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Freixa A, Ortiz-Rivero J, Sabater S. Artificial substrata to assess ecological and ecotoxicological responses in river biofilms: Use and recommendations. MethodsX 2023; 10:102089. [PMID: 36915862 PMCID: PMC10006700 DOI: 10.1016/j.mex.2023.102089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
River biofilms are biological consortia of autotrophs and heterotrophs colonizing most solid surfaces in rivers. Biofilm composition and biomass differ according to the environmental conditions, having different characteristics between systems and even between river habitats. Artificial substrata (AS) are an alternative for in situ or laboratory experiments to handle the natural variability of biofilms. However, specific research goals may require decisions on colonization time or type of substrata. Substrata properties (i.e., texture, roughness, hydrophobicity) and the colonization period and site are selective factors of biofilm characteristics. Here we describe the uses of artificial substrata in the assessment of ecological and ecotoxicological responses and propose a decision tree for the best use of artificial substrata in river biofilm studies. We propose departing from the purpose of the study to define the necessity of obtaining a realistic biofilm community, from which it may be defined the colonization time, the colonization site, and the type of artificial substratum. Having a simple or mature biofilm community should guide our decisions on the colonization time and type of substrata to be selected for the best use of AS in biofilm studies. Tests involving contaminants should avoid adsorbing materials while those ecologically oriented may use any AS mimicking those substrata occurring in the streambed.•We review the utilization of different artificial substrata to colonize biofilm in river ecology and ecotoxicology.•We propose a decision tree to guide on selecting the appropriate artificial substrata and colonization site and duration.•Type of artificial substrata (material, size, shape...) and colonization duration are to be decided according to the specific purpose of the study.
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Affiliation(s)
- Anna Freixa
- Catalan Institute for Water Research (ICRA-CERCA), Carrer Emili Grahit 101, 17003 Girona, Spain.,University of Girona, Plaça de Sant Domènec 3, 17004, Girona, Spain
| | - Javier Ortiz-Rivero
- Catalan Institute for Water Research (ICRA-CERCA), Carrer Emili Grahit 101, 17003 Girona, Spain.,University of Girona, Plaça de Sant Domènec 3, 17004, Girona, Spain
| | - Sergi Sabater
- Catalan Institute for Water Research (ICRA-CERCA), Carrer Emili Grahit 101, 17003 Girona, Spain.,Institute of Aquatic Ecology, University of Girona, Campus de Montilivi, 17071 Girona, Spain
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2
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Matviichuk O, Mondamert L, Geffroy C, Gaschet M, Dagot C, Labanowski J. River Biofilms Microbiome and Resistome Responses to Wastewater Treatment Plant Effluents Containing Antibiotics. Front Microbiol 2022; 13:795206. [PMID: 35222329 PMCID: PMC8863943 DOI: 10.3389/fmicb.2022.795206] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/14/2022] [Indexed: 11/17/2022] Open
Abstract
Continuous exposure to low concentrations of antibiotics (sub-minimal inhibitory concentration: sub-MIC) is thought to lead to the development of antimicrobial resistance (AMR) in the environmental microbiota. However, the relationship between antibiotic exposure and resistance selection in environmental bacterial communities is still poorly understood and unproven. Therefore, we measured the concentration of twenty antibiotics, resistome quality, and analyzed the taxonomic composition of microorganisms in river biofilms collected upstream (UPS) and downstream (DWS) (at the point of discharge) from the wastewater treatment plant (WWTP) of Poitiers (France). The results of statistical analysis showed that the antibiotic content, resistome, and microbiome composition in biofilms collected UPS were statistically different from that collected DWS. According to Procrustes analysis, microbial community composition and antibiotics content may be determinants of antibiotic resistance genes (ARGs) composition in samples collected DWS. However, network analysis showed that the occurrence and concentration of antibiotics measured in biofilms did not correlate with the occurrence and abundance of antibiotic resistance genes and mobile genetic elements. In addition, network analysis suggested patterns of co-occurrence between several ARGs and three classes of bacteria/algae: Bacteroidetes incertae sedis, Cyanobacteria/Chloroplast, and Nitrospira, in biofilm collected UPS. The absence of a direct effect of antibiotics on the selection of resistance genes in the collected samples suggests that the emergence of antibiotic resistance is probably not only due to the presence of antibiotics but is a more complex process involving the cumulative effect of the interaction between the bacterial communities (biotic) and the abiotic matrix. Nevertheless, this study confirms that WWTP is an important reservoir of various ARGs, and additional efforts and legislation with clearly defined concentration limits for antibiotics and resistance determinants in WWTP effluents are needed to prevent their spread and persistence in the environment.
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Affiliation(s)
- Olha Matviichuk
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, Poitiers, France.,UMR INSERM 1092, Limoges, France
| | - Leslie Mondamert
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, Poitiers, France
| | - Claude Geffroy
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, Poitiers, France
| | | | | | - Jérôme Labanowski
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, Poitiers, France
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Cai X, Yao L, Sheng Q, Jiang L, Wang T, Dahlgren RA, Deng H. Influence of a biofilm bioreactor on water quality and microbial communities in a hypereutrophic urban river. ENVIRONMENTAL TECHNOLOGY 2021; 42:1452-1460. [PMID: 31539312 DOI: 10.1080/09593330.2019.1670267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 09/14/2019] [Indexed: 06/10/2023]
Abstract
Biofilms play an important role in degradation, transformation and assimilation of anthropogenic pollutants in aquatic ecosystems. In this study, we assembled a tubular bioreactor containing a biofilm substrate and aeration device, which was introduced into mesocosms to explore the effects of bioreactor on physicochemical and microbial characteristics of a hypereutrophic urban river. The biofilm bioreactor greatly improved water quality, especially by decreasing dissolved inorganic nitrogen (DIN) concentrations, suggesting that biofilms were the major sites of nitrification and denitrification with an oxygen concentration gradient. The biofilm bioreactor increased the abundance of planktonic bacteria, whereas diversity of the planktonic microbial community decreased. Sequencing revealed that Proteobacteria, Bacteroidetes, Planctomycetes, and Actinobacteria were the four predominant phyla in the planktonic microbial community, and the presence of the biofilm bioreactor increased the relative abundance of Proteobacteria. Variations in microbial communities were most strongly affected by the presence of the biofilm bioreactor, as indicated by principal component analysis (PCA) and redundancy analysis (RDA). This study provides valuable insights into changes in ecological characteristics associated with self-purification processes in hypereutrophic urban rivers, and may be of important for the application of biofilm bioreactor in natural urban river.
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Affiliation(s)
- Xianlei Cai
- Zhejiang Provincial Key Laboratory of Watershed Science and Health, Wenzhou Medical University, Wenzhou, People's Republic of China
- Southern Zhejiang Water Research Institute, Wenzhou, People's Republic of China
| | - Ling Yao
- Zhejiang Provincial Key Laboratory of Watershed Science and Health, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Qiyue Sheng
- Zhejiang Provincial Key Laboratory of Watershed Science and Health, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Luyao Jiang
- Zhejiang Provincial Key Laboratory of Watershed Science and Health, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Ting Wang
- Zhejiang Provincial Key Laboratory of Watershed Science and Health, Wenzhou Medical University, Wenzhou, People's Republic of China
- Southern Zhejiang Water Research Institute, Wenzhou, People's Republic of China
| | - Randy A Dahlgren
- Zhejiang Provincial Key Laboratory of Watershed Science and Health, Wenzhou Medical University, Wenzhou, People's Republic of China
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Huanhuan Deng
- Zhejiang Provincial Key Laboratory of Watershed Science and Health, Wenzhou Medical University, Wenzhou, People's Republic of China
- Southern Zhejiang Water Research Institute, Wenzhou, People's Republic of China
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Ting ASY, Zoqratt MZHM, Tan HS, Hermawan AA, Talei A, Khu ST. Bacterial and eukaryotic microbial communities in urban water systems profiled via Illumina MiSeq platform. 3 Biotech 2021; 11:40. [PMID: 33479595 PMCID: PMC7794265 DOI: 10.1007/s13205-020-02617-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/26/2020] [Indexed: 01/04/2023] Open
Abstract
Microbial communities from a lake and river flowing through a highly dense urbanized township in Malaysia were profiled by sequencing amplicons of the 16S V3-V4 and 18S V9 hypervariable rRNA gene regions via Illumina MiSeq. Results revealed that Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the dominant prokaryotic phyla; whereas, eukaryotic communities were predominantly of the SAR clade and Opisthokonta. The abundance of Pseudomonas and Flavobacterium in all sites suggested the possible presence of pathogens in the urban water systems, supported by the most probable number (MPN) values of more than 1600 per 100 mL. Urbanization could have impacted the microbial communities as transient communities (clinical, water-borne and opportunistic pathogens) coexisted with common indigenous aquatic communities (Cyanobacteria). It was concluded that in urban water systems, microbial communities vary in their abundance of microbial phyla detected along the water systems. The influences of urban land use and anthropogenic activities influenced the physicochemical properties and the microbial dynamics in the water systems. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02617-3.
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Affiliation(s)
- Adeline Su Yien Ting
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 46150 Bandar Sunway, Selangor Darul Ehsan Malaysia
| | - Muhammad Zarul Hanifah Md Zoqratt
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor Malaysia
| | - Hock Siew Tan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
| | - Andreas Aditya Hermawan
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
| | - Amin Talei
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
| | - Soon Thiam Khu
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
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Cook S, Price O, King A, Finnegan C, van Egmond R, Schäfer H, Pearson JM, Abolfathi S, Bending GD. Bedform characteristics and biofilm community development interact to modify hyporheic exchange. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141397. [PMID: 32841855 DOI: 10.1016/j.scitotenv.2020.141397] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
The physical and biological attributes of riverine ecosystems interact in a complex manner which can affect the hydrodynamic behaviour of the system. This can alter the mixing characteristics of a river at the sediment-water interface. Research on hyporheic exchange has increased in recent years driven by a greater appreciation for the importance of this dynamic ecotone in connecting and regulating river systems. An understanding of process-based interactions driving hyporheic exchange is still limited, specifically the feedbacks between the physical and biological controlling factors. The interplay between bed morphology and sediment size on biofilm community development and the impact on hyporheic exchange mechanisms, was experimentally considered. Purpose built recirculating flume systems were constructed and three profiles of bedform investigated: i) flat, ii) undulating λ = 1 m, ii) undulating λ = 0.2 m, across two different sized sediments (0.5 mm and 5 mm). The influence of biofilm growth and bedform interaction on hyporheic exchange was explored, over time, using discrete repeat injections of fluorescent dye into the flumes. Hyporheic exchange rates were greatest in systems with larger sediment sizes (5 mm) and with more bedforms (undulating λ = 0.2). Sediment size was a dominant control in governing biofilm growth and hyporheic exchange in systems with limited bedform. In systems where bedform was prevalent, sediment size and biofilm appeared to no longer be a control on exchange due to the physical influence of advective pumping. Here, exchange rates within these environments were more consistent overtime, despite greater microbial growth. As such, bedform has the potential to overcome the rate limiting effects of biotic factors on hyporheic exchange and sediment size on microbial penetration. This has implications for pollutant and nutrient penetration; bedforms increase hydrological connectivity, generating the opportunity to support microbial communities at depth and as such, improve the self-purification ability of river systems.
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Affiliation(s)
- Sarah Cook
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK; School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | | | - Andrew King
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | | | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | | | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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He J, Guo J, Fu X, Cai J. Potential use of high-throughput sequencing of bacterial communities for postmortem submersion interval estimation. Braz J Microbiol 2019; 50:999-1010. [PMID: 31364013 DOI: 10.1007/s42770-019-00119-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023] Open
Abstract
Microorganisms play vital roles in the natural decomposition of carcasses in aquatic systems. Using high-throughput sequencing techniques, we evaluated the composition and succession of microbial communities throughout the decomposition of rat carcasses in freshwater. A total of 4,428,781 high-quality 16S rRNA gene sequences and 2144 operational taxonomic units were obtained. Further analysis revealed that the microbial composition differed significantly between the epinecrotic (rat skins) and the epilithic (rocks) samples. During the carcass decomposition process, Proteobacteria became the dominant phylum in the epinecrotic, epilithic, and environmental (water) samples, followed by Firmicutes in the epinecrotic samples and Bacteroidetes in the epilithic and water samples. Microbial communities were influenced by numerous environmental factors, such as dissolved oxygen content and conductivity. Our study provides new insight about postmortem submersion interval (PMSI) estimation in aquatic environments.
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Affiliation(s)
- Jing He
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Juanjuan Guo
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Xiaoliang Fu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Jifeng Cai
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China.
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