Denmark, Copenhagen, Denmark; Danish Environmental Protection Agency, Denmark
| | | | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Warkworth, New Zealand
| | - Thomas Dahlgren
- Norwegian Research Centre NORCE, Bergen, Norway; University of Gothenburg, Dept. of Marine Sciences, Gothenburg, Sweden
| | - Raymond Bannister
- Institute of Marine Research, Tromsø, Norway; Environmental Protection Agency, Tasmania, Australia
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28
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Liang Y, Zhang Y, Zhou C, Li H, Kang X, Wang L, Song J, Jiao N. Cumulative impact of long-term intensive mariculture on total and active bacterial communities in the core sediments of the Ailian Bay, North China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 691:1212-1224. [PMID: 31466202 DOI: 10.1016/j.scitotenv.2019.07.200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/10/2019] [Accepted: 07/13/2019] [Indexed: 06/10/2023]
Abstract
The exponential growth of off-shore mariculture worldwide over the last 20 years has had significant impact on coastal sediment biogeochemistry. However, there are no long-term records of the cumulative impacts of mariculture on the benthic bacterial community. Here, total (DNA) and active (RNA) bacterial community compositions were characterized using MiSeq sequencing of 16S rRNA gene in four core sediments of the Ailian Bay, one of the typical intensive mariculture areas in China with more than fifty-year history of kelp and scallop cultivation. The γ-Proteobacteria, δ-Proteobacteria, Acidobacteria and Acitinobacteria were more abundant in the total bacterial communities, while β-Proteobacteria, Anaerolineae, Clostridia, Spirochaetes and Cyanobacteria were enriched in the active bacterial communities. Significant differences were observed between total and active benthic bacterial communities. The influences of different mariculture modes on the total bacterial communities were more significant than those on the active bacterial communities. Only limited groups of the total bacterial communities were significant influenced by the cumulative effects of the long-term mariculture. The bacterial genera with the function in the sulfide cycling and organic consumption were enriched in the total bacterial population of the integrated multi-trophic aquaculture (IMTA) areas. The variations of both total and active bacterial communities were significantly influenced by grain sizes, total organic carbon and nutrients. Both total and active bacterial communities exhibited a slightly stronger response to environmental factors than to spatial (distance) factors. The effects of mutualism might dominate the total and active bacterial networks in the Ailian Bay. The present study demonstrated that the cumulative influences of the long-term and intensive IMTA mariculture on total benthic bacterial communities in the sub-surface sediments of the Ailian Bay were stronger than those on the active benthic bacterial communities, which provided some insights into the potential ecological roles of specific taxa in the sediments of the IMTA ecosystems.
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Affiliation(s)
- Yantao Liang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Chao Zhou
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Hongmei Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Xuming Kang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Long Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Jinming Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nianzhi Jiao
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
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29
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Zeng J, Lin Y, Zhao D, Huang R, Xu H, Jiao C. Seasonality overwhelms aquacultural activity in determining the composition and assembly of the bacterial community in Lake Taihu, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 683:427-435. [PMID: 31141745 DOI: 10.1016/j.scitotenv.2019.05.256] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/29/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Aquaculture accounts for an extremely valuable and rapidly expanding sector of global food production, yet its environmental impacts on aquatic ecosystems have attracted much concern. In this study, we collected water samples from eastern Lake Taihu, China. We targeted sites varying in their intensity of aquacultural activities and sampled them over multiple seasons. For each sample, we measured physicochemical variables, and we sequenced the 16S rRNA gene of the respective bacterial communities using an Illumina second-generation sequencing platform. Marked differences in diversity and bacterial community composition were observed between seasons, whereas we observed relatively weak differences between sites. Remarkable differences in the abundance of the bacterial community were observed at the phylum and genus levels across the different seasons. Stochastic processes dominated the assembly of bacterial communities in the aquaculture-influenced systems, and the assembly processes of bacterial community differed between seasons. Our observations highlight the effect of seasonality on bacterial communities and provide a more complete knowledge base for the proper assessment of the effects of aquacultural activities on freshwater ecosystems.
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Affiliation(s)
- Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Yuqing Lin
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing 210098, China
| | - Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing 210098, China
| | - Rui Huang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing 210098, China
| | - Huimin Xu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing 210098, China
| | - Congcong Jiao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing 210098, China
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Shi R, Xu S, Qi Z, Zhu Q, Huang H, Weber F. Influence of suspended mariculture on vertical distribution profiles of bacteria in sediment from Daya Bay, Southern China. MARINE POLLUTION BULLETIN 2019; 146:816-826. [PMID: 31426223 DOI: 10.1016/j.marpolbul.2019.07.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
Mariculture is known to contribute to oxygen depletion, pH decline and accumulation of nutrients and organic matter in sediments. However, studies on the bacterial vertical distribution of mariculture area are very limited. The bacterial abundance in the non-culture site (3.8 ± 0.8 × 109 copies g-1) was significantly higher than that in the three mariculture sites (1.2 ± 0.2 × 109 copies g-1), and bacterial diversity in the non-culture site was significantly higher than that in fish cage-TF (p < 0.05). The vertical distribution profiles of bacteria in non-culture and oyster culture sites were similar but very different from that of fish cage-TF. In addition, significant downward trends in bacterial abundance and diversity were observed as sediment depth increased (p < 0.05), and the most relevant environmental factors were moisture content, total nitrogen, total organic carbon and carbon/nitrogen. The dominant bacterial phyla in sediment were Proteobacteria, Chloroflexi and Bacteroidetes.
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Affiliation(s)
- Rongjun Shi
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China
| | - Shumin Xu
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China
| | - Zhanhui Qi
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China.
| | - Qingzhi Zhu
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA.
| | - Honghui Huang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China
| | - Felix Weber
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA
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Cordier T, Lanzén A, Apothéloz-Perret-Gentil L, Stoeck T, Pawlowski J. Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring. Trends Microbiol 2019; 27:387-397. [DOI: 10.1016/j.tim.2018.10.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/17/2018] [Accepted: 10/30/2018] [Indexed: 01/28/2023]
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He X, Sutherland TF, Pawlowski J, Abbott CL. Responses of foraminifera communities to aquaculture‐derived organic enrichment as revealed by environmental
DNA
metabarcoding. Mol Ecol 2019; 28:1138-1153. [DOI: 10.1111/mec.15007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/28/2018] [Accepted: 12/26/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Xiaoping He
- Pacific Biological Station, Fisheries and Oceans Canada Nanaimo British Columbia Canada
| | - Terri F. Sutherland
- Pacific Science Enterprise Centre, Fisheries and Oceans Canada West Vancouver British Columbia Canada
| | - Jan Pawlowski
- Department of Genetics and Evolution University of Geneva Geneva Switzerland
| | - Cathryn L. Abbott
- Pacific Biological Station, Fisheries and Oceans Canada Nanaimo British Columbia Canada
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Cordier T, Frontalini F, Cermakova K, Apothéloz-Perret-Gentil L, Treglia M, Scantamburlo E, Bonamin V, Pawlowski J. Multi-marker eDNA metabarcoding survey to assess the environmental impact of three offshore gas platforms in the North Adriatic Sea (Italy). MARINE ENVIRONMENTAL RESEARCH 2019; 146:24-34. [PMID: 30890270 DOI: 10.1016/j.marenvres.2018.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
The environmental DNA (eDNA) metabarcoding represents a new promising tool for biomonitoring and environmental impact assessment. One of the main advantages of eDNA metabarcoding, compared to the traditional morphotaxonomy-based methods, is to provide a more holistic biodiversity information that includes inconspicuous morphologically non-identifiable taxa. Here, we use eDNA metabarcoding to survey marine biodiversity in the vicinity of the three offshore gas platforms in North Adriatic Sea (Italy). We isolated eDNA from 576 water and sediment samples collected at 32 sampling sites situated along four axes at increasing distances from the gas platforms. We obtained about 46 million eDNA sequences for 5 markers from nuclear 18S V1V2, 18S V4, 18S 37F and mitochondrial 16S and COI genes that cover a wide diversity of benthic and planktonic eukaryotes. Our results showed some impact of platform activities on benthic and pelagic communities at very close distance (<50 m), while communities for intermediate (125 m, 250 m, 500 m) and reference (1000 m, 2000 m) sites did not show any particular biodiversity changes that could be related to platforms activities. The most significant community change along the distance gradient was obtained with the 18S V1V2 marker targeting benthic eukaryotes, even though other markers showed similar trends, but to a lesser extent. These results were congruent with the AMBI index inferred from the eDNA sequences assigned to benthic macrofauna. We finally explored the relation between various physicochemical parameters, including hydrocarbons, on benthic community in the case of one of the platforms. Our results showed that these communities were not significantly impacted by most of hydrocarbons, but rather by macro-elements and sediment texture.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Switzerland.
| | - Fabrizio Frontalini
- Dipartimento di Scienze Pure e Applicate (DiSPeA), Università degli Studi di Urbino "Carlo Bo", 61029, Urbino, Italy
| | - Kristina Cermakova
- ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202, Geneva, Switzerland
| | - Laure Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Switzerland; ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202, Geneva, Switzerland
| | - Mauro Treglia
- SGS Italia S.p.A., 35010, Villafranca Padovana, Italy
| | | | | | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Switzerland; ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202, Geneva, Switzerland
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Verhoeven JTP, Salvo F, Knight R, Hamoutene D, Dufour SC. Temporal Bacterial Surveillance of Salmon Aquaculture Sites Indicates a Long Lasting Benthic Impact With Minimal Recovery. Front Microbiol 2018; 9:3054. [PMID: 30631310 PMCID: PMC6315143 DOI: 10.3389/fmicb.2018.03054] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/27/2018] [Indexed: 12/30/2022] Open
Abstract
Coastal aquaculture has experienced substantial growth in the last few decades and associated impacts on natural environments are of increasing importance. Understanding both the effects of aquaculture on marine ecosystems and the processes of recovery during fallowing periods is crucial for the development of a more environmentally sustainable industry. Because bacteria are sensitive to environmental change, surveying fluctuations in bacterial communities is a promising tool for monitoring the status of benthic environments. Here, we used 16S rRNA gene high-throughput sequencing to characterize bacterial communities in flocculent matter samples collected over a period of 3 years and at various distances from cages (0–200 meters) at production and fallow (3–35 months) salmon aquaculture sites in southern Newfoundland to evaluate the environmental impact of aquaculture on predominantly hard-bottom substrates. Bacterial composition analysis revealed four clusters, three of which (defined as “recently disturbed,” “intermediate impact,” and “high impact”) differed markedly from a fourth “low impact” cluster that contained far-field samples collected >500 m from cages. Samples within the high impact group were most often collected directly under cages, whereas those in the intermediate impact group were mainly sampled from 20 to 40 m from cages. Large scale phylum shifts (increases of Bacteroidetes, Firmicutes, Spirochaetes, and decreases in Proteobacteria and Epsilonbacteraeota) and a decline in bacterial diversity were observed in the high impact cluster, indicating significant ecological change. Samples from sites of different fallow duration were found in the high impact cluster, indicating a lack of recovery, even after 35 months of fallowing. Finally, we identified 28 genera as bacterial biomarkers, specific to one or more clusters, including genera associated with organically enriched environments and previously reported in the context of aquaculture impacts. Tracking the relative abundance of biomarkers in relation to different lengths of fallowing in the three more impacted clusters showed that these markers remained significantly above low impact cluster levels at all times, further pointing toward incomplete recovery. Our results suggest that coastal aquaculture on hard-bottom substrates is prone to long lasting impacts on bacterial communities, especially below cages, and that effects can be accurately tracked using bacterial community profiles or specific biomarkers.
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Affiliation(s)
- Joost T P Verhoeven
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Flora Salvo
- Aquaculture, Biotechnology and Aquatic Animal Health Section, Fisheries and Oceans Canada, Northwest Atlantic Fisheries Center, St. John's, NL, Canada
| | - Robyn Knight
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Dounia Hamoutene
- Aquaculture, Biotechnology and Aquatic Animal Health Section, Fisheries and Oceans Canada, Northwest Atlantic Fisheries Center, St. John's, NL, Canada
| | - Suzanne C Dufour
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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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: 197] [Impact Index Per Article: 32.8] [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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Zhong L, Li D, Wang M, Chen X, Bian W, Zhu G. Dynamics of the bacterial community in a channel catfish nursery pond with a cage-pond integration system. Can J Microbiol 2018; 64:954-967. [PMID: 30118606 DOI: 10.1139/cjm-2018-0268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The changes in the bacterial community composition in a channel catfish nursery pond with a cage-pond integration system were investigated by sequencing of the 16S rRNA gene through Illumina MiSeq sequencing platforms. A total of 1 362 877 sequences and 1440 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in the cage and pond groups were similar, including Actinobacteria, Cyanobacteria, Proteobacteria, and Bacteroidetes, although a significant difference was detected between them by ANOSIM (P < 0.05). Temporal changes and site variation were significantly related to the variation of the bacterial community. A comprehensive analysis of the diversity and evenness of the bacterial 16S rRNA gene, redundancy analysis (RDA), and partial Mantel test showed that the bacterial community composition in a cage-pond integration system was shaped more by temporal variation than by site variation. RDA also indicated that water temperature, total dissolved solids, and Secchi depth had the largest impact on bacterial populations.
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Affiliation(s)
- Liqiang Zhong
- a Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,b Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China.,c University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daming Li
- b Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Minghua Wang
- b Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Xiaohui Chen
- b Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Wenji Bian
- b Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Guangwei Zhu
- a Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,c University of Chinese Academy of Sciences, Beijing 100049, China
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37
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Forster D, Filker S, Kochems R, Breiner HW, Cordier T, Pawlowski J, Stoeck T. A Comparison of Different Ciliate Metabarcode Genes as Bioindicators for Environmental Impact Assessments of Salmon Aquaculture. J Eukaryot Microbiol 2018; 66:294-308. [DOI: 10.1111/jeu.12670] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/22/2018] [Accepted: 07/18/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Dominik Forster
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Sabine Filker
- Molecular Ecology; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Rebecca Kochems
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Hans-Werner Breiner
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Tristan Cordier
- Department of Genetics and Evolution; University of Geneva; 1211 Geneva Switzerland
| | - Jan Pawlowski
- Department of Genetics and Evolution; University of Geneva; 1211 Geneva Switzerland
- ID-Gene ecodiagnostics Ltd.; Campus Biotech Innovation Park 1202 Geneva Switzerland
| | - Thorsten Stoeck
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
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38
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PCR-based assay for Mya arenaria detection from marine environmental samples and tracking its invasion in coastal ecosystems. J Nat Conserv 2018. [DOI: 10.1016/j.jnc.2018.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Stoeck T, Frühe L, Forster D, Cordier T, Martins CIM, Pawlowski J. Environmental DNA metabarcoding of benthic bacterial communities indicates the benthic footprint of salmon aquaculture. MARINE POLLUTION BULLETIN 2018; 127:139-149. [PMID: 29475645 DOI: 10.1016/j.marpolbul.2017.11.065] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/29/2017] [Indexed: 06/08/2023]
Abstract
We evaluated benthic bacterial communities as bioindicators in environmental impact assessments of salmon aquaculture, a rapidly growing sector of seafood industry. Sediment samples (n=72) were collected from below salmon cages towards distant reference sites. Bacterial community profiles inferred from DNA metabarcodes were compared to reference data from standard macrofauna biomonitoring surveys of the same samples. Deltaproteobacteria were predominant in immediate vicinity of the salmon cages. Along the transect, significant shifts in bacterial community structures were observed with Gammaproteobacteria dominating the less-impacted sites. Alpha- and beta-diversity measures of bacterial communities correlated significantly with macrofauna diversity metrics and with five ecological status indices. Benthic bacterial communities mirror the reaction of macrofauna bioindicators to environmental disturbances caused by salmon farming. The implementation of bacterial eDNA metabarcoding in future Strategic Framework Directives is an alternative cost-effective high-throughput biomonitoring solution, providing a basis for management strategies in a matter of days rather than months.
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Affiliation(s)
- Thorsten Stoeck
- University of Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany.
| | - Larissa Frühe
- University of Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - Dominik Forster
- University of Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - Tristan Cordier
- University of Geneva, Department of Genetics and Evolution, 1211 Geneva, Switzerland
| | | | - Jan Pawlowski
- University of Geneva, Department of Genetics and Evolution, 1211 Geneva, Switzerland; ID-Gene ecodiagnostics Ltd. 1228 Plan-les-Ouates, Switzerland
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40
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Laroche O, Wood SA, Tremblay LA, Ellis JI, Lear G, Pochon X. A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations. MARINE POLLUTION BULLETIN 2018; 127:97-107. [PMID: 29475721 DOI: 10.1016/j.marpolbul.2017.11.042] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 06/08/2023]
Abstract
Standardized ecosystem-based monitoring surveys are critical for providing information on marine ecosystem health. Environmental DNA/RNA (eDNA/eRNA) metabarcoding may facilitate such surveys by quickly and effectively characterizing multi-trophic levels. In this study, we assessed the suitability of eDNA/eRNA metabarcoding to evaluate changes in benthic assemblages of bacteria, Foraminifera and other eukaryotes along transects at three offshore oil and gas (O&G) drilling and production sites, and compared these to morphologically characterized macro-faunal assemblages. Bacterial communities were the most responsive to O&G activities, followed by Foraminifera, and macro-fauna (the latter assessed by morphology). The molecular approach enabled detection of hydrocarbon degrading taxa such as the bacteria Alcanivorax and Microbulbifer at petroleum impacted stations. Most identified indicator taxa, notably among macro-fauna, were highly specific to site conditions. Based on our results we suggest that eDNA/eRNA metabarcoding can be used as a stand-alone method for biodiversity assessment or as a complement to morphology-based monitoring approaches.
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Affiliation(s)
- Olivier Laroche
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand.
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Environmental Research Institute, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Louis A Tremblay
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Joanne I Ellis
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Centre, Thuwal 23955-6900, Saudi Arabia
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
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Hornick KM, Buschmann AH. Insights into the diversity and metabolic function of bacterial communities in sediments from Chilean salmon aquaculture sites. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1317-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Pochon X, Zaiko A, Fletcher LM, Laroche O, Wood SA. Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications. PLoS One 2017; 12:e0187636. [PMID: 29095959 PMCID: PMC5667844 DOI: 10.1371/journal.pone.0187636] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/23/2017] [Indexed: 11/19/2022] Open
Abstract
High-throughput sequencing metabarcoding studies in marine biosecurity have largely focused on targeting environmental DNA (eDNA). DNA can persist extracellularly in the environment, making discrimination of living organisms difficult. In this study, bilge water samples (i.e., water accumulating on-board a vessel during transit) were collected from 15 small recreational and commercial vessels. eDNA and eRNA molecules were co-extracted and the V4 region of the 18S ribosomal RNA gene targeted for metabarcoding. In total, 62.7% of the Operational Taxonomic Units (OTUs) were identified at least once in the corresponding eDNA and eRNA reads, with 19.5% unique to eDNA and 17.7% to eRNA. There were substantial differences in diversity between molecular compartments; 57% of sequences from eDNA-only OTUs belonged to fungi, likely originating from legacy DNA. In contrast, there was a higher percentage of metazoan (50.2%) and ciliate (31.7%) sequences in the eRNA-only OTUs. Our data suggest that the presence of eRNA-only OTUs could be due to increased cellular activities of some rare taxa that were not identified in the eDNA datasets, unusually high numbers of rRNA transcripts in ciliates, and/or artefacts produced during the reverse transcriptase, PCR and sequencing steps. The proportions of eDNA/eRNA shared and unshared OTUs were highly heterogeneous within individual bilge water samples. Multiple factors including boat type and the activities performed on-board, such as washing of scientific equipment, may play a major role in contributing to this variability. For some marine biosecurity applications analysis, eDNA-only data may be sufficient, however there are an increasing number of instances where distinguishing the living portion of a community is essential. For these circumstances, we suggest only including OTUs that are present in both eDNA and eRNA data. OTUs found only in the eRNA data need to be interpreted with caution until further research provides conclusive evidence for their origin.
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Affiliation(s)
- Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
- * E-mail:
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
- Marine Science and Technology Centre, Klaipeda University, Klaipeda, Lithuania
| | | | - Olivier Laroche
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Environmental Research Institute, University of Waikato, Hamilton, New Zealand
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Pimentel T, Marcelino J, Ricardo F, Soares AMVM, Calado R. Bacterial communities 16S rDNA fingerprinting as a potential tracing tool for cultured seabass Dicentrarchus labrax. Sci Rep 2017; 7:11862. [PMID: 28928412 PMCID: PMC5605529 DOI: 10.1038/s41598-017-11552-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/25/2017] [Indexed: 11/12/2022] Open
Abstract
Traceability of seafood has become crucial with market globalization and consumer’s awareness. The present study used PCR-DGGE and 454 pyrosequencing to assess if bacterial communities fingerprint associated to seabass (Dicentrarchus labrax) skin mucus can be used to discriminate the geographic origin of fishes cultured in three semi-intensive fish farms. PCR-DGGE and pyrosequencing results were congruent and suggested that this molecular approach has the potential to trace fish farms with a spatial resolution <500 m. Pyrosequencing results provided a detailed insight into the bacterial community composition of seabass skin mucus and revealed the existence of a core of bacterial communities within family Pseudomonadaceae and Rhodobacteraceae. This approach also allowed to recognized key OTUs that are potentially relevant to discriminate the geographic origin of the fish being surveyed. Overall, the present study increased our knowledge on farmed seabass microbiome and demonstrated that specific and unique bacterial taxa can act as natural signatures that allow us to trace fish to its respective geographic origin. Our study provides valuable clues that should be more investigated in future studies as a way to fulfill current traceability needs in the global trade of seafood.
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Affiliation(s)
- Tânia Pimentel
- Departamento de Biologia & CESAM & ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Joana Marcelino
- Instituto Universitário de Lisboa (ISCTE-IUL), DINÂMIA'CET, Avenida das Forças Armadas, 1649-026, Lisbon, Portugal
| | - Fernando Ricardo
- Departamento de Biologia & CESAM & ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Amadeu M V M Soares
- Departamento de Biologia & CESAM & ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Ricardo Calado
- Departamento de Biologia & CESAM & ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
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White CA, Nichols PD, Ross DJ, Dempster T. Dispersal and assimilation of an aquaculture waste subsidy in a low productivity coastal environment. MARINE POLLUTION BULLETIN 2017; 120:309-321. [PMID: 28535958 DOI: 10.1016/j.marpolbul.2017.05.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 06/07/2023]
Abstract
To understand dispersal and assimilation of aquaculture waste subsidies in a naturally low-productivity environment, we applied a novel, rapid transmethylation technique to analyse sediment and biota fatty acid composition. This technique was initially validated at Atlantic salmon farms in Macquarie Harbour, Australia, where sediments were collected at farm and control locations. Subsequently, sediment, benthic polychaete and zooplankton were sampled at sites 0, 50, 250, 500 and 1000m distant from multiple cages. Results demonstrated an acute deposition zone up to 50m from cages and a diffuse zone extending 500m from cages. Changes in sediment concentration of linoleic acid, oleic acid and total fatty acids were effective tracers of farm deposition. Bacterial biomarkers indicated that aquaculture waste stimulates bacterial productivity in sediments, with elevated biomarker concentrations also detected in benthic polychaetes. Overall, fatty acid analysis was a sensitive technique to characterize the benthic footprint of aquaculture influence.
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Affiliation(s)
- C A White
- Sustainable Aquaculture Laboratory - Temperate and Tropical, School of BioSciences, University of Melbourne, VIC 3010, Australia; Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organization, Castray Esplanade, Hobart, TAS 7000, Australia.
| | - P D Nichols
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organization, Castray Esplanade, Hobart, TAS 7000, Australia
| | - D J Ross
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 49, Hobart, TAS 7000, Australia
| | - T Dempster
- Sustainable Aquaculture Laboratory - Temperate and Tropical, School of BioSciences, University of Melbourne, VIC 3010, Australia
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Laroche O, Wood SA, Tremblay LA, Lear G, Ellis JI, Pochon X. Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. PeerJ 2017; 5:e3347. [PMID: 28533985 PMCID: PMC5437860 DOI: 10.7717/peerj.3347] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/22/2017] [Indexed: 11/20/2022] Open
Abstract
Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil production activity. Overall, the data appeared more robust when trimmed by shared OTUs, showing a greater effect of the platform on alpha- and beta-diversity. Trimming by shared OTUs likely removes taxa derived from legacy DNA and technical artefacts introduced through reverse transcriptase, polymerase-chain-reaction and sequencing. Findings from our scoping study suggest that metabarcoding-based biomonitoring surveys should, if funds, time and expertise allow, be assessed using both eDNA and eRNA products.
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Affiliation(s)
- Olivier Laroche
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Susanna A Wood
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Environmental Research Institute, University of Waikato, Hamilton, New Zealand
| | - Louis A Tremblay
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joanne I Ellis
- Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xavier Pochon
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
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Laroche O, Wood SA, Tremblay LA, Ellis JI, Lejzerowicz F, Pawlowski J, Lear G, Atalah J, Pochon X. First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site. MARINE ENVIRONMENTAL RESEARCH 2016; 120:225-235. [PMID: 27595900 DOI: 10.1016/j.marenvres.2016.08.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/12/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
At present, environmental impacts from offshore oil and gas activities are partly determined by measuring changes in macrofauna diversity. Morphological identification of macrofauna is time-consuming, expensive and dependent on taxonomic expertise. In this study, we evaluated the applicability of using foraminiferal-specific metabarcoding for routine monitoring. Sediment samples were collected along distance gradients from two oil platforms off Taranaki (New Zealand) and their physico-chemical properties, foraminiferal environmental DNA/RNA, and macrofaunal composition analyzed. Macrofaunal and foraminiferal assemblages showed similar shifts along impact gradients, but responded differently to environmental perturbations. Macrofauna were affected by hypoxia, whereas sediment grain size appeared to drive shifts in foraminifera. We identified eight foraminiferal molecular operational taxonomic units that have potential to be used as bioindicator taxa. Our results show that metabarcoding represents an effective tool for assessing foraminiferal communities near offshore oil and gas platforms, and that it can be used to complement current monitoring techniques.
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Affiliation(s)
- Olivier Laroche
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Susanna A Wood
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Environmental Research Institute, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Louis A Tremblay
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Joanne I Ellis
- Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Switzerland
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Javier Atalah
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Xavier Pochon
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
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Dowle EJ, Pochon X, C. Banks J, Shearer K, Wood SA. Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates. Mol Ecol Resour 2015; 16:1240-54. [DOI: 10.1111/1755-0998.12488] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/12/2015] [Accepted: 11/12/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Eddy J. Dowle
- Cawthron Institute; 98 Halifax Street 7010 Nelson New Zealand
- Department of Entomology; Kansas State University; Waters Hall Manhattan KS 66502 USA
| | - Xavier Pochon
- Cawthron Institute; 98 Halifax Street 7010 Nelson New Zealand
- Institute of Marine Science; University of Auckland; PO Box 349 Warkworth 0941 New Zealand
| | | | - Karen Shearer
- Cawthron Institute; 98 Halifax Street 7010 Nelson New Zealand
| | - Susanna A. Wood
- Cawthron Institute; 98 Halifax Street 7010 Nelson New Zealand
- Environmental Research Insitute University of Waikato; Private Bag 3105 3240 Hamilton New Zealand
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Pochon X, Wood SA, Keeley NB, Lejzerowicz F, Esling P, Drew J, Pawlowski J. Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding. MARINE POLLUTION BULLETIN 2015; 100:370-382. [PMID: 26337228 DOI: 10.1016/j.marpolbul.2015.08.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 08/09/2015] [Accepted: 08/11/2015] [Indexed: 06/05/2023]
Abstract
Assessing the environmental impact of salmon farms on benthic systems is traditionally undertaken using biotic indices derived from microscopic analyses of macrobenthic infaunal (MI) communities. In this study, we tested the applicability of using foraminiferal-specific high-throughput sequencing (HTS) metabarcoding for monitoring these habitats. Sediment samples and physico-chemical data were collected along an enrichment gradient radiating out from three Chinook salmon (Oncorhynchus tshawytscha) farms in New Zealand. HTS of environmental DNA and RNA (eDNA/eRNA) resulted in 1,875,300 sequences that clustered into 349 Operational Taxonomic Units. Strong correlations were observed among various biotic indices calculated from MI data and normalized fourth-root transformed HTS data. Correlations were stronger using eRNA compared to eDNA data. Quantile regression spline analyses identified 12 key foraminiferal taxa that have potential to be used as bioindicator species. This study demonstrates the huge potential for using this method for biomonitoring of fish-farming and other marine industrial activities.
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Affiliation(s)
- X Pochon
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand.
| | - S A Wood
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Environmental Research Institute, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - N B Keeley
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Research, PO Box 1870, Bergen 5817, Norway
| | - F Lejzerowicz
- Department of Genetics and Evolution, University of Geneva, Switzerland
| | - P Esling
- Department of Genetics and Evolution, University of Geneva, Switzerland; IRCAM, UMR 9912, Université Pierre et Marie Curie, Paris, France
| | - J Drew
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Switzerland
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