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Papaioannou C, Geladakis G, Kommata V, Batargias C, Lagoumintzis G. Insights in Pharmaceutical Pollution: The Prospective Role of eDNA Metabarcoding. TOXICS 2023; 11:903. [PMID: 37999555 PMCID: PMC10675236 DOI: 10.3390/toxics11110903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/25/2023]
Abstract
Environmental pollution is a growing threat to natural ecosystems and one of the world's most pressing concerns. The increasing worldwide use of pharmaceuticals has elevated their status as significant emerging contaminants. Pharmaceuticals enter aquatic environments through multiple pathways related to anthropogenic activity. Their high consumption, insufficient waste treatment, and the incapacity of organisms to completely metabolize them contribute to their accumulation in aquatic environments, posing a threat to all life forms. Various analytical methods have been used to quantify pharmaceuticals. Biotechnology advancements based on next-generation sequencing (NGS) techniques, like eDNA metabarcoding, have enabled the development of new methods for assessing and monitoring the ecotoxicological effects of pharmaceuticals. eDNA metabarcoding is a valuable biomonitoring tool for pharmaceutical pollution because it (a) provides an efficient method to assess and predict pollution status, (b) identifies pollution sources, (c) tracks changes in pharmaceutical pollution levels over time, (d) assesses the ecological impact of pharmaceutical pollution, (e) helps prioritize cleanup and mitigation efforts, and (f) offers insights into the diversity and composition of microbial and other bioindicator communities. This review highlights the issue of aquatic pharmaceutical pollution while emphasizing the importance of using modern NGS-based biomonitoring actions to assess its environmental effects more consistently and effectively.
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Affiliation(s)
- Charikleia Papaioannou
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - George Geladakis
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - Vasiliki Kommata
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - Costas Batargias
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
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Zhang C, Zhao G, Jiao Y, Quan B, Lu W, Su P, Tang Y, Wang J, Wu M, Xiao N, Zhang Y, Tong J. Critical analysis on the transformation and upgrading strategy of Chinese municipal wastewater treatment plants: Towards sustainable water remediation and zero carbon emissions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165201. [PMID: 37406711 DOI: 10.1016/j.scitotenv.2023.165201] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/13/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
In the light of circular economy aspects, processing of large-scale municipal wastewater treatment plants (WWTPs) needs reconsideration to limit the overuse of energy, implement of non-green technologies and emit abundant greenhouse gas. Along with the huge increase in the worldwide population and agro-industrial activities, global environmental organizations have issued several recent roles to boost scientific and industrial communities towards sustainable development. Over recent years, China has imposed national and regional standards to control and manage the discharged liquid and solid waste, as well as to achieve carbon peaking and carbon neutrality. The aim of this report is to analyze the current state of Chinese WWTPs routing and related issues such as climate change and air pollution. The used strategies in Chinese WWTPs and upgrading trends were critically discussed. Several points were addressed including the performance, environmental impact, and energy demand of bio-enhanced technologies, including hydrolytic acidification pretreatment, efficient (toxic) strain treatment, and anaerobic ammonia oxidation denitrification technology, as well as advanced treatment technologies composed of physical and chemical treatment technologies, biological treatment technology and combined treatment technology. Discussion and critical analysis based on the current data and national policies were provided and employed to develop the future development trend of municipal WWTPs in China from the construction of sustainable and "Zero carbon" WWTPs.
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Affiliation(s)
- Chunhui Zhang
- College of Chemistry and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China.
| | - Guifeng Zhao
- College of Chemistry and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
| | - Yanan Jiao
- College of Chemistry and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
| | - Bingxu Quan
- College of Chemistry and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
| | - Wenjing Lu
- College of Chemistry and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
| | - Peidong Su
- College of Chemistry and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China.
| | - Yuanhui Tang
- College of Chemistry and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
| | - Jianbing Wang
- College of Chemistry and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
| | - Mengmeng Wu
- Zhongguancun Summit Enviro-Protection Co., Ltd., Beijing 100081, China
| | - Nan Xiao
- Zhongguancun Summit Enviro-Protection Co., Ltd., Beijing 100081, China
| | - Yizhen Zhang
- Zhongguancun Summit Enviro-Protection Co., Ltd., Beijing 100081, China
| | - Jinghua Tong
- Zhongguancun Summit Enviro-Protection Co., Ltd., Beijing 100081, China
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3
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Li C, Yao Y, Liu X, Chen H, Li X, Zhao M, Zhao H, Wang Y, Cheng Z, Wang L, Cheng J, Sun H. Integrated metabolomics, transcriptomics, and proteomics analyses reveal co-exposure effects of polycyclic aromatic hydrocarbons and cadmium on ryegrass (Lolium perenne L.). ENVIRONMENT INTERNATIONAL 2023; 178:108105. [PMID: 37517176 DOI: 10.1016/j.envint.2023.108105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023]
Abstract
Cadmium (Cd) and polycyclic aromatic hydrocarbons (PAHs) are prominent soil contaminants found in industrial sites, and their combined effects on plants are not yet fully understood. To investigate the mechanisms underlying the co-exposure of Cd and PAHs and identify key biomarkers for their co-effects, an integrated analysis of metabolomics, transcriptomics, and proteomics was conducted on ryegrass leaves cultivated in soil. In nontarget metabolomics analysis, nine differentially expressed metabolites that were specifically induced by the compound exposure were identified. When combined with the analysis of differentially expressed genes and proteins, it was determined that the major pathways involved in the response to the co-stress of Cd and PAHs were linoleic acid metabolism and phenylpropanoid biosynthesis. The upregulation of 12,13-dihydroxy-9Z-octadecenoic acid and the downregulation of sinapyl alcohol were identified as typical biomarkers, respectively. Compared to scenarios of single exposures, the compound exposure to Cd and PAHs disrupted the oxidation of linoleic acid, leading to alterations in the profiles of linoleate metabolites. Additionally, it intensified hydroxylation, carboxylation, and methylation processes, and interfered with reactions involving coenzyme A, thus inhibiting lignin production. As a result, oxidative stress was elevated, and the cell wall defense system in ryegrass was weakened. The findings of this study highlight the ecological risks associated with unique biological responses in plants co-exposed to Cd and PAHs in polluted soils.
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Affiliation(s)
- Cheng Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China; College of Geography and Environment, Shandong Normal University, Jinan 250358, China
| | - Yiming Yao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China.
| | - Xiaosong Liu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Hao Chen
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Xiaoxiao Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Maosen Zhao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Hongzhi Zhao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Yu Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Zhipeng Cheng
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Lei Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Jiemin Cheng
- College of Geography and Environment, Shandong Normal University, Jinan 250358, China
| | - Hongwen Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
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Ríos-Castro R, Cabo A, Teira E, Cameselle C, Gouveia S, Payo P, Novoa B, Figueras A. High-throughput sequencing as a tool for monitoring prokaryote communities in a wastewater treatment plant. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160531. [PMID: 36470389 DOI: 10.1016/j.scitotenv.2022.160531] [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: 09/14/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
In this study, the DNA metabarcoding technique was used to explore the prokaryote diversity and community structure in wastewater collected in spring and winter 2020-2021 as well as the efficiency of the treatment in a wastewater treatment plant (WWTP) in Ría de Vigo (NW Spain). The samplings included raw wastewater from the inlet stream (M1), the discharge water after the disinfection treatment (M3) and mussels used as bioindicators of possible contamination of the marine environment. Significant differences were discovered in the microbiome of each type of sample (M1, M3 and mussels), with 92 %, 45 % and 44 % of exclusive OTUs found in mussel, M3 and M1 samples respectively. Seasonal differences were also detected in wastewater samples, with which abiotic parameters (temperature, pH) could be strongly involved. Bacteria present in raw wastewater (M1) were associated with the human gut microbiome, and therefore, potential pathogens that could be circulating in the population in specific periods were detected (e.g., Arcobacter sp. and Clostridium sp.). A considerable decrease in putative pathogenic organisms from the M1 to M3 wastewater fractions and the scarce presence in mussels (<0.5 % total reads) confirmed the effectiveness of pathogen removal in the wastewater treatment plant. Our results showed the potential of the DNA metabarcoding technique for monitoring studies and confirmed its application in wastewater-based epidemiology (WBE) and environmental contamination studies. Although this technique cannot determine if the infective pathogens are present, it can characterize the microbial communities and the putative pathogens that are circulating through the population (microbiome of M1) and also confirm the efficacy of depuration treatment, which can directly affect the aquaculture sector and even human and veterinary health.
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Affiliation(s)
- Raquel Ríos-Castro
- Marine Research Institute IIM-CSIC, Spanish National Research Council, Eduardo Cabello 6, 36208 Vigo, Spain.
| | - Adrián Cabo
- University of Vigo, BiotecnIA Group, Department of Chemical Engineering, 36310 Vigo, Spain.
| | - Eva Teira
- University of Vigo, Departamento de Ecología y Biología Animal, Centro de Investigación Marina (CIM), Universidad de Vigo, Facultad de Ciencias do Mar, 36310 Vigo, Spain.
| | - Claudio Cameselle
- University of Vigo, BiotecnIA Group, Department of Chemical Engineering, 36310 Vigo, Spain
| | - Susana Gouveia
- University of Vigo, BiotecnIA Group, Department of Chemical Engineering, 36310 Vigo, Spain
| | - Pedro Payo
- GESECO Aguas S.A., Teixugueiras 13, 36212 Vigo, Spain.
| | - Beatriz Novoa
- Marine Research Institute IIM-CSIC, Spanish National Research Council, Eduardo Cabello 6, 36208 Vigo, Spain.
| | - Antonio Figueras
- Marine Research Institute IIM-CSIC, Spanish National Research Council, Eduardo Cabello 6, 36208 Vigo, Spain.
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Ciliate Morpho-Taxonomy and Practical Considerations before Deploying Metabarcoding to Ciliate Community Diversity Surveys in Urban Receiving Waters. Microorganisms 2022; 10:microorganisms10122512. [PMID: 36557765 PMCID: PMC9787992 DOI: 10.3390/microorganisms10122512] [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: 10/26/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Disentangling biodiversity and community assembly effects on ecosystem function has always been an important topic in ecological research. The development and application of a DNA metabarcoding method has fundamentally changed the way we describe prokaryotic communities and estimate biodiversity. Compared to prokaryotes (bacteria and archaea), the eukaryotic microbes (unicellular eukaryotes) also fulfill extremely important ecological functions in different ecosystems regarding their intermediate trophic positions. For instance, ciliated microbes (accounting for a substantial portion of the diversity of unicellular eukaryotes) perform pivotal roles in microbial loops and are essential components in different ecosystems, especially in water purification processes. Therefore, the community composition of ciliated species has been widely utilized as a proxy for water quality and biological assessment in urban river ecosystems and WWTPs (wastewater treatment plants). Unfortunately, investigating the dynamic changes and compositions in ciliate communities relies heavily on existing morpho-taxonomical descriptions, which is limited by traditional microscopic approaches. To deal with this dilemma, we discuss the DNA-based taxonomy of ciliates, the relative merits and challenges of deploying its application using DNA metabarcoding for surveys of ciliate community diversity in urban waterbodies, and provide suggestions for minimizing relevant sources of biases in its implementation. We expect that DNA metabarcoding could untangle relationships between community assembly and environmental changes affecting ciliate communities. These analyses and discussions could offer a replicable method in support of the application of evaluating communities of ciliated protozoa as indicators of urban freshwater ecosystems.
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Bohmann K, Elbrecht V, Carøe C, Bista I, Leese F, Bunce M, Yu DW, Seymour M, Dumbrell AJ, Creer S. Strategies for sample labelling and library preparation in DNA metabarcoding studies. Mol Ecol Resour 2022; 22:1231-1246. [PMID: 34551203 PMCID: PMC9293284 DOI: 10.1111/1755-0998.13512] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022]
Abstract
Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to target a taxonomically informative marker within a taxonomic group, and sample-specific nucleotide identifiers are added to the amplicons prior to sequencing. The latter enables assignment of the sequences back to the samples they originated from. Nucleotide identifiers can be added during the metabarcoding PCR and during "library preparation", that is, when amplicons are prepared for sequencing. Different strategies to achieve this labelling exist. All have advantages, challenges and limitations, some of which can lead to misleading results, and in the worst case compromise the fidelity of the metabarcoding data. Given the range of questions addressed using metabarcoding, ensuring that data generation is robust and fit for the chosen purpose is critically important for practitioners seeking to employ metabarcoding for biodiversity assessments. Here, we present an overview of the three main workflows for sample-specific labelling and library preparation in metabarcoding studies on Illumina sequencing platforms; one-step PCR, two-step PCR, and tagged PCR. Further, we distill the key considerations for researchers seeking to select an appropriate metabarcoding strategy for their specific study. Ultimately, by gaining insights into the consequences of different metabarcoding workflows, we hope to further consolidate the power of metabarcoding as a tool to assess biodiversity across a range of applications.
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Affiliation(s)
- Kristine Bohmann
- Faculty of Health and Medical SciencesSection for Evolutionary GenomicsGlobe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Vasco Elbrecht
- Department of Environmental Systems ScienceETH ZurichZürichSwitzerland
| | - Christian Carøe
- Faculty of Health and Medical SciencesSection for Evolutionary GenomicsGlobe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Iliana Bista
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Tree of LifeWellcome Sanger InstituteHinxtonUK
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) LaboratorySchool of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- School of Biological SciencesNorwich Research ParkUniversity of East AngliaNorwichUK
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming YunnanChina
| | - Mathew Seymour
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Simon Creer
- Molecular Ecology and Evolution GroupSchool of Natural SciencesBangor UniversityGwyneddUK
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Bonfantine KL, Trevathan-Tackett SM, Matthews TG, Neckovic A, Gan HM. Dumpster diving for diatom plastid 16S rRNA genes. PeerJ 2021; 9:e11576. [PMID: 34249491 PMCID: PMC8255066 DOI: 10.7717/peerj.11576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 05/18/2021] [Indexed: 11/20/2022] Open
Abstract
High throughput sequencing is improving the efficiency of monitoring diatoms, which inhabit and support aquatic ecosystems across the globe. In this study, we explored the potential of a standard V4 515F-806RB primer pair in recovering diatom plastid 16S rRNA sequences. We used PhytoREF to classify the 16S reads from our freshwater biofilm field sampling from three stream segments across two streams in south-eastern Australia and retrieved diatom community data from other, publicly deposited, Australian 16S amplicon datasets. When these diatom operational taxonomic units (OTUs) were traced using the default RDPII and NCBI databases, 68% were characterized as uncultured cyanobacteria. We analysed the 16S rRNA sequences from 72 stream biofilm samples, separated the chloroplast OTUs, and classified them using the PhytoREF database. After filtering the reads attributed to Bacillariophyta (relative abundance >1%), 71 diatom OTUs comprising more than 90% of the diatom reads in each stream biofilm sample were identified. Beta-diversity analyses demonstrated significantly different diatom assemblages and discrimination among river segments. To further test the approach, the diatom OTUs from our biofilm sampling were used as reference sequences to identify diatom reads from other Australian 16S rRNA datasets in the NCBI-SRA database. Across the three selected public datasets, 67 of our 71 diatom OTUs were detected in other Australian ecosystems. Our results show that diatom plastid 16S rRNA genes are readily amplified with existing 515F-806RB primer sets. Therefore, the volume of existing 16S rRNA amplicon datasets initially generated for microbial community profiling can also be used to detect, characterize, and map diatom distribution to inform phylogeny and ecological health assessments, and can be extended into a range of ecological and industrial applications. To our knowledge, this study represents the first attempt to classify freshwater samples using this approach and the first application of PhytoREF in Australia.
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Affiliation(s)
- Krista L Bonfantine
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Stacey M Trevathan-Tackett
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Ty G Matthews
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Ana Neckovic
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,GeneSEQ Sdn Bhd, Rawang, Selangor, Malaysia
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Sagova-Mareckova M, Boenigk J, Bouchez A, Cermakova K, Chonova T, Cordier T, Eisendle U, Elersek T, Fazi S, Fleituch T, Frühe L, Gajdosova M, Graupner N, Haegerbaeumer A, Kelly AM, Kopecky J, Leese F, Nõges P, Orlic S, Panksep K, Pawlowski J, Petrusek A, Piggott JJ, Rusch JC, Salis R, Schenk J, Simek K, Stovicek A, Strand DA, Vasquez MI, Vrålstad T, Zlatkovic S, Zupancic M, Stoeck T. Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring. WATER RESEARCH 2021; 191:116767. [PMID: 33418487 DOI: 10.1016/j.watres.2020.116767] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/14/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.
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Affiliation(s)
- M Sagova-Mareckova
- Dept. of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, Prague 6, 16500, Czechia.
| | - J Boenigk
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - A Bouchez
- UMR CARRTEL, INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - K Cermakova
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, 15, av. Sécheron, 1202 Geneva, Switzerland
| | - T Chonova
- UMR CARRTEL, INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Science III, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland
| | - U Eisendle
- University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - T Elersek
- National Institute of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Via Salaria km 29,300 - C.P. 10, 00015 Monterotondo St., Rome, Italy
| | - T Fleituch
- Institute of Nature Conservation, Polish Academy of Sciences, ul. Adama Mickiewicza 33, 31-120 Krakow, Poland
| | - L Frühe
- Ecology Group, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - M Gajdosova
- Dept. of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czechia
| | - N Graupner
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - A Haegerbaeumer
- Dept. of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - A-M Kelly
- School of Natural Sciences, Trinity College Dublin, University of Dublin, College Green, Dublin 2, D02 PN40, Ireland
| | - J Kopecky
- Epidemiology and Ecology of Microoganisms, Crop Research Institute, Drnovská 507, 16106 Prague 6, Czechia
| | - F Leese
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany; Aquatic Ecosystem Resarch, University of Duisburg-Essen, Universitaetsstrasse 5 D-45141 Essen, Germany
| | - P Nõges
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
| | - S Orlic
- Institute Ruđer Bošković, Bijenička 54, 10000 Zagreb, Croatia; Center of Excellence for Science and Technology Integrating Mediterranean, Bijenička 54,10 000 Zagreb, Croatia
| | - K Panksep
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
| | - J Pawlowski
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, 15, av. Sécheron, 1202 Geneva, Switzerland; Department of Genetics and Evolution, University of Geneva, Science III, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - A Petrusek
- Dept. of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czechia
| | - J J Piggott
- School of Natural Sciences, Trinity College Dublin, University of Dublin, College Green, Dublin 2, D02 PN40, Ireland
| | - J C Rusch
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway; Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - R Salis
- Department of Biology, Faculty of Science, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
| | - J Schenk
- Dept. of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - K Simek
- Institute of Hydrobiology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czechia
| | - A Stovicek
- Dept. of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, Prague 6, 16500, Czechia
| | - D A Strand
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway
| | - M I Vasquez
- Department of Chemical Engineering, Cyprus University of Technology, 30 Arch. Kyprianos Str., 3036 Limassol, Cyprus
| | - T Vrålstad
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway
| | - S Zlatkovic
- Ministry of Environmental Protection, Omladinskih brigada 1, 11070 Belgrade, Serbia; Agency "Akvatorija", 11. krajiške divizije 49, 11090 Belgrade, Serbia
| | - M Zupancic
- National Institute of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
| | - T Stoeck
- Ecology Group, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
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Tian L, Wang L. Multi-omics analysis reveals structure and function of biofilm microbial communities in a pre-denitrification biofilter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143908. [PMID: 33316516 DOI: 10.1016/j.scitotenv.2020.143908] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
The highly complex microbial communities in biofilm play crucial roles in the pollutant removal performance of wastewater treatment plants (WWTPs). In the present study, using multi-omics analysis, we studied microbial structure, key enzymes, functional traits, and key metabolic pathways of pre-denitrification biofilter in an urban WWTP in China. The analysis results of metagenomic and metaproteomic showed that Betaproteobacteria and Flavobacteriia were dominant in biofilms. The integrated metagenomic and metaproteomic data showed that the expression of nitrogen metabolism genes was high, and the high proportion of denitrification module indicating that denitrification was the main nitrogen removal pathway. The most abundant denitrifying bacterial genera were: Dechloromonas, Acidovorax, Bosea, Polaromonas, and Chryseobacterium. And microorganisms with denitrification potential may not be able to denitrify in the actual operation of the filter. The integrated analysis of metaproteomic and metabolomic showed that there was a correlation between biofilm microorganisms and metabolites. Metabolomic analysis indicated that metabolic profiles of biofilms varied with layer height. This study provides the first detailed microbial communities and metabolic profiles in a full-scale pre-denitrification biofilter and clarifies the mechanism of denitrification.
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Affiliation(s)
- Lu Tian
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Lin Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
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10
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Carøe C, Bohmann K. Tagsteady: A metabarcoding library preparation protocol to avoid false assignment of sequences to samples. Mol Ecol Resour 2020; 20:1620-1631. [PMID: 32663358 DOI: 10.1111/1755-0998.13227] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 11/30/2022]
Abstract
Metabarcoding of environmental DNA (eDNA) and DNA extracted from bulk specimen samples is a powerful tool in studies of biodiversity, diet and ecological interactions as its inherent labelling of amplicons allows sequencing of taxonomically informative genetic markers from many samples in parallel. However, the occurrence of so-called 'tag-jumps' can cause incorrect assignment of sequences to samples and artificially inflate diversity. Two steps during library preparation of pools of 5' nucleotide-tagged amplicons have been suggested to cause tag-jumps: (a) T4 DNA polymerase blunt-ending in the end-repair step and (b) postligation PCR amplification of amplicon libraries. The discovery of tag-jumps has led to recommendations to only carry out metabarcoding PCR amplifications with primers carrying twin-tags to ensure that tag-jumps cannot result in false assignments of sequences to samples. As this increases both cost and workload, a metabarcoding library preparation protocol which circumvents the two steps that causes tag-jumps is needed. Here, we demonstrate Tagsteady, a PCR-free metabarcoding Illumina library preparation protocol for pools of nucleotide-tagged amplicons that enables efficient and cost-effective generation of metabarcoding data with virtually no tag-jumps. We use pools of twin-tagged amplicons to investigate the effect of T4 DNA polymerase blunt-ending and postligation PCR on the occurrence of tag-jumps and demonstrate that both blunt-ending and postligation PCR, alone or together, can result in detrimental amounts of tag-jumps (here, up to ca. 49% of total sequences), while leaving both steps out (the Tagsteady protocol) results in amounts of sequences carrying new combinations of used tags (tag-jumps) comparable to background contamination.
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Affiliation(s)
- Christian Carøe
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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11
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Lequette K, Ait-Mouheb N, Wéry N. Drip irrigation biofouling with treated wastewater: bacterial selection revealed by high-throughput sequencing. BIOFOULING 2019; 35:217-229. [PMID: 30935236 DOI: 10.1080/08927014.2019.1591377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/18/2019] [Accepted: 03/03/2019] [Indexed: 06/09/2023]
Abstract
Clogging of drippers due to the development of biofilms weakens the advantages and impedes the implementation of drip irrigation technology. The objective of this study was to characterise the bacterial community of biofilms that develop in a drip irrigation system supplied with treated wastewater. High-throughput sequencing of 16S rRNA gene amplicons indicated that the bacterial community composition differed between drippers and pipes, mainly due to changes in the abundance of the genus Aquabacterium. Cyanobacteria were found to be involved in the biological fouling of drippers. Moreover, bacterial genera including opportunistic pathogenic bacteria such as Legionella and Pseudomonas were more abundant in dripper and pipe biofilms than in the incoming water. Some genera such as Pseudomonas were mostly recovered from drippers, while others (ie Bacillus, Brevundimonas) mainly occurred in pipes. Variations in the hydraulic conditions and properties of the materials likely explain the shift in bacterial communities observed between pipes and drippers.
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Affiliation(s)
- Kévin Lequette
- a LBE, Univ Montpellier, INRA , Narbonne , France
- b IRSTEA, UMR G-EAU, University of Montpellier , Montpellier , France
| | - Nassim Ait-Mouheb
- b IRSTEA, UMR G-EAU, University of Montpellier , Montpellier , France
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