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Kang M, Le VV, Ko SR, Chun SJ, Choi DY, Shin Y, Kim K, Baek SH, Ahn CY. Effect of rainfall in shaping microbial community during Microcystis bloom in Nakdong River, Korea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172482. [PMID: 38621529 DOI: 10.1016/j.scitotenv.2024.172482] [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: 01/26/2024] [Revised: 03/20/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
Various environmental factors play a role in the formation and collapse of Microcystis blooms. This study investigates the impact of heavy rainfall on cyanobacterial abundance, microbial community composition, and functional dynamics in the Nakdong River, South Korea, during typical and exceptionally rainy years. The results reveal distinct responses to rainfall variations, particularly in cyanobacterial dominance and physicochemical characteristics. In 2020, characterized by unprecedented rainfall from mid-July to August, Microcystis blooms were interrupted significantly, exhibiting lower cell densities and decreased water temperature, compared to normal bloom patterns in 2019. Moreover, microbial community composition varied, with increases in Gammaproteobacteria and notably in genera of Limnohabitans and Fluviicola. These alterations in environmental conditions and bacterial community were similar to those of the post-bloom period in late September 2019. It shows that heavy rainfall during summer leads to changes in environmental factors, consequently causing shifts in bacterial communities akin to those observed during the autumn-specific post-bloom period in typical years. These changes also accompany shifts in bacterial functions, primarily involved in the degradation of organic matter such as amino acids, fatty acids, and terpenoids, which are assumed to have been released due to the significant collapse of cyanobacteria. Our results demonstrate that heavy rainfall in early summer induces changes in the environmental factors and subsequently microbial communities and their functions, similar to those of the post-bloom period in autumn, leading to the earlier breakdown of Microcystis blooms.
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Affiliation(s)
- Mingyeong Kang
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Ve Van Le
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seong-Jun Chun
- LMO Research Team, National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon 33657, Republic of Korea
| | - Dong-Yun Choi
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yuna Shin
- Water Quality Assessment Research Division, National Institute of Environmental Research, Incheon 22689, Republic of Korea
| | - Kyunghyun Kim
- Water Quality Assessment Research Division, National Institute of Environmental Research, Incheon 22689, Republic of Korea
| | - Seung Ho Baek
- Ecological Risk Research Department, Korea Institute of Ocean Science and Technology (KIOST), Geoje 53201, Republic of Korea; Department of Ocean Science, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
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Anju VT, Busi S, Mohan MS, Salim SA, Ar S, Imchen M, Kumavath R, Dyavaiah M, Prasad R. Surveillance and mitigation of soil pollution through metagenomic approaches. Biotechnol Genet Eng Rev 2024; 40:589-622. [PMID: 36881114 DOI: 10.1080/02648725.2023.2186330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.
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Affiliation(s)
- V T Anju
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Mahima S Mohan
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Simi Asma Salim
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Sabna Ar
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ranjith Kumavath
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ram Prasad
- Department of Botany, School of Life Sciences, Mahatma Gandhi Central University, Bihar, India
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Koloti LE, Nkuna R, Matambo TS. Impact of current anthropogenic activities on Blesbokspruit wetland microbiome and functions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170010. [PMID: 38219994 DOI: 10.1016/j.scitotenv.2024.170010] [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: 05/16/2023] [Revised: 01/03/2024] [Accepted: 01/06/2024] [Indexed: 01/16/2024]
Abstract
Till present, natural wetlands have been continuously subjected to intensive pollution stress in recent years, mainly because of the rapidly growing industrialization and urbanization that are associated with a myriad of anthropogenic activities and land use practices. These man-made sources of pollution change the chemical properties of the natural wetlands, which in turn alter their microbial ecological biodiversity and functions. For the first time, the impact of the current anthropogenic activities and land use practices on the Blesbokspruit wetland chemical status and their consequential effect on the microbial structure and functions were investigated. Sites of high pollution intensity were identified using geographic information systems mapping (GISMapping) and the wetland microbiome and functional profile were studied through the use of high throughput shotgun metagenomics sequencing analysis. The predominant phyla that stemmed along the Blesbokspruit wetland were found to be Proteobacteria which was more dominant in water (93 %) than in the sediments (89 %), followed by firmicutes which was more abundant in sediments (9 %) than in water (6 %), and Bacteroidetes were relatively low in abundance within both the sediments (2 %) and the overlying water (1 %). The genera Klebsiella (70.4 %-28.2 %), Citrobacter (52.0 %-30.6 %), Escherichia (51.0 %-8.4 %), and Lynsinibacillus (9.3 %-1.5 %) were observed in most water and sediment samples. Within the six polluted sites, Site 2 was found to be the most highly polluted site in the Blesbokspruit wetland with very high COD (900 mg/L), TOC (11.60 mg/L), NO3- (39.74 mg/L), NO2- (12.64 mg/L), PO43 (4.14 mg/L), Fl- (143.88 mg/L), Cl- (145.95 mg/L) concentrations recorded in the water and high levels of TOC (0.37 mg/L), TC (6.92 %), TN (1.82 %), TS (0.53 %) in sediments. The microbial community structure and functions were found to be strongly influenced by the high organic content from the intense agricultural activities and sewage spillages and heavy metals from the mining activities nearby.
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Affiliation(s)
- Lebohang E Koloti
- Institute for the Development of Energy for African Sustainability (IDEAS), University of South Africa, Christiaan De Wet/Pioneer, P.O. Box X6, FL 1710, South Africa
| | - Rosina Nkuna
- Institute for the Development of Energy for African Sustainability (IDEAS), University of South Africa, Christiaan De Wet/Pioneer, P.O. Box X6, FL 1710, South Africa
| | - Tonderayi S Matambo
- Institute for the Development of Energy for African Sustainability (IDEAS), University of South Africa, Christiaan De Wet/Pioneer, P.O. Box X6, FL 1710, South Africa; Centre of Competence in Environmental Biotechnology, College of Agriculture and Environmental Sciences, University of South Africa, Christiaan De Wet/Pioneer, P.O. Box X6, FL 1710, South Africa.
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Knorr S, Weisener CG, Phillips LA. The role of agricultural drainage, storm-events, and natural filtration on the biogeochemical cycling capacity of aquatic and sediment environments in Lake Erie's drainage basin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167102. [PMID: 37717759 DOI: 10.1016/j.scitotenv.2023.167102] [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: 04/27/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
Lake Erie is the most at risk of the Great Lakes for degraded water quality due to non-point source pollution caused by agricultural activities in the lake's watershed. The extent and temporal patterns of nutrient loading from these agricultural activities is influenced by the timing of agronomic events, precipitation events, and water flow through areas of natural filtration within the watershed. Downstream impacts of these nutrient loading events may be moderated by the co-loading of functionally relevant biogeochemical cycling microbial communities from agricultural soils. This study quantified loading patterns of these communities from tile drain sources, assessed whether functional communities from agricultural sources influenced downstream microbial functionality, and investigated how distance from agricultural sources, storm events, and areas of natural filtration altered nutrient cycling and nutrient fluxes in aquatic and sediment environments. Water and sediment samples were collected in the Wigle Creek watershed in Ontario, from tile drains through to Lake Erie, from May to November 2021, and microbial nitrogen (N) and phosphorous (P) cycling capacity (quantitative PCR), and nutrient levels were evaluated. Results showed that N and P functional groups were co-loaded with nutrients, with increased loading occurring during storm events and during agricultural activities including fertilization and harvest. Overall functional capacity in the aquatic environment decreased with distance from the agricultural sources and as water transited through natural filtration areas. In contrast, the sediment environment was more resilient to both agricultural disturbances and abiotic factors. This study expands our understanding of when and where different stages of N and P cycling occurs in agriculturally impacted watersheds, and identifies both seasons and regions to target with nutrient mitigation strategies.
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Affiliation(s)
- S Knorr
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON N0R 1G0, Canada; Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - C G Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - L A Phillips
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON N0R 1G0, Canada.
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Campos MA, Zhang Q, Acuña JJ, Rilling JI, Ruiz T, Carrazana E, Reyno C, Hollenback A, Gray K, Jaisi DP, Ogram A, Bai J, Zhang L, Xiao R, Elias M, Sadowsky MJ, Hu J, Jorquera MA. Structure and Functional Properties of Bacterial Communities in Surface Sediments of the Recently Declared Nutrient-Saturated Lake Villarrica in Southern Chile. MICROBIAL ECOLOGY 2023; 86:1513-1533. [PMID: 36752910 DOI: 10.1007/s00248-023-02173-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Lake Villarrica, one of Chile's main freshwater water bodies, was recently declared a nutrient-saturated lake due to increased phosphorus (P) and nitrogen (N) levels. Although a decontamination plan based on environmental parameters is being established, it does not consider microbial parameters. Here, we conducted high-throughput DNA sequencing and quantitative polymerase chain reaction (qPCR) analyses to reveal the structure and functional properties of bacterial communities in surface sediments collected from sites with contrasting anthropogenic pressures in Lake Villarrica. Alpha diversity revealed an elevated bacterial richness and diversity in the more anthropogenized sediments. The phylum Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria dominated the community. The principal coordinate analysis (PCoA) and redundancy analysis (RDA) showed significant differences in bacterial communities of sampling sites. Predicted functional analysis showed that N cycling functions (e.g., nitrification and denitrification) were significant. The microbial co-occurrence networks analysis suggested Chitinophagaceae, Caldilineaceae, Planctomycetaceae, and Phycisphaerae families as keystone taxa. Bacterial functional genes related to P (phoC, phoD, and phoX) and N (nifH and nosZ) cycling were detected in all samples by qPCR. In addition, an RDA related to N and P cycling revealed that physicochemical properties and functional genes were positively correlated with several nitrite-oxidizing, ammonia-oxidizing, and N-fixing bacterial genera. Finally, denitrifying gene (nosZ) was the most significant factor influencing the topological characteristics of co-occurrence networks and bacterial interactions. Our results represent one of a few approaches to elucidate the structure and role of bacterial communities in Chilean lake sediments, which might be helpful in conservation and decontamination plans.
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Affiliation(s)
- Marco A Campos
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Qian Zhang
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, 361100, People's Republic of China
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Joaquin I Rilling
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Tay Ruiz
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Elizabeth Carrazana
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Doctorado en Ciencias mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Cristóbal Reyno
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Doctorado en Ciencias mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Anthony Hollenback
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Katelyn Gray
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Deb P Jaisi
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Andrew Ogram
- Soil and Water Sciences Department, University of Florida, PO Box 110290, Gainesville, FL, 32608-32611, USA
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Ling Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Rong Xiao
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Mikael Elias
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
| | - Jingming Hu
- College of the Environment & Ecology, Xiamen University, Xiamen, 361100, People's Republic of China
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
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Wiesner-Friedman C, Beattie RE, Stewart JR, Hristova KR, Serre ML. Identifying sources of antibiotic resistance genes in the environment using the microbial Find, Inform, and Test framework. Front Microbiol 2023; 14:1223876. [PMID: 37731922 PMCID: PMC10508347 DOI: 10.3389/fmicb.2023.1223876] [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: 05/16/2023] [Accepted: 08/07/2023] [Indexed: 09/22/2023] Open
Abstract
Introduction Antimicrobial resistance (AMR) is an increasing public health concern for humans, animals, and the environment. However, the contributions of spatially distributed sources of AMR in the environment are not well defined. Methods To identify the sources of environmental AMR, the novel microbial Find, Inform, and Test (FIT) model was applied to a panel of five antibiotic resistance-associated genes (ARGs), namely, erm(B), tet(W), qnrA, sul1, and intI1, quantified from riverbed sediment and surface water from a mixed-use region. Results A one standard deviation increase in the modeled contributions of elevated AMR from bovine sources or land-applied waste sources [land application of biosolids, sludge, and industrial wastewater (i.e., food processing) and domestic (i.e., municipal and septage)] was associated with 34-80% and 33-77% increases in the relative abundances of the ARGs in riverbed sediment and surface water, respectively. Sources influenced environmental AMR at overland distances of up to 13 km. Discussion Our study corroborates previous evidence of offsite migration of microbial pollution from bovine sources and newly suggests offsite migration from land-applied waste. With FIT, we estimated the distance-based influence range overland and downstream around sources to model the impact these sources may have on AMR at unsampled sites. This modeling supports targeted monitoring of AMR from sources for future exposure and risk mitigation efforts.
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Affiliation(s)
- Corinne Wiesner-Friedman
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, United States
| | - Rachelle E. Beattie
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, United States
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Jill R. Stewart
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | - Marc L. Serre
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Stach TL, Sieber G, Shah M, Simon SA, Soares A, Bornemann TLV, Plewka J, Künkel J, Becker C, Meyer F, Boenigk J, Probst AJ. Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater. Microbiologyopen 2023; 12:e1347. [PMID: 37186231 PMCID: PMC10012233 DOI: 10.1002/mbo3.1347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/02/2023] [Accepted: 02/17/2023] [Indexed: 03/15/2023] Open
Abstract
Microbial communities in freshwater streams play an essential role in ecosystem functioning via biogeochemical cycling. Yet, the impacts of treated wastewater influx into stream ecosystems on microbial strain diversity remain mostly unexplored. Here, we coupled full-length 16S ribosomal RNA gene Nanopore sequencing and strain-resolved metagenomics to investigate the impact of treated wastewater on a mesocosm system (AquaFlow) run with restored river water. Over 10 days, community Bray-Curtis dissimilarities between treated and control mesocosm decreased (0.57 ± 0.058 to 0.26 ± 0.046) based on ribosomal protein S3 gene clustering, finally converging to nearly identical communities. Similarly, strain-resolved metagenomics revealed a high diversity of bacteria and viruses after the introduction of treated wastewater; these microbes also decreased over time resulting in the same strain clusters in control and treatment at the end of the experiment. Specifically, 39.2% of viral strains detected in all samples were present after the introduction of treated wastewater only. Although bacteria present at low abundance in the treated wastewater introduced additional antibiotic resistance genes, signals of naturally occurring ARG-encoding organisms resembled the resistome at the endpoint. Our results suggest that the previously stressed freshwater stream and its microbial community are resilient to a substantial introduction of treated wastewater.
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Affiliation(s)
- Tom L. Stach
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
| | - Guido Sieber
- Department of BiodiversityUniversity of Duisburg‐EssenEssenGermany
| | - Manan Shah
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
- Department of BiodiversityUniversity of Duisburg‐EssenEssenGermany
| | - Sophie A. Simon
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
| | - André Soares
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
| | - Till L. V. Bornemann
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
| | - Julia Plewka
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
| | - Julian Künkel
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
| | | | - Folker Meyer
- Institute for Artificial IntelligenceUniversity of Duisburg‐EssenEssenGermany
| | - Jens Boenigk
- Department of BiodiversityUniversity of Duisburg‐EssenEssenGermany
- Centre of Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Alexander J. Probst
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
- Centre of Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
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Vignale FA, Bernal Rey D, Pardo AM, Almasqué FJ, Ibarra JG, Fernández Do Porto D, Turjanski AG, López NI, Helman RJM, Raiger Iustman LJ. Spatial and Seasonal Variations in the Bacterial Community of an Anthropogenic Impacted Urban Stream. MICROBIAL ECOLOGY 2023; 85:862-874. [PMID: 35701635 DOI: 10.1007/s00248-022-02055-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/02/2022] [Indexed: 05/04/2023]
Abstract
Environmental changes and human activities can alter the structure and diversity of aquatic microbial communities. In this work, we analyzed the bacterial community dynamics of an urban stream to understand how these factors affect the composition of river microbial communities. Samples were taken from a stream situated in Buenos Aires, Argentina, which flows through residential, peri-urban horticultural, and industrial areas. For sampling, two stations were selected: one influenced by a series of industrial waste treatment plants and horticultural farms (PL), and the other influenced by residential areas (R). Microbial communities were analyzed by sequence analysis of 16S rRNA gene amplicons along an annual cycle. PL samples showed high nutrient content compared with R samples. The diversity and richness of the R site were more affected by seasonality than those of the PL site. At the amplicon sequence variants level, beta diversity analysis showed a differentiation between cool-season (fall and winter) and warm-season (spring and summer) samples, as well as between PL and R sites. This demonstrated that there is spatial and temporal heterogeneity in the composition of the bacterial community, which should be considered if a bioremediation strategy is applied. The taxonomic composition analysis also revealed a differential seasonal cycle of phototrophs and chemoheterotrophs between the sampling sites, as well as different taxa associated with each sampling site. This analysis, combined with a comparative analysis of global rivers, allowed us to determine the genera Arcobacter, Simplicispira, Vogesella, and Sphingomonas as potential bioindicators of anthropogenic disturbance.
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Affiliation(s)
- Federico A Vignale
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Daissy Bernal Rey
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
- Instituto de Química Física de los Materiales, Medio Ambiente Y Energía (INQUIMAE)-CONICET, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Agustín M Pardo
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
- Facultad de Ciencias Exactas Y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Facundo J Almasqué
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - José G Ibarra
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Darío Fernández Do Porto
- Facultad de Ciencias Exactas Y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Adrián G Turjanski
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Nancy I López
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Renata J Menéndez Helman
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Laura J Raiger Iustman
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina.
- Departamento de Química Biológica, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina.
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9
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Odhiambo KA, Ogola HJO, Onyango B, Tekere M, Ijoma GN. Contribution of pollution gradient to the sediment microbiome and potential pathogens in urban streams draining into Lake Victoria (Kenya). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:36450-36471. [PMID: 36543987 DOI: 10.1007/s11356-022-24517-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
In sub-Saharan Africa (SSA), urban rivers/streams have long been subjected to anthropogenic pollution caused by urbanization, resulting in significantly altered chemical and biological properties of surface water and sediments. However, little is known about the diversity and structure of river microbial community composition and pathogens, as well as how they respond to anthropogenic inputs. High-throughput 16S rRNA amplicon sequencing and PICRUSt predictive function profiling were used in this study to conduct a comprehensive analysis of the spatial bacterial distribution and metabolic functions in sediment of two urban streams (Kisat and Auji) flowing through Kisumu City, Kenya. Results revealed that sediment samples from the highly urbanized mid and lower stream catchment zones of both streams had significantly higher levels of total organic carbon (TOC), total nitrogen (TN), total phosphorous (TP) than the less urbanized upper catchment zone, and were severely polluted with toxic heavy metals lead (Pb), cadmium (Cd), and copper (Cu). Differential distribution of Actinobacteria, Proteobacteria, Chloroflexi, and Verrucomicrobia in sediment bacterial composition was detected along stream catchment zones. The polluted mid and lower catchment zones were rich in Actinobacteria and Proteobacteria, as well as a variety of potential pathogenic taxa such as Corynebacterium, Staphylococcus, Cutibacterium, Turicella, Acinetobacter, and Micrococcus, as well as enteric bacteria such as Faecalibacterium, Shewanella, Escherichia, Klebsiella, Enterococcus, Prevotella, Legionella, Vibrio and Salmonella. Furthermore, PICRUSt metabolic inference analysis revealed an increasing enrichment in the sediments of genes associated with carbon and nitrogen metabolism, disease pathogenesis, and virulence. Environmental factors (TOC, Pb, Cd, TN, pH) and geographical distance as significant drivers of sediment bacterial community assembly, with the environmental selection to play a dominant role. In polluted river catchment zone sediment samples, Pb content was the most influential sediment property, followed by TOC and Cd content. Given the predicted increase in urbanization in SSA, further alteration of surface water and sediment microbiome due to urban river pollution is unavoidable, with potential long-term effects on ecosystem function and potential health hazards. As a result, this study provides valuable information for ecological risk assessment and management of urban rivers impacted by diffuse and point source anthropogenic inputs, which is critical for future proactive and sustainable urban waste management, monitoring, and water pollution control in low-income countries.
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Affiliation(s)
- Kennedy Achieng Odhiambo
- Department of Biological Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O Box 210, Bondo, 40601, Kenya
| | - Henry Joseph Oduor Ogola
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, 1709, South Africa.
| | - Benson Onyango
- Department of Biological Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O Box 210, Bondo, 40601, Kenya
| | - Memory Tekere
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, 1709, South Africa
| | - Grace N Ijoma
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, Florida, Roodepoort, 1709, South Africa
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10
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Alaniz AJ, Smith-Ramírez C, Rendón-Funes A, Hidalgo-Corrotea C, Carvajal MA, Vergara PM, Fuentes N. Multiscale spatial analysis of headwater vulnerability in South-Central Chile reveals a high threat due to deforestation and climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157930. [PMID: 35952895 DOI: 10.1016/j.scitotenv.2022.157930] [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: 04/06/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Headwaters represent an essential component of hydrological, ecological, and socioeconomical systems, by providing constant water streams to the complete basin. However, despite the high importance of headwaters, there is a lack of vulnerability assessments worldwide. Identifying headwaters and their vulnerability in a spatially explicit manner can enable restauration and conservation programs. In this study, we assess the vulnerability of headwaters in South-Central Chile (38.4 to 43.2°S) considering multiple degradation factors related to climate change and land cover change. We analyzed 2292 headwaters, characterizing multiple factors at five spatial scales by using remote sensing data related to Land Use and Cover Change (LUCC), human disturbances, vegetation cover, climate change, potential water demand, and physiography. We then generated an index of vulnerability by integrating all the analyzed variables, which allowed us to map the spatial distribution of headwater vulnerability. Finally, to estimate the main drivers of degradation, we performed a Principal Components Analysis with an Agglomerative Hierarchical Clustering, that allowed us to group headwaters according to the analyzed factors. The largest proportion of most vulnerable headwaters are located in the north of our study area with 48.1 %, 62.1 %, and 28.1 % of headwaters classified as highly vulnerable at 0, 10, and 30 m scale, respectively. The largest proportion of headwaters are affected by Climate Change (63.66 %) and LUCC (23.02 %) on average across all scales. However, we identified three clusters, in which the northern cluster is mainly affected by LUCC, while the Andean and Coastal clusters are mainly affected by climate change. Our results and methods present an informative picture of the current state of headwater vulnerability, identifying spatial patterns and drivers at multiple scales. We believe that the approach developed in this study could be useful for new studies in other zones of the world and can also promote Chilean headwater conservation.
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Affiliation(s)
- Alberto J Alaniz
- Departamento de Ingeniería Geográfica, Facultad de Ingeniería, Universidad de Santiago de Chile, Chile; Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Cecilia Smith-Ramírez
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, 1305 Av. Fuchslocher, Osorno, Chile; Instituto de Ecología y Biodiversidad-Chile (IEB), Las Palmeras 3425, Santiago, Chile; Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, Isla Teja s/n, Valdivia, Chile
| | - Adriana Rendón-Funes
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, 1305 Av. Fuchslocher, Osorno, Chile; Instituto de Ecología y Biodiversidad-Chile (IEB), Las Palmeras 3425, Santiago, Chile; Área de Ecología, Museo de Historia Natural Alcide d'Orbigny, 1458 Av. Potosí, Cochabamba, Bolivia
| | | | - Mario A Carvajal
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile; Departamento de Gestión Agraria, Facultad Tecnológica, Universidad de Santiago de Chile, Chile
| | - Pablo M Vergara
- Departamento de Gestión Agraria, Facultad Tecnológica, Universidad de Santiago de Chile, Chile
| | - Norka Fuentes
- Departamento de Acuicultura y Recursos Agroalimentarios, Universidad de Los Lagos, Av. Fuchslocher 1305, Osorno, Chile
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11
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Jin L, Gerson JR, Rocca JD, Bernhardt ES, Simonin M. Alkaline mine drainage drives stream sediment microbial community structure and function. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:150189. [PMID: 34818783 DOI: 10.1016/j.scitotenv.2021.150189] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/24/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
With advances in eDNA metabarcoding, environmental microbiomes are increasingly used as cost-effective tools for monitoring ecosystem health. Stream ecosystems in Central Appalachia, heavily impacted by alkaline drainage from mountaintop coal mining, present ideal opportunities for biomonitoring using stream microbiomes, but the structural and functional responses of microbial communities in different environmental compartments are not well understood. We investigated sediment microbiomes in mining impacted streams to determine how community composition and function respond to mining and to look for potential microbial bioindicators. Using 16s rRNA gene amplicon sequencing, we found that mining leads to shifts in microbial community structure, with the phylum Planctomycetes enriched by 1-6% at mined sites. We observed ~51% increase in species richness in bulk sediments. In contrast, of the 31 predicted metabolic pathways that changed significantly with mining, 23 responded negatively. Mining explained 15-18% of the variance in community structure and S, Se, %C and %N were the main drivers of community and functional pathway composition. We identified 12 microbial indicators prevalent in the ecosystem and sensitive to mining. Overall, alkaline mountaintop mining drainage causes a restructuration of the sediment microbiome, and our study identified promising microbial indicators for the long-term monitoring of these impacted streams.
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Affiliation(s)
- Lingrong Jin
- Department of Biology, Duke University, Durham, NC 27708, United States.
| | | | - Jennifer D Rocca
- Department of Biology, Duke University, Durham, NC 27708, United States
| | - Emily S Bernhardt
- Department of Biology, Duke University, Durham, NC 27708, United States.
| | - Marie Simonin
- Department of Biology, Duke University, Durham, NC 27708, United States.
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12
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Beattie RE, Hristova KR. Manure derived nutrients alter microbial community composition and increase the presence of potential pathogens in freshwater sediment. J Appl Microbiol 2021; 132:747-757. [PMID: 34312944 DOI: 10.1111/jam.15232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/01/2022]
Abstract
AIM To determine the impact of an acute, pulse disturbance of nutrients from manure on freshwater sediment microbiomes in an experimental system. METHODS AND RESULTS A controlled freshwater mesocosm experiment was designed to compare the effect of disturbance from nutrients derived from sterile manure (SM), disturbance from equivalent concentrations of laboratory-derived nutrients, and a nondisturbed control on freshwater sediment microbial community composition and function using 16S rRNA amplicon sequencing. Sediment microbiomes impacted by nutrients from SM showed no sign of compositional recovery after 28 days but those impacted by laboratory-derived chemicals lead to a new steady-state (p < 0.05). Carbon and nitrate sources within disturbed mesocosms were the primary drivers of altered microbial community composition. Additionally, multiple potential pathogens (based on exact sequence matching at the species level) were enriched in mesocosms treated with SM. CONCLUSIONS Nutrient disturbance from SM, in the absence of the manure microbial community, alters the microbiome of sediments without recovery after 28 days and enriches potential pathogens. SIGNIFICANCE AND IMPACT OF THE STUDY These results suggest manure land application practices should be re-evaluated to account for impact of nutrient disturbance on environmental microbiomes in addition to the impact of the manure microbial community.
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Affiliation(s)
- Rachelle E Beattie
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
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13
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Short- and long-term effects of copper on anammox under gradually increased copper concentrations. Biodegradation 2021; 32:273-286. [PMID: 33745118 DOI: 10.1007/s10532-021-09934-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
This study aims to determine both short- and long-term response of enriched anammox culture to Cu. Assessment of short-term inhibition is based both on total applied Cu concentration and potential bioavailable fractions like intracellular, surface-bound, soluble and free Cu ion. The half maximal inhibitory concentration (IC50) values for total applied, soluble, intracellular and cell-associated concentrations were determined as 4.57 mg/L, 1.97 mg/L, 0.71 mg/L, 1.11 mg/L, respectively. Correlation between the surface-bound fraction of Cu and inhibition response was weak, suggesting that Cu sorbed to biomass was not directly responsible for the effects on anammox activity. There was a disparity between the results of short- and long-term experiments in terms of inhibition threshold concentration (i.e. short-term IC50 = 4.57 mg/L vs long-term IC50 = 6.74 mg/L). Candidatus Kuenenia (59.8%) and Candidatus Brocadia (40.2%) were the two main anammox genera within the initial biomass sample. One of the most interesting finding of the study is the demonstration that a complete wash-out of C. Brocadia genus at an applied Cu concentration of 6.5 mg/L. This strongly indicates that C. Brocadia were not able to tolerate high copper concentrations and all nitrogen conversion was carried out by C. Kuenenia during the Cu exposure period.
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