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Lancaster E, Winston R, Martin J, Lee J. Urban stormwater green infrastructure: Evaluating the public health service role of bioretention using microbial source tracking and bacterial community analyses. WATER RESEARCH 2024; 259:121818. [PMID: 38815337 DOI: 10.1016/j.watres.2024.121818] [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: 02/12/2024] [Revised: 04/30/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024]
Abstract
Bioretention cells (BRCs) control stormwater flow on-site during precipitation, reducing runoff and improving water quality through chemical, physical, and biological processes. While BRCs are effective in these aspects, they provide habitats for wildlife and may face microbial hazards from fecal shedding, posing a potential threat to human health and the nearby environment. However, limited knowledge exists regarding the ability to control microbial hazards (e.g., beyond using typical indicator bacteria) through stormwater biofiltration. Therefore, the purpose of this study is to characterize changes in the bacterial community of urban stormwater undergoing bioretention treatment, with the goal of assessing the public health implications of these green infrastructure solutions. Samples from BRC inflow and outflow in Columbus, Ohio, were collected post-heavy storms from October 2021 to March 2022. Conventional culture-based E. coli monitoring and microbial source tracking (MST) were conducted to identify major fecal contamination extent and its sources (i.e., human, canine, avian, and ruminant). Droplet digital polymerase chain reaction (ddPCR) was utilized to quantify the level of host-associated fecal contamination in addition to three antibiotic resistant genes (ARGs): tetracycline resistance gene (tetQ), sulfonamide resistance gene (sul1), and Klebsiella pneumoniae carbapenemase resistance gene (blaKPC). Subsequently, 16S rRNA gene sequencing was conducted to characterize bacterial community differences between stormwater BRC inflow and outflow. Untreated urban stormwater reflects anthropogenic contamination, suggesting it as a potential source of contamination to waterbodies and urban environments. When comparing inlet and outlet BRC samples, urban stormwater treated via biofiltration did not increase microbial hazards, and changes in bacterial taxa and alpha diversity were negligible. Beta diversity results reveal a significant shift in bacterial community structure, while simultaneously enhancing the water quality (i.e., reduction of metals, total suspended solids, total nitrogen) of urban stormwater. Significant correlations were found between the bacterial community diversity of urban stormwater with fecal contamination (e.g. dog) and ARG (sul1), rainfall intensity, and water quality (hardness, total phosphorous). The study concludes that bioretention technology can sustainably maintain urban microbial water quality without posing additional public health risks, making it a viable green infrastructure solution for heavy rainfall events exacerbated by climate change.
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Affiliation(s)
- Emma Lancaster
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Ryan Winston
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA; Department of Food, Agricultural, and Biological Engineering, The Ohio State University, Columbus, OH, USA; Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Jay Martin
- Department of Food, Agricultural, and Biological Engineering, The Ohio State University, Columbus, OH, USA; Sustainability Institute, The Ohio State University, Columbus, OH, USA
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA; Department of Food Science & Technology, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.
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Mills M, Davis A, Lancaster E, Choi B, Martin J, Winston R, Lee J. Longitudinal Analysis of Urban Stormwater Microbiome and Resistome from Watersheds with and without Green Infrastructure using Long-Read Sequencing. WATER RESEARCH 2024; 259:121873. [PMID: 38852387 DOI: 10.1016/j.watres.2024.121873] [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: 02/26/2024] [Revised: 05/14/2024] [Accepted: 06/02/2024] [Indexed: 06/11/2024]
Abstract
Since stormwater conveys a variety of contaminants into water bodies, green infrastructure (GI) is increasingly being adopted as an on-site treatment solution in addition to controlling peak flows. The purpose of this study was to identify differences in microbial water quality of stormwater in watersheds retrofitted with GI vs. those without GI. Considering stormwater is recently recognized as a contributor to the antibiotic resistance (AR) threat, another goal of this study was to characterize changes in the microbiome and collection of AR genes (resistome) of urban stormwater with season, rainfall characteristics, and fecal contamination. MinION long-read sequencing was used to analyze stormwater microbiome and resistome from watersheds with and without GI in Columbus, Ohio, United States, over 18 months. We characterized fecal contamination in stormwater via culturing Escherichia coli and with molecular microbial source tracking (MST) to identify sources of fecal contamination. Overall, season and storm event (rainfall) characteristics had the strongest relationships with changes in the stormwater microbiome and resistome. We found no significant differences in microbial water quality or the microbiome of stormwater in watersheds with and without GI implemented. However, there were differences between the communities of microorganisms hosting antibiotic resistance genes (ARGs) in stormwater from watersheds with and without GI, indicating the potential sensitivity of AR bacteria to treatment. Stormwater was contaminated with high concentrations of human-associated fecal bacterial genes, and the ARG host bacterial community had considerable similarities to human feces/wastewater. We also identified 15 potential pathogens hosting ARGs in these stormwater resistome, including vancomycin-resistant Enterococcus faecium (VRE) and multidrug-resistant Pseudomonas aeruginosa. In summary, urban stormwater is highly contaminated and has a great potential to spread AR and microbial hazards to nearby environments. This study presents the most comprehensive analysis of stormwater microbiome and resistome to date, which is crucial to understanding the potential microbial risk from this matrix. This information can be used to guide future public health policy, stormwater reuse programs, and urban runoff treatment initiatives.
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Affiliation(s)
- Molly Mills
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Angela Davis
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Emma Lancaster
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Boseung Choi
- Division of Big Data Science, Korea University, Sejong, Republic of Korea
| | - Jay Martin
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA; Department of Food, Agricultural and Biological Engineering, The Ohio State University, Columbus, OH, USA; Sustainability Institute, The Ohio State University, Columbus, OH, USA
| | - Ryan Winston
- Department of Food, Agricultural and Biological Engineering, The Ohio State University, Columbus, OH, USA; Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Department of Food Science & Technology, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.
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Zhong W, Agarwal V. Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty. Beilstein J Org Chem 2024; 20:1635-1651. [PMID: 39076296 PMCID: PMC11285056 DOI: 10.3762/bjoc.20.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/02/2024] [Indexed: 07/31/2024] Open
Abstract
Microbulbifer is a genus of halophilic bacteria that are commonly detected in the commensal marine microbiomes. These bacteria have been recognized for their ability to degrade polysaccharides and other polymeric materials. Increasingly, Microbulbifer genomes indicate these bacteria to be an untapped reservoir for novel natural product discovery and biosynthetic novelty. In this review, we summarize the distribution of Microbulbifer bacteria, activities of the various polymer degrading enzymes that these bacteria produce, and an up-to-date summary of the natural products that have been isolated from Microbulbifer strains. We argue that these bacteria have been hiding in plain sight, and contemporary efforts into their genome and metabolome mining are going to lead to a proliferation of Microbulbifer-derived natural products in the future. We also describe, where possible, the ecological interactions of these bacteria in marine microbiomes.
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Affiliation(s)
- Weimao Zhong
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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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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Saleem F, Li E, Edge TA, Tran KL, Schellhorn HE. Identification of potential microbial risk factors associated with fecal indicator exceedances at recreational beaches. ENVIRONMENTAL MICROBIOME 2024; 19:4. [PMID: 38225663 PMCID: PMC10790499 DOI: 10.1186/s40793-024-00547-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024]
Abstract
BACKGROUND Fecal bacterial densities are proxy indicators of beach water quality, and beach posting decisions are made based on Beach Action Value (BAV) exceedances for a beach. However, these traditional beach monitoring methods do not reflect the full extent of microbial water quality changes associated with BAV exceedances at recreational beaches (including harmful cyanobacteria). This proof of concept study evaluates the potential of metagenomics for comprehensively assessing bacterial community changes associated with BAV exceedances compared to non-exceedances for two urban beaches and their adjacent river water sources. RESULTS Compared to non-exceedance samples, BAV exceedance samples exhibited higher alpha diversity (diversity within the sample) that could be further differentiated into separate clusters (Beta-diversity). For Beach A, Cyanobacterial sequences (resolved as Microcystis and Pseudanabaena at genus level) were significantly more abundant in BAV non-exceedance samples. qPCR validation supported the Cyanobacterial abundance results from metagenomic analysis and also identified saxitoxin genes in 50% of the non-exceedance samples. Microcystis sp and saxitoxin gene sequences were more abundant on non-exceedance beach days (when fecal indicator data indicated the beach should be open for water recreational purposes). For BAV exceedance days, Fibrobacteres, Pseudomonas, Acinetobacter, and Clostridium sequences were significantly more abundant (and positively correlated with fecal indicator densities) for Beach A. For Beach B, Spirochaetes (resolved as Leptospira on genus level) Burkholderia and Vibrio sequences were significantly more abundant in BAV exceedance samples. Similar bacterial diversity and abundance trends were observed for river water sources compared to their associated beaches. Antibiotic Resistance Genes (ARGs) were also consistently detected at both beaches. However, we did not observe a significant difference or correlation in ARGs abundance between BAV exceedance and non-exceedance samples. CONCLUSION This study provides a more comprehensive analysis of bacterial community changes associated with BAV exceedances for recreational freshwater beaches. While there were increases in bacterial diversity and some taxa of potential human health concern associated with increased fecal indicator densities and BAV exceedances (e.g. Pseudomonas), metagenomics analyses also identified other taxa of potential human health concern (e.g. Microcystis) associated with lower fecal indicator densities and BAV non-exceedances days. This study can help develop more targeted beach monitoring strategies and beach-specific risk management approaches.
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Affiliation(s)
- Faizan Saleem
- Department of Biology, McMaster University, 1280 Main St W., Hamilton, ON, L8S 4L8, Canada
| | - Enze Li
- Department of Biology, McMaster University, 1280 Main St W., Hamilton, ON, L8S 4L8, Canada
| | - Thomas A Edge
- Department of Biology, McMaster University, 1280 Main St W., Hamilton, ON, L8S 4L8, Canada
| | - Kevin L Tran
- Department of Biology, McMaster University, 1280 Main St W., Hamilton, ON, L8S 4L8, Canada
| | - Herb E Schellhorn
- Department of Biology, McMaster University, 1280 Main St W., Hamilton, ON, L8S 4L8, Canada.
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Srivastava A, Verma D. Comparative bacteriome and antibiotic resistome analysis of water and sediment of the Ganga River of India. World J Microbiol Biotechnol 2023; 39:294. [PMID: 37656255 DOI: 10.1007/s11274-023-03730-0] [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: 05/15/2023] [Accepted: 08/13/2023] [Indexed: 09/02/2023]
Abstract
A comparative analysis between water and sediment can provide better information to understand the dynamics of the inhabitant microbiome and their respective antibiotic resistance genes of a river. Therefore, the present investigation was carried to explore the limited information available on bacterial microbiome and their predictive antibiotic resistance genes (ARGs) from water and sediment of the Ganga River. The study utilized the NGS-based sequences previously submitted under the accession number (PRJNA847424 and PRJNA892876). Overall analysis revealed that twenty phyla and fifty-four genera were shared between the water and sediment of the Ganga River. Of them, nine phyla and nineteen genera were observed as significantly different (p-value < 0.05). Where the majority of the genera were associated with the sediment samples over the water that identify the sediment samples as more diverse for species richness. Similarly, seventy-six ARGs were shared between water and sediment samples. Of the ten abundant antibiotic resistance pathways, seven were relatively abundant in sediment samples as compared to the water. Vancomycin resistance genes were significantly more abundant among sediment samples, whereas β-lactam resistance genes were equally distributed in water and sediment samples. The network analysis further revealed that five genera (Flavobacterium, Pseudomonas, Acinetobacter, Candidatus_divison CL5003, and Candidatus_division SWB02) showed a significantly positive correlation with six antibiotic resistance pathways (β-lactam, vancomycin, multidrug resistance, tetracycline, aminoglycoside, and macrolide resistance pathways). The study comes out with several findings where sediment may be considered as a more atrocious habitat for evolving the resistance mechanisms against threatful antibiotics over the water samples of the Ganga River.
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Affiliation(s)
- Ankita Srivastava
- Department of Environmental Microbiology, School of Earth and Environemntal Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India
| | - Digvijay Verma
- Department of Environmental Microbiology, School of Earth and Environemntal Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India.
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Lee J, Lee S, Hu C, Marion JW. Beyond cyanotoxins: increased Legionella, antibiotic resistance genes in western Lake Erie water and disinfection-byproducts in their finished water. Front Microbiol 2023; 14:1233327. [PMID: 37700867 PMCID: PMC10493389 DOI: 10.3389/fmicb.2023.1233327] [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: 06/01/2023] [Accepted: 08/15/2023] [Indexed: 09/14/2023] Open
Abstract
Background Western Lake Erie is suffering from harmful cyanobacterial blooms, primarily toxic Microcystis spp., affecting the ecosystem, water safety, and the regional economy. Continued bloom occurrence has raised concerns about public health implications. However, there has been no investigation regarding the potential increase of Legionella and antibiotic resistance genes in source water, and disinfection byproducts in municipal treated drinking water caused by these bloom events. Methods Over 2 years, source water (total n = 118) and finished water (total n = 118) samples were collected from drinking water plants situated in western Lake Erie (bloom site) and central Lake Erie (control site). Bloom-related parameters were determined, such as microcystin (MC), toxic Microcystis, total organic carbon, N, and P. Disinfection byproducts (DBPs) [total trihalomethanes (THMs) and haloacetic acids (HAAs)] were assessed in finished water. Genetic markers for Legionella, antibiotic resistance genes, and mobile genetic elements were quantified in source and finished waters. Results Significantly higher levels of MC-producing Microcystis were observed in the western Lake Erie site compared to the control site. Analysis of DBPs revealed significantly elevated THMs concentrations at the bloom site, while HAAs concentrations remained similar between the two sites. Legionella spp. levels were significantly higher in the bloom site, showing a significant relationship with total cyanobacteria. Abundance of ARGs (tetQ and sul1) and mobile genetic elements (MGEs) were also significantly higher at the bloom site. Discussion Although overall abundance decreased in finished water, relative abundance of ARGs and MGE among total bacteria increased after treatment, particularly at the bloom site. The findings underscore the need for ongoing efforts to mitigate bloom frequency and intensity in the lake. Moreover, optimizing water treatment processes during bloom episodes is crucial to maintain water quality. The associations observed between bloom conditions, ARGs, and Legionella, necessitate future investigations into the potential enhancement of antibiotic-resistant bacteria and Legionella spp. due to blooms, both in lake environments and drinking water distribution systems.
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Affiliation(s)
- Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, United States
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Seungjun Lee
- Department of Food Science and Nutrition, Pukyong National University, Busan, Republic of Korea
| | - Chenlin Hu
- College of Pharmacy, University of Houston, Houston, TX, United States
| | - Jason W. Marion
- Department of Public Health and Clinical Sciences, Eastern Kentucky University, Richmond, KY, United States
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Flocco CG, Methner A, Burkart F, Geppert A, Overmann J. Touching the (almost) untouchable: a minimally invasive workflow for microbiological and biomolecular analyses of cultural heritage objects. Front Microbiol 2023; 14:1197837. [PMID: 37601377 PMCID: PMC10435870 DOI: 10.3389/fmicb.2023.1197837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/27/2023] [Indexed: 08/22/2023] Open
Abstract
Microbiological and biomolecular approaches to cultural heritage research have expanded the established research horizon from the prevalent focus on the cultural objects' conservation and human health protection to the relatively recent applications to provenance inquiry and assessment of environmental impacts in a global context of a changing climate. Standard microbiology and molecular biology methods developed for other materials, specimens, and contexts could, in principle, be applied to cultural heritage research. However, given certain characteristics common to several heritage objects-such as uniqueness, fragility, high value, and restricted access, tailored approaches are required. In addition, samples of heritage objects may yield low microbial biomass, rendering them highly susceptible to cross-contamination. Therefore, dedicated methodology addressing these limitations and operational hurdles is needed. Here, we review the main experimental challenges and propose a standardized workflow to study the microbiome of cultural heritage objects, illustrated by the exploration of bacterial taxa. The methodology was developed targeting the challenging side of the spectrum of cultural heritage objects, such as the delicate written record, while retaining flexibility to adapt and/or upscale it to heritage artifacts of a more robust constitution or larger dimensions. We hope this tailored review and workflow will facilitate the interdisciplinary inquiry and interactions among the cultural heritage research community.
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Affiliation(s)
- Cecilia G. Flocco
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Anika Methner
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Franziska Burkart
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Alicia Geppert
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
- Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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Matsui K, Miki T. Microbial community composition and function in an urban waterway with combined sewer overflows before and after implementation of a stormwater storage pipe. PeerJ 2023; 11:e14684. [PMID: 36650829 PMCID: PMC9840855 DOI: 10.7717/peerj.14684] [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: 08/19/2022] [Accepted: 12/13/2022] [Indexed: 01/15/2023] Open
Abstract
When the wastewater volume exceeds the sewer pipe capacity during extreme rainfall events, untreated sewage discharges directly into rivers as combined sewer overflow (CSO). To compare the impacts of CSOs and stormwater on urban waterways, we assessed physicochemical water quality, the 16S rRNA gene-based bacterial community structure, and EcoPlate-based microbial functions during rainfall periods in an urban waterway before and after a stormwater storage pipe was commissioned. A temporal variation analysis showed that CSOs have significant impacts on microbial function and bacterial community structure, while their contributions to physicochemical parameters, bacterial abundance, and chlorophyll a were not confirmed. Heat map analysis showed that the impact of CSO on the waterway bacterial community structure was temporal and the bacterial community composition in CSO is distinct from that in sewers. Hierarchical clustering analysis revealed that the waterway physicochemical water qualities, bacterial community composition, and microbial community function were distinguishable from the upper reach of the river, rather than between CSO and stormwater. Changes in the relative abundance of tetracycline resistance (tet) genes-especially tet(M)-were observed after CSOs but did not coincide with changes in the microbial community composition, suggesting that the parameters affecting the microbial community composition and relative abundance of tet genes differ. After pipe implementation, however, stormwater did not contribute to the abundance of tet genes in the waterway. These results indicate that CSO-induced acute microbial disturbances in the urban waterway were alleviated by the implementation of a stormwater storage pipe and will support the efficiency of storage pipe operation for waterway management in urban areas.
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Affiliation(s)
- Kazuaki Matsui
- Department of Civil and Environmental Engineering, Kindai University, Higashiosaka, Japan
| | - Takeshi Miki
- Faculty of Advanced Science and Technology, Ryukoku University, Otsu, Shiga, Japan
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Gao N, Liang Y, Li J, Cui K, Lu W. Bacterial community composition and indicators of water quality in Caizi lake, a typical Yangtze-connected freshwater lake. FEMS Microbiol Lett 2022; 369:6674759. [PMID: 36001998 DOI: 10.1093/femsle/fnac084] [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: 04/11/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/14/2022] Open
Abstract
Caizi Lake is an important lake connected to the Yangtze River in Anhui Province and a crucial connection for the Yangtze-to-Huaihe Water Diversion Project (YHWD). There were marked differences in trophic status of the six sampling sites based on the physicochemical characterization. The Bacterial Eutrophic Index (BEI), used to quantify water quality, was well related to Carlson's trophic state index (TSI) (Spearman's ρ = 0.829, P < 0.05). Mean TSI and BEI were 54 and 0.58, respectively, indicating that Caizi Lake was slightly eutrophic. Actinobacteriota were the predominant bacterial phylum in the water and Acidobacteriota in sediments. The diversity and composition of the bacterial community was markedly different between sites for water but not sediment samples. Unlike other Yangtze-connected freshwater lakes, the distance-based redundancy analysis (db-RDA) revealed that dissolved oxygen (DO) affected the composition of the planktonic bacterial community (P < 0.001) while total phosphorus (TP) was the major factor in the sediments (P < 0.05). Water quality of Caizi Lake significantly improved since a few years ago. These results contribute to the long-term monitoring of the ecological quality of the water environment along the Yangtze River to the Huaihe River.
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Affiliation(s)
- Na Gao
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Yangyang Liang
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Jing Li
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Kai Cui
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Wenxuan Lu
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
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Chaganti SR, Plouff C, Madani M, Shahraki AH, Vasquez AA, Seth R, Heath DD, Ram JL. Variation in the diversity of bacterial communities and potential sources of fecal contamination of beaches in the Huron to Erie corridor. WATER RESEARCH 2022; 222:118913. [PMID: 35940154 DOI: 10.1016/j.watres.2022.118913] [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: 02/28/2022] [Revised: 07/03/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Understanding the diversity of bacteria and E.coli levels at beaches is important for managing health risks. This study compared temporal changes of the bacterial communities of Belle Isle Beach (Detroit, MI) and Sand Point Beach (Windsor, ONT), both located near the Lake St. Clair origin of the Detroit River. Water samples collected 4 days/week for 12 weeks in summer, were subjected to 16S rRNA analysis of amplicon sequencing and E. coli enumeration. Bacterial communities changed over time, as determined by cluster dendrogram analysis, exhibiting different communities in July and August than in June and different communities at the two beaches. After June, alpha diversity decreased and relative abundance of Enterobacter (Gammaproteobacteria) increased at Sand Point; whereas, Belle Isle maintained its alpha diversity and dominance by Betaproteobacteria and Actinobacteria. Contamination at both beaches is dominated by birds (23% to 50% of samples), while only ∼10% had evidence of human-associated bacteria. High E. coli at both beaches was often associated with precipitation. Nearshore sampling counts were higher than waist-deep sampling counts. Despite the dynamic changes in bacterial communities between the two beaches, this analysis based on 16S rRNA amplicon sequencing is able to provide information about bacterial types associated with high E. coli levels and to use bacterial sequences to more precisely determine sources and health relevance of contaminants.
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Affiliation(s)
- Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Claire Plouff
- Belle Isle Aquarium Field Research Laboratory, Facility of Healthy Urban Waters, Department of Physiology, Wayne State University, Detroit, MI 48201, United States
| | - Mohammad Madani
- Department of Civil & Environmental Engineering, University of Windsor, 401 Sunset Ave. Windsor, ON N9B 3P4, Canada
| | | | - Adrian A Vasquez
- Belle Isle Aquarium Field Research Laboratory, Facility of Healthy Urban Waters, Department of Physiology, Wayne State University, Detroit, MI 48201, United States; Department of Physiology, Wayne State University, 540 E. Canfield St., Detroit, MI 48201, United States
| | - Rajesh Seth
- Department of Civil & Environmental Engineering, University of Windsor, 401 Sunset Ave. Windsor, ON N9B 3P4, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada; Department of Integrative Biology, University of Windsor, Windsor, ON, Canada
| | - Jeffrey L Ram
- Belle Isle Aquarium Field Research Laboratory, Facility of Healthy Urban Waters, Department of Physiology, Wayne State University, Detroit, MI 48201, United States; Department of Physiology, Wayne State University, 540 E. Canfield St., Detroit, MI 48201, United States.
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12
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Cho KH, Wolny J, Kase JA, Unno T, Pachepsky Y. Interactions of E. coli with algae and aquatic vegetation in natural waters. WATER RESEARCH 2022; 209:117952. [PMID: 34965489 DOI: 10.1016/j.watres.2021.117952] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 11/27/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
Both algae and bacteria are essential inhabitants of surface waters. Their presence is of ecological significance and sometimes of public health concern triggering various control actions. Interactions of microalgae, macroalgae, submerged aquatic vegetation, and bacteria appear to be important phenomena necessitating a deeper understanding by those involved in research and management of microbial water quality. Given the long-standing reliance on Escherichia coli as an indicator of the potential presence of pathogens in natural waters, understanding its biology in aquatic systems is necessary. The major effects of algae and aquatic vegetation on E. coli growth and survival, including changes in the nutrient supply, modification of water properties and constituents, impact on sunlight radiation penetration, survival as related to substrate attachment, algal mediation of secondary habitats, and survival inhibition due to the release of toxic substances and antibiotics, are discussed in this review. An examination of horizontal gene transfer and antibiotic resistance potential, strain-specific interactions, effects on the microbial, microalgae, and grazer community structure, and hydrodynamic controls is given. Outlooks due to existing and expected consequences of climate change and advances in observation technologies via high-resolution satellite imaging, unmanned aerial vehicles (drones), and mathematical modeling are additionally covered. The multiplicity of interactions among bacteria, algae, and aquatic vegetation as well as multifaceted impacts of these interactions, create a wide spectrum of research opportunities and technology developments.
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Affiliation(s)
- Kyung Hwa Cho
- Department of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jennifer Wolny
- Division of Microbiology, Office of Regulatory Science, Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, USA
| | - Julie A Kase
- Division of Microbiology, Office of Regulatory Science, Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, USA
| | - Tatsui Unno
- College of Applied Life Science, Jeju National University, Republic of Korea
| | - Yakov Pachepsky
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, U.S. Department of Agriculture, USA.
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13
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Mathan Kumar R, Jani K, Parvathi JR, Thomas BM, Raja SSS, Pandey A, Sharma A. Bacterial diversity of geochemically distinct hot springs located in Maharashtra, India. Arch Microbiol 2022; 204:110. [PMID: 34978617 DOI: 10.1007/s00203-021-02728-2] [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: 07/11/2021] [Revised: 11/25/2021] [Accepted: 12/14/2021] [Indexed: 11/29/2022]
Abstract
Bacterial diversity of four thermally different hot springs of Ratnagiri district, Maharashtra, India, was investigated using culture-dependent and culture-independent approaches. A total of 144 bacterial cultures were isolated and identified using MALDI-TOF MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) and 16S rRNA gene sequencing. Culture-independent analysis by Ion Torrent sequencing targeting the V3 region of the 16S rRNA gene revealed the predominance of Firmicutes across all the hot springs, followed by Chloroflexi, Bacteroidetes, Cyanobacteria, Proteobacteria, Armatimonadetes, Actinobacteria, Nitrospirae, Acidobacteria, and Deinococcus-Thermus, with subtle differences in their abundance. At the lower taxonomic rank of genus, we noted the prevalence of Acinetobacter followed by Clostridium, Planomicrobium, Bacillus, Streptomyces, and Leptolyngbya. Metagenomics imputation using in silico approach revealed divergence in the metabolic capabilities of bacterial communities along the thermal gradient of host springs, with site TS (63 °C) featuring the abundant functional gene families.
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Affiliation(s)
- R Mathan Kumar
- Government College of Arts and Science, Kurumbalur, Perambalur, (Formerly, Bharathidasan University Constituent College, Perambalur), Kurumbalur, Tamil Nadu, 621212, India
| | - Kunal Jani
- DBT-National Centre for Cell Science, Pune, 411007, India
| | - J R Parvathi
- Somaiya Institute for Research and Consultancy (SIRAC), Somaiya Vidyavihar University, Mumbai, 400077, India
| | - Becky M Thomas
- Somaiya Institute for Research and Consultancy (SIRAC), Somaiya Vidyavihar University, Mumbai, 400077, India.,CHRIST (Deemed to be University), Pune, 412112, India
| | - Suresh S S Raja
- Government College of Arts and Science, Kurumbalur, Perambalur, (Formerly, Bharathidasan University Constituent College, Perambalur), Kurumbalur, Tamil Nadu, 621212, India
| | - Anita Pandey
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehra Dun, 248002, India
| | - Avinash Sharma
- DBT-National Centre for Cell Science, Pune, 411007, India.
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14
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Devi SP, Jani K, Sharma A, Jha DK. Bacterial communities and their bioremediation capabilities in oil-contaminated agricultural soils. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 194:9. [PMID: 34874481 DOI: 10.1007/s10661-021-09669-9] [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: 05/22/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
Rapid industrialization and development in petrochemical industries have resulted in increased hydrocarbon pollution causing substantial damage to the natural ecosystems including agricultural soils. In the recent, past efforts have been made to treat the contaminated soils using microorganisms by natural processes. Soil bacteria, known for their potential to degrade the soil contaminants, play a vital role in maintaining soil health. In the current study, we observed the influence of hydrocarbon contamination on the physicochemical characteristics and enzymatic activities of the soil. Proteobacteria (30.48%), Actinobacteria (13.91%), and Acidobacteria (12.57%) flourished in the non-contaminated soil whereas contaminated sites were dominated by Proteobacteria (44.02 ± 15.65%). In contrast, the sites experiencing the different degrees of exposure to the hydrocarbon pollution allowed specific augmentation of bacterial taxa (in decreasing order of exposure time), viz. Proteobacteria (60.47%), Firmicutes (32.48%), and Bacteroidetes(13.59%), based on culture-independent approach that suggested their potential role in hydrocarbon degradation as compared to the non-contaminated site. The imputation of metabolic function also supported the positive correlation to the exposure to hydrocarbon pollution, with site 2 being highly abundant for gene families involved in xenobiotics biodegradation. The study provides insights into bacterial community structure with special emphasis on their efficiency to degrade hydrocarbons. The results from the study can help in designing appropriate biodegradation strategies to mitigate the serious problems of oil contamination in agricultural soil.
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Affiliation(s)
- Sashi Prava Devi
- Microbial Ecology Laboratory, Department of Botany, Gauhati University, Guwahati, 781014, India
| | - Kunal Jani
- DBT-National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Avinash Sharma
- DBT-National Centre for Cell Science, Pune, Maharashtra, 411007, India.
| | - Dhruva Kumar Jha
- Microbial Ecology Laboratory, Department of Botany, Gauhati University, Guwahati, 781014, India.
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15
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Bell RL, Kase JA, Harrison LM, Balan KV, Babu U, Chen Y, Macarisin D, Kwon HJ, Zheng J, Stevens EL, Meng J, Brown EW. The Persistence of Bacterial Pathogens in Surface Water and Its Impact on Global Food Safety. Pathogens 2021; 10:1391. [PMID: 34832547 PMCID: PMC8617848 DOI: 10.3390/pathogens10111391] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
Water is vital to agriculture. It is essential that the water used for the production of fresh produce commodities be safe. Microbial pathogens are able to survive for extended periods of time in water. It is critical to understand their biology and ecology in this ecosystem in order to develop better mitigation strategies for farmers who grow these food crops. In this review the prevalence, persistence and ecology of four major foodborne pathogens, Shiga toxin-producing Escherichia coli (STEC), Salmonella, Campylobacter and closely related Arcobacter, and Listeria monocytogenes, in water are discussed. These pathogens have been linked to fresh produce outbreaks, some with devastating consequences, where, in a few cases, the contamination event has been traced to water used for crop production or post-harvest activities. In addition, antimicrobial resistance, methods improvements, including the role of genomics in aiding in the understanding of these pathogens, are discussed. Finally, global initiatives to improve our knowledge base of these pathogens around the world are touched upon.
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Affiliation(s)
- Rebecca L. Bell
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Julie A. Kase
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Lisa M. Harrison
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD 20708, USA; (L.M.H.); (K.V.B.); (U.B.)
| | - Kannan V. Balan
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD 20708, USA; (L.M.H.); (K.V.B.); (U.B.)
| | - Uma Babu
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD 20708, USA; (L.M.H.); (K.V.B.); (U.B.)
| | - Yi Chen
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Dumitru Macarisin
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Hee Jin Kwon
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Jie Zheng
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Eric L. Stevens
- Office of the Center Director, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA;
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA;
| | - Eric W. Brown
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
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16
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Shahraki AH, Chaganti SR, Heath D. Spatio-temporal dynamics of bacterial communities in the shoreline of Laurentian great Lake Erie and Lake St. Clair's large freshwater ecosystems. BMC Microbiol 2021; 21:253. [PMID: 34548037 PMCID: PMC8454060 DOI: 10.1186/s12866-021-02306-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Background Long-term trends in freshwater bacterial community composition (BCC) and dynamics are not yet well characterized, particularly in large lake ecosystems. We addressed this gap by temporally (15 months) and spatially (6 sampling locations) characterizing BCC variation in lakes Erie and St. Clair; two connected ecosystems in the Laurentian Great Lakes. Results We found a spatial variation of the BCC between the two lakes and among the sampling locations (significant changes in the relative abundance of 16% of the identified OTUs at the sampling location level). We observed five distinct temporal clusters (UPGMA broad-scale temporal variation) corresponding to seasonal variation over the 15 months of sampling. Temporal variation among months was high, with significant variation in the relative abundance of 69% of the OTUs. We identified significant differences in taxonomic composition between summer months of 2016 and 2017, with a corresponding significant reduction in the diversity of BCC in summer 2017. Conclusions As bacteria play a key role in biogeochemical cycling, and hence in healthy ecosystem function our study defines the scope for temporal and spatial variation in large lake ecosystems. Our data also show that freshwater BCC could serve as an effective proxy and monitoring tool to access large lake health. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02306-y.
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Affiliation(s)
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada. .,Present Address: Cooperative Institute for Great Lakes Research, School of Environmental and Sustainability, University of Michigan, Ann Arbor, MI, USA.
| | - Daniel Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada. .,Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada.
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17
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Jing G, Zhang Y, Liu L, Wang Z, Sun Z, Knight R, Su X, Xu J. A Scale-Free, Fully Connected Global Transition Network Underlies Known Microbiome Diversity. mSystems 2021; 6:e0039421. [PMID: 34254819 PMCID: PMC8407412 DOI: 10.1128/msystems.00394-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/24/2021] [Indexed: 12/14/2022] Open
Abstract
Microbiomes are inherently linked by their structural similarity, yet the global features of such similarity are not clear. Here, we propose as a solution a search-based microbiome transition network. By traversing a composition-similarity-based network of 177,022 microbiomes, we show that although the compositions are distinct by habitat, each microbiome is on-average only seven neighbors from any other microbiome on Earth, indicating the inherent homology of microbiomes at the global scale. This network is scale-free, suggesting a high degree of stability and robustness in microbiome transition. By tracking the minimum spanning tree in this network, a global roadmap of microbiome dispersal was derived that tracks the potential paths of formulating and propagating microbiome diversity. Such search-based global microbiome networks, reconstructed within hours on just one computing node, provide a readily expanded reference for tracing the origin and evolution of existing or new microbiomes. IMPORTANCE It remains unclear whether and how compositional changes at the "community to community" level among microbiomes are linked to the origin and evolution of global microbiome diversity. Here we propose a microbiome transition model and a network-based analysis framework to describe and simulate the variation and dispersal of the global microbial beta-diversity across multiple habitats. The traversal of a transition network with 177,022 samples shows the inherent homology of microbiome at the global scale. Then a global roadmap of microbiome dispersal derived from the network tracks the potential paths of formulating and propagating microbiome diversity. Such search-based microbiome network provides a readily expanded reference for tracing the origin and evolution of existing or new microbiomes at the global scale.
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Affiliation(s)
- Gongchao Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yufeng Zhang
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, China
| | - Lu Liu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zengbin Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Sun
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rob Knight
- University of California, San Diego, California, USA
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
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18
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Bacterial Diversity of Water and Sediment Samples from Gull Point State Park (West Okoboji, Iowa) Determined Using 16S rRNA Gene Amplicon Sequencing. Microbiol Resour Announc 2021; 10:e0072621. [PMID: 34410154 PMCID: PMC8375475 DOI: 10.1128/mra.00726-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Gull Point State Park is located on a peninsula on the west shore of West Okoboji Lake (Iowa, USA). It is the primary state park in the Iowa Great Lakes region. Sediment and water samples from three locations at the Gull Point pond were analyzed for their microbial composition.
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19
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Jani K, Bandal J, Shouche Y, Shafi S, Azhar EI, Zumla A, Sharma A. Extended Ecological Restoration of Bacterial Communities in the Godavari River During the COVID-19 Lockdown Period: a Spatiotemporal Meta-analysis. MICROBIAL ECOLOGY 2021; 82:365-376. [PMID: 34219185 PMCID: PMC8255117 DOI: 10.1007/s00248-021-01781-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/20/2021] [Indexed: 05/04/2023]
Abstract
The unprecedented COVID-19 pandemic has had major impact on human health worldwide. Whilst national and international COVID-19 lockdown and travel restriction measures have had widespread negative impact on economies and mental health, they may have beneficial effect on the environment, reducing air and water pollution. Mass bathing events (MBE) also known as Kumbh Mela are known to cause perturbations of the ecosystem affecting resilient bacterial populations within water of rivers in India. Lockdowns and travel restrictions provide a unique opportunity to evaluate the impact of minimum anthropogenic activity on the river water ecosystem and changes in bacterial populations including antibiotic-resistant strains. We performed a spatiotemporal meta-analysis of bacterial communities of the Godavari River, India. Targeted metagenomics revealed a 0.87-fold increase in the bacterial diversity during the restricted activity of lockdown. A significant increase in the resilient phyla, viz. Proteobacteria (70.6%), Bacteroidetes (22.5%), Verrucomicrobia (1.8%), Actinobacteria (1.2%) and Cyanobacteria (1.1%), was observed. There was minimal incorporation of allochthonous bacterial communities of human origin. Functional profiling using imputed metagenomics showed reduction in infection and drug resistance genes by - 0.71-fold and - 0.64-fold, respectively. These observations may collectively indicate the positive implications of COVID-19 lockdown measures which restrict MBE, allowing restoration of the river ecosystem and minimise the associated public health risk.
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Affiliation(s)
- Kunal Jani
- DBT-National Centre for Cell Science, Pune, India
| | | | | | - Shuja Shafi
- Mass Gatherings and Global Health Network, London, UK
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, and Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alimuddin Zumla
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, UK
- NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, London, UK
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20
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Alexyuk M, Bogoyavlenskiy A, Alexyuk P, Moldakhanov Y, Berezin V, Digel I. Epipelagic microbiome of the Small Aral Sea: Metagenomic structure and ecological diversity. Microbiologyopen 2021; 10:e1142. [PMID: 33305509 PMCID: PMC7882900 DOI: 10.1002/mbo3.1142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/04/2020] [Accepted: 11/07/2020] [Indexed: 11/11/2022] Open
Abstract
Microbial diversity studies regarding the aquatic communities that experienced or are experiencing environmental problems are essential for the comprehension of the remediation dynamics. In this pilot study, we present data on the phylogenetic and ecological structure of microorganisms from epipelagic water samples collected in the Small Aral Sea (SAS). The raw data were generated by massive parallel sequencing using the shotgun approach. As expected, most of the identified DNA sequences belonged to Terrabacteria and Actinobacteria (40% and 37% of the total reads, respectively). The occurrence of Deinococcus-Thermus, Armatimonadetes, Chloroflexi in the epipelagic SAS waters was less anticipated. Surprising was also the detection of sequences, which are characteristic for strict anaerobes-Ignavibacteria, hydrogen-oxidizing bacteria, and archaeal methanogenic species. We suppose that the observed very broad range of phylogenetic and ecological features displayed by the SAS reads demonstrates a more intensive mixing of water masses originating from diverse ecological niches of the Aral-Syr Darya River basin than presumed before.
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Affiliation(s)
- Madina Alexyuk
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | | | - Pavel Alexyuk
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | - Yergali Moldakhanov
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | - Vladimir Berezin
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | - Ilya Digel
- Institute for BioengineeringAachen University of Applied SciencesJülichGermany
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21
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Cullen CM, Aneja KK, Beyhan S, Cho CE, Woloszynek S, Convertino M, McCoy SJ, Zhang Y, Anderson MZ, Alvarez-Ponce D, Smirnova E, Karstens L, Dorrestein PC, Li H, Sen Gupta A, Cheung K, Powers JG, Zhao Z, Rosen GL. Emerging Priorities for Microbiome Research. Front Microbiol 2020; 11:136. [PMID: 32140140 PMCID: PMC7042322 DOI: 10.3389/fmicb.2020.00136] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
Microbiome research has increased dramatically in recent years, driven by advances in technology and significant reductions in the cost of analysis. Such research has unlocked a wealth of data, which has yielded tremendous insight into the nature of the microbial communities, including their interactions and effects, both within a host and in an external environment as part of an ecological community. Understanding the role of microbiota, including their dynamic interactions with their hosts and other microbes, can enable the engineering of new diagnostic techniques and interventional strategies that can be used in a diverse spectrum of fields, spanning from ecology and agriculture to medicine and from forensics to exobiology. From June 19-23 in 2017, the NIH and NSF jointly held an Innovation Lab on Quantitative Approaches to Biomedical Data Science Challenges in our Understanding of the Microbiome. This review is inspired by some of the topics that arose as priority areas from this unique, interactive workshop. The goal of this review is to summarize the Innovation Lab's findings by introducing the reader to emerging challenges, exciting potential, and current directions in microbiome research. The review is broken into five key topic areas: (1) interactions between microbes and the human body, (2) evolution and ecology of microbes, including the role played by the environment and microbe-microbe interactions, (3) analytical and mathematical methods currently used in microbiome research, (4) leveraging knowledge of microbial composition and interactions to develop engineering solutions, and (5) interventional approaches and engineered microbiota that may be enabled by selectively altering microbial composition. As such, this review seeks to arm the reader with a broad understanding of the priorities and challenges in microbiome research today and provide inspiration for future investigation and multi-disciplinary collaboration.
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Affiliation(s)
- Chad M. Cullen
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
| | | | - Sinem Beyhan
- Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, United States
| | - Clara E. Cho
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, Logan, UT, United States
| | - Stephen Woloszynek
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
- College of Medicine, Drexel University, Philadelphia, PA, United States
| | - Matteo Convertino
- Nexus Group, Faculty of Information Science and Technology, Gi-CoRE Station for Big Data & Cybersecurity, Hokkaido University, Sapporo, Japan
| | - Sophie J. McCoy
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Yanyan Zhang
- Department of Civil Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Matthew Z. Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | | | - Ekaterina Smirnova
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, United States
| | - Lisa Karstens
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, United States
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ananya Sen Gupta
- Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, IA, United States
| | - Kevin Cheung
- Department of Dermatology, The University of Iowa, Iowa City, IA, United States
| | | | - Zhengqiao Zhao
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
| | - Gail L. Rosen
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
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22
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Alves J, Dias L, Mateus J, Marques J, Graças D, Ramos R, Seldin L, Henriques I, Silva A, Folador A. Resistome in Lake Bolonha, Brazilian Amazon: Identification of Genes Related to Resistance to Broad-Spectrum Antibiotics. Front Microbiol 2020; 11:67. [PMID: 32117110 PMCID: PMC7010645 DOI: 10.3389/fmicb.2020.00067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 01/14/2020] [Indexed: 01/02/2023] Open
Abstract
Resistance to antibiotics is one of the most relevant public health concerns in the world. Aquatic environments play an important role because they are reservoirs for antibiotic resistance genes and antibiotic-resistant strains, contributing to the spread of resistance. The present study investigated the resistome in Lake Bolonha (three sampling sites) in the Amazon region using a metagenomics approach and culture-dependent methods. Whole-metagenome-based results showed that the most abundant phyla were Protobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. The composition of the resistome demonstrated that the genes that confer resistance to β-lactams were prevalent at all sampling sites, followed by genes conferring resistance to aminoglycosides and tetracycline. Acquired genes encoding extended-spectrum β-lactamases (e.g., blaCTX–M) and resistance to carbapenems (e.g., blaIMP and blaVIM) were detected through metagenome analysis. Bacteria were isolated from culture medium supplemented with cefotaxime or imipenem, and isolates were identified and analyzed for their antibiotic susceptibility profiles and resistance genes. In total, 98 bacterial isolates belonging to the genera Pseudomonas (37), Acinetobacter (32), Klebsiella (13), Enterobacter (9), Pantoe (3), Stenotrophomonas (3), and Methylobacterium (1) were obtained. Among isolates, the most abundant genes were blaCTX–M (28.3%), blaSHV (22.6%) and blaTEM (18.8%) in isolates from cefotaxime-supplemented medium and blaVIM (28.8%) and blaIMP (22.2%) in isolates recovered from imipenem-supplemented medium. The genes intl1 and intl2 were detected in 19.3% and 7.1% of isolates. Antibiograms showed that 94.9% (from cefotaxime-supplemented medium) and 85.7% (from imipenem-supplemented medium) of the isolates were multidrug resistant. Besides cefotaxime and imipenem, isolates were mostly resistant to aztreonam (91.8%), amoxicillin (98.8%), ampicillin (82.6%), and nalidixic acid (77.5%). Hence, the present study demonstrates that Lake Bolonha is a reservoir of bacteria resistant to antibiotics and resistance genes, some of which are of critical importance to human health.
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Affiliation(s)
- Jorianne Alves
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
| | - Larissa Dias
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
| | - Jackeline Mateus
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joana Marques
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
| | - Diego Graças
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
| | - Rommel Ramos
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Isabel Henriques
- Center for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal.,Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Coimbra, Portugal
| | - Artur Silva
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
| | - Adriana Folador
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
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23
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Jani K, Bandal J, Rale V, Shouche Y, Sharma A. Antimicrobial resistance pattern of microorganisms isolated and identified from Godavari River across the mass gathering event. J Biosci 2019; 44:121. [PMID: 31719230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The Kumbh Mela is considered the world's largest mass gathering event (MGE). It represents a unique anthropogenic burden on the river ecosystem and may confer antimicrobial resistance among microbial communities. The present study explains the characterization of microbial isolates associated with Godavari River under the advent of the mass bathing event using culture dependent approach. The isolates were identified by sequencing of 16S rRNA gene and ITS region. Further, the isolates were screened for antibiotic susceptibility against 22 antibiotics using disc diffusion method. A total of 63 bacterial and 21 fungal isolates were isolated under the temporal variation of the event. Kocuria and Staphylococcus were the most prevalent bacterial genera in the samples collected before and during the event, while Meyerozyma and Candida predominate among fungal communities. A group of antibiotics impeding the bacterial protein synthesis were found to be most effective against greater than or equal to 67% of bacterial isolates. However, greater than or equal to 37-67% of isolates could escape the action of inhibitors of bacterial cell wall synthesis. Moreover, bacterial isolates belonging to genera Acinetobacter, Corynebacterium and Brevibacterium showed higher resistance towards the antibiotics. Observations from the current study suggest likely microbial taxa as targets to mitigate the waterborne infections during the MGE.
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Affiliation(s)
- Kunal Jani
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411 021, India
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24
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Jani K, Bandal J, Rale V, Shouche Y, Sharma A. Antimicrobial resistance pattern of microorganisms isolated and identified from Godavari River across the mass gathering event. J Biosci 2019. [DOI: 10.1007/s12038-019-9941-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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Ji B, Liang J, Ma Y, Zhu L, Liu Y. Bacterial community and eutrophic index analysis of the East Lake. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:682-688. [PMID: 31185357 DOI: 10.1016/j.envpol.2019.05.138] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/18/2019] [Accepted: 05/26/2019] [Indexed: 06/09/2023]
Abstract
This study investigated bacterial diversities in surface water and sediment of the East Lake located in Wuhan, China. Bacterial community of lake water was mainly composed of Proteobacteria (31.1%), Actinobacteria (25.0%), Bacteroidetes (18.6%), Cyanobacteria (18.9%), Planctomycetes (2.4%) and Verrucomicrobia (1.4%), while more abundant and richer bacterial community was found in the sediments, e.g. 46.1% for Proteobacteria, 10.1% for Bacteroidetes, 8.7% for Chloroflexi, 8.4% for Acidobacteria, 5.0% for Cyanobacteria, 3.6% for Firmicutes, 3.1% for Planctomycetes, 2.8% for Actinobacteria and 2.3% for Nitrospirae. The decreased bacterial community richness and abundance was found in poor-quality water. Moreover, Bacterial Eutrophic Index (BEI) was firstly put forward to quantitatively describe the water quality of a freshwater ecosystem, which was defined as the ratio of abundance of Cyanobacteria and Actinobacteria in water. It was demonstrated BEI was well correlated to Carlson's Trophic State Index (TSI) (Spearman's ρ = 0.848, p < 0.01). The average TSI and BEI were determined to be 64 and 0.81, suggesting that East Lake could be classified as a medium eutrophic level.
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Affiliation(s)
- Bin Ji
- Department of Water and Wastewater Engineering, Wuhan University of Science and Technology, Wuhan, 430065, China; Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore, 637141, Singapore.
| | - Jiechao Liang
- Department of Water and Wastewater Engineering, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Yingqun Ma
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore, 637141, Singapore
| | - Lin Zhu
- Department of Water and Wastewater Engineering, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Yu Liu
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore, 637141, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
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26
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Casero MC, Velázquez D, Medina-Cobo M, Quesada A, Cirés S. Unmasking the identity of toxigenic cyanobacteria driving a multi-toxin bloom by high-throughput sequencing of cyanotoxins genes and 16S rRNA metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 665:367-378. [PMID: 30772567 DOI: 10.1016/j.scitotenv.2019.02.083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/14/2019] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
Cyanobacterial harmful algal blooms (CyanoHABs) are complex communities that include coexisting toxic and non-toxic strains only distinguishable by genetic methods. This study shows a water-management oriented use of next generation sequencing (NGS) to specifically pinpoint toxigenic cyanobacteria within a bloom simultaneously containing three of the most widespread cyanotoxins (the hepatotoxins microcystins, MCs; and the neurotoxins anatoxin-a, ATX, and saxitoxins, STXs). The 2013 summer bloom in Rosarito reservoir (Spain) comprised 33 cyanobacterial OTUs based on 16S rRNA metabarcoding, 7 of which accounted for as much as 96.6% of the community. Cyanotoxins and their respective biosynthesis genes were concurrently present throughout the entire bloom event including: MCs and mcyE gene; ATX and anaF gene; and STXs and sxtI gene. NGS applied to amplicons of cyanotoxin-biosynthesis genes unveiled 6 toxigenic OTUs, comprising 3 involved in MCs production (Planktothrix agardhii and 2 Microcystis spp.), 2 in ATX production (Cuspidothrix issatschenkoi and Phormidium/Tychonema spp.) and 1 in STXs production (Aphanizomenon gracile). These toxigenic taxa were also present in 16S rRNA OTUs list and their relative abundance was positively correlated with the respective toxin concentrations. Our results point at MC-producing P. agardhii and ATX-producing C. issatschenkoi as the main contributors to the moderate toxin concentrations observed, and suggest that their distribution in Southern Europe is broader than previously thought. Our findings also stress the need for monitoring low-abundance cyanobacteria (<1% relative abundance) in cyanotoxicity studies, and provide novel data on the presence of picocyanobacteria and potentially ATX-producing benthic taxa (e.g., Phormidium) in deep thermally-stratified water bodies. This study showcases a straightforward use of amplicon metagenomics of cyanotoxin biosynthesis genes in a multi-toxin bloom thus illustrating the broad applicability of NGS for water management in risk-oriented monitoring of CyanoHABs.
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Affiliation(s)
- María Cristina Casero
- Departamento de Biología, C/Darwin, 2, Universidad Autónoma de Madrid, ES-28049 Madrid, Spain
| | - David Velázquez
- Departamento de Biología, C/Darwin, 2, Universidad Autónoma de Madrid, ES-28049 Madrid, Spain
| | - Miguel Medina-Cobo
- Centro de Estudios Hidrográficos, Paseo Bajo de la Virgen del Puerto, 3, CEDEX, ES-28005 Madrid, Spain
| | - Antonio Quesada
- Departamento de Biología, C/Darwin, 2, Universidad Autónoma de Madrid, ES-28049 Madrid, Spain
| | - Samuel Cirés
- Departamento de Biología, C/Darwin, 2, Universidad Autónoma de Madrid, ES-28049 Madrid, Spain.
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27
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Batrich M, Maskeri L, Schubert R, Ho B, Kohout M, Abdeljaber M, Abuhasna A, Kholoki M, Psihogios P, Razzaq T, Sawhney S, Siddiqui S, Xoubi E, Cooper A, Hatzopoulos T, Putonti C. Pseudomonas Diversity Within Urban Freshwaters. Front Microbiol 2019; 10:195. [PMID: 30828321 PMCID: PMC6384249 DOI: 10.3389/fmicb.2019.00195] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/23/2019] [Indexed: 11/23/2022] Open
Abstract
Freshwater lakes are home to bacterial communities with 1000s of interdependent species. Numerous high-throughput 16S rRNA gene sequence surveys have provided insight into the microbial taxa found within these waters. Prior surveys of Lake Michigan waters have identified bacterial species common to freshwater lakes as well as species likely introduced from the urban environment. We cultured bacterial isolates from samples taken from the Chicago nearshore waters of Lake Michigan in an effort to look more closely at the genetic diversity of species found there within. The most abundant genus detected was Pseudomonas, whose presence in freshwaters is often attributed to storm water or runoff. Whole genome sequencing was conducted for 15 Lake Michigan Pseudomonas strains, representative of eight species and three isolates that could not be resolved with named species. These genomes were examined specifically for genes encoding functionality which may be advantageous in their urban environment. Antibiotic resistance, amidst other known virulence factors and defense mechanisms, were identified in the genome annotations and verified in the lab. We also tested the Lake Michigan Pseudomonas strains for siderophore production and resistance to the heavy metals mercury and copper. As the study presented here shows, a variety of pseudomonads have inhabited the urban coastal waters of Lake Michigan.
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Affiliation(s)
- Mary Batrich
- Niehoff School of Nursing, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Laura Maskeri
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Ryan Schubert
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States.,Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Brian Ho
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States.,Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Melanie Kohout
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Malik Abdeljaber
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Ahmed Abuhasna
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Mutah Kholoki
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Penelope Psihogios
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Tahir Razzaq
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Samrita Sawhney
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Salah Siddiqui
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Eyad Xoubi
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Alexandria Cooper
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Thomas Hatzopoulos
- Department of Computer Science, Loyola University Chicago, Chicago, IL, United States
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States.,Department of Biology, Loyola University Chicago, Chicago, IL, United States.,Department of Computer Science, Loyola University Chicago, Chicago, IL, United States.,Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
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28
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Jani K, Dhotre D, Bandal J, Shouche Y, Suryavanshi M, Rale V, Sharma A. World's Largest Mass Bathing Event Influences the Bacterial Communities of Godavari, a Holy River of India. MICROBIAL ECOLOGY 2018. [PMID: 29536131 DOI: 10.1007/s00248-018-1169-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Kumbh Mela is one of the largest religious mass gathering events (MGE) involving bathing in rivers. The exponential rise in the number of devotees, from around 0.4 million in 1903 to 120 million in 2013, bathing in small specified sites can have a dramatic impact on the river ecosystem. Here, we present the spatiotemporal profiling of bacterial communities in Godavari River, Nashik, India, comprising five sites during the Kumbh Mela, held in 2015. Assessment of environmental parameters indicated deterioration of water quality. Targeted amplicon sequencing demonstrates approximately 37.5% loss in microbial diversity because of anthropogenic activity during MGE. A significant decrease in phyla viz. Actinobacteria, Chloroflexi, Proteobacteria, and Bacteroidetes was observed, while we noted substantial increase in prevalence of the phylum Firmicutes (94.6%) during MGE. qPCR estimations suggested nearly 130-fold increase in bacterial load during the event. Bayesian mixing model accounted the source of enormous incorporation of bacterial load of human origin. Further, metagenomic imputations depicted increase in virulence and antibiotic resistance genes during the MGE. These observations suggest the striking impact of the mass bathing on river ecosystem. The subsequent increase in infectious diseases and drug-resistant microbes pose a critical public health concern.
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Affiliation(s)
- Kunal Jani
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
- Symbiosis School of Biological Sciences, Symbiosis International University, Pune, 412115, India
| | - Dhiraj Dhotre
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Jayashree Bandal
- Department of Microbiology, KTHM College, Nashik, Maharashtra, 422002, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Mangesh Suryavanshi
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Vinay Rale
- Symbiosis School of Biological Sciences, Symbiosis International University, Pune, 412115, India
| | - Avinash Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India.
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29
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Mrdjen I, Fennessy S, Schaal A, Dennis R, Slonczewski JL, Lee S, Lee J. Tile Drainage and Anthropogenic Land Use Contribute to Harmful Algal Blooms and Microbiota Shifts in Inland Water Bodies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:8215-8223. [PMID: 29952549 DOI: 10.1021/acs.est.8b03269] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Freshwater harmful algal blooms (HABs), driven by nutrient inputs from anthropogenic sources, pose unique risks to human and ecological health worldwide. A major nutrient contributor is agricultural land use, specifically tile drainage discharge. Small lakes and ponds are at elevated risk for HAB appearance, as they are uniquely sensitive to nutrient input. HABs introduce exposure risk to microcystin (MC), hepatotoxic and potentially carcinogenic cyanotoxins. To investigate the impact of anthropogenic land use on small lakes and ponds, 24 sites in central Ohio were sampled over a 3-month period in late summer of 2015. MC concentration, microbial community structure, and water chemistry were analyzed. Land use intensity, including tile drainage systems, was the driver of clustering in principle component analysis, ultimately contributing to nutrient deposition, a driver of HABs. Relative abundance of HAB-forming genera was correlated with elevated concentrations of nitrate and soluble reactive phosphate. One location (FC) showed MC concentrations exceeding 875 μg/L and large community shifts in ciliates (Oligohymenophorea) associated with hypoxic conditions. The prokaryotic community at FC was dominated by Planktothrix sp. These results demonstrate the impact of HABs in small lakes and ponds, and that prevailing issues extend beyond cyanotoxins, such as cascading impacts on other trophic levels.
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Affiliation(s)
- Igor Mrdjen
- Division of Environmental Health Sciences, College of Public Health , The Ohio State University , 1841 Neil Avenue , Columbus , Ohio 43210 , United States
| | - Siobhan Fennessy
- Department of Biology , Kenyon College , 202 North College Road , Gambier , Ohio 43022 , United States
| | - Alex Schaal
- Department of Biology , Kenyon College , 202 North College Road , Gambier , Ohio 43022 , United States
| | - Richard Dennis
- Department of Biology , Kenyon College , 202 North College Road , Gambier , Ohio 43022 , United States
| | - Joan L Slonczewski
- Department of Biology , Kenyon College , 202 North College Road , Gambier , Ohio 43022 , United States
| | - Seungjun Lee
- Division of Environmental Health Sciences, College of Public Health , The Ohio State University , 1841 Neil Avenue , Columbus , Ohio 43210 , United States
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health , The Ohio State University , 1841 Neil Avenue , Columbus , Ohio 43210 , United States
- Department of Food Science and Technology , The Ohio State University , Columbus , Ohio 43210 , United States
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30
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Roguet A, Therial C, Catherine A, Bressy A, Varrault G, Bouhdamane L, Tran V, Lemaire BJ, Vincon-Leite B, Saad M, Moulin L, Lucas FS. Importance of Local and Regional Scales in Shaping Mycobacterial Abundance in Freshwater Lakes. MICROBIAL ECOLOGY 2018; 75:834-846. [PMID: 29063147 DOI: 10.1007/s00248-017-1088-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
Biogeographical studies considering the entire bacterial community may underestimate mechanisms of bacterial assemblages at lower taxonomic levels. In this context, the study aimed to identify factors affecting the spatial and temporal dynamic of the Mycobacterium, a genus widespread in aquatic ecosystems. Nontuberculous mycobacteria (NTM) density variations were quantified in the water column of freshwater lakes at the regional scale (annual monitoring of 49 lakes in the Paris area) and at the local scale (2-year monthly monitoring in Créteil Lake) by real-time quantitative PCR targeting the atpE gene. At the regional scale, mycobacteria densities in water samples ranged from 6.7 × 103 to 1.9 × 108 genome units per liter. Density variations were primarily explained by water pH, labile iron, and dispersal processes through the connection of the lakes to a river. In Créteil Lake, no spatial variation of mycobacterial densities was noticed over the 2-year monthly survey, except after large rainfall events. Indeed, storm sewer effluents locally and temporarily increased NTM densities in the water column. The temporal dynamic of the NTM densities in Créteil Lake was associated with suspended solid concentrations. No clear seasonal variation was noticed despite a shift in NTM densities observed over the 2012-2013 winter. Temporal NTM densities fluctuations were well predicted by the neutral community model, suggesting a random balance between loss and gain of mycobacterial taxa within Créteil Lake. This study highlights the importance of considering multiple spatial scales for understanding the spatio-temporal dynamic of bacterial populations in natural environments.
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Affiliation(s)
- Adélaïde Roguet
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France.
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA.
| | - Claire Therial
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Arnaud Catherine
- Unité Molécules de Communication et Adaptation des Micro-organismes (MCAM UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, Case 39, 57 rue Cuvier, FR 75005, Paris, France
| | - Adèle Bressy
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Gilles Varrault
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Lila Bouhdamane
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Viet Tran
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Bruno J Lemaire
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | | | - Mohamed Saad
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Laurent Moulin
- Eau de Paris, Direction Recherche et Développement Qualité de l'Eau (DRDQE), 33 avenue Jean Jaurès, FR 94200, Ivry-sur-Seine, France
| | - Françoise S Lucas
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
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31
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Zhang H, Wang Y, Chen S, Zhao Z, Feng J, Zhang Z, Lu K, Jia J. Water Bacterial and Fungal Community Compositions Associated with Urban Lakes, Xi'an, China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018. [PMID: 29518989 PMCID: PMC5877014 DOI: 10.3390/ijerph15030469] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Urban lakes play a vital role in the sustainable development of urbanized areas. In this freshwater ecosystem, massive microbial communities can drive the recycling of nutrients and regulate the water quality. However, water bacterial and fungal communities in the urban lakes are not well understood. In the present work, scanning electron microscopy (SEM) was combined with community level physiological profiles (CLPPs) and Illumina Miseq sequence techniques to determine the diversity and composition of the water bacterial and fungal community in three urban lakes, namely Xingqing lake (LX), Geming lake (LG) and Lianhu lake (LL), located in Xi’an City (Shaanxi Province, China). The results showed that these three lakes were eutrophic water bodies. The highest total nitrogen (TN) was observed in LL, with a value of 12.1 mg/L, which is 2 times higher than that of LG. The permanganate index (CODMn) concentrations were 21.6 mg/L, 35.4 mg/L and 28.8 mg/L in LG, LL and LX, respectively (p < 0.01). Based on the CLPPs test, the results demonstrated that water bacterial communities in the LL and LX urban lakes had higher carbon source utilization ability. A total of 62,742 and 55,346 high quality reads were grouped into 894 and 305 operational taxonomic units (OTUs) for bacterial and fungal communities, respectively. Water bacterial and fungal community was distributed across 14 and 6 phyla. The most common phyla were Proteobacteriaand Cyanobacteria. Cryptomycota was particularly dominant in LL, while Chytridiomycota and Entomophthormycota were the most abundant fungal phyla, accounting for 95% of the population in the LL and 56% in the LG. Heat map and redundancy analysis (RDA) highlighted the dramatic differences of water bacterial communities among three urban lakes. Meanwhile, the profiles of fungal communities were significantly correlated with the water quality parameters (e.g., CODMn and total nitrogen, TN). Several microbes (Legionella sp. and Streptococcus sp.) related to human diseases, such as infectious diseases, were also found. The results from this study provides useful information related to the water quality and microbial community compositions harbored in the aquatic ecosystems of urban lakes.
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Affiliation(s)
- Haihan Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Yue Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Shengnan Chen
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Zhenfang Zhao
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Ji Feng
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Zhonghui Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Kuanyu Lu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Jingyu Jia
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, China.
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Subhan F, Shahzad R, Tauseef I, Haleem KS, Rehman AU, Mahmood S, Lee IJ. Isolation, identification, and pathological effects of beach sand bacterial extract on human skin keratinocytes in vitro. PeerJ 2018; 6:e4245. [PMID: 29441229 PMCID: PMC5807979 DOI: 10.7717/peerj.4245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/18/2017] [Indexed: 01/22/2023] Open
Abstract
Background Beaches are recreational spots for people. However, beach sand contains harmful microbes that affect human health, and there are no established methods for either sampling and identifying beach-borne pathogens or managing the quality of beach sand. Method This study was conducted with the aim of improving human safety at beaches and augmenting the quality of the beach experience. Beach sand was used as a resource to isolate bacteria due to its distinctive features and the biodiversity of the beach sand biota. A selected bacterial isolate termed FSRS was identified as Pseudomonas stutzeri using 16S rRNA sequencing and phylogenetic analysis, and the sequence was deposited in the NCBI GenBank database under the accession number MF599548. The isolated P. stutzeri bacterium was cultured in Luria-Bertani growth medium, and a crude extract was prepared using ethyl acetate to examine the potential pathogenic effect of P. stutzeri on human skin. A human skin keratinocyte cell line (HaCaT) was used to assess cell adhesion, cell viability, and cell proliferation using a morphological analysis and a WST-1 assay. Result The crude P. stutzeri extract inhibited cell adhesion and decreased cell viability in HaCaT cells. We concluded that the crude extract of P. stutzeri FSRS had a strong pathological effect on human skin cells. Discussion Beach visitors frequently get skin infections, but the exact cause of the infections is yet to be determined. The beach sand bacterium P. stutzeri may, therefore, be responsible for some of the dermatological problems experienced by people visiting the beach.
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Affiliation(s)
- Fazli Subhan
- Department of Microbiology, Hazara University, Mansehra, Pakistan
| | - Raheem Shahzad
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Isfahan Tauseef
- Department of Microbiology, Hazara University, Mansehra, Pakistan
| | | | - Atta-Ur Rehman
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | - Sajid Mahmood
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.,Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Republic of Korea
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Scherer PI, Millard AD, Miller A, Schoen R, Raeder U, Geist J, Zwirglmaier K. Temporal Dynamics of the Microbial Community Composition with a Focus on Toxic Cyanobacteria and Toxin Presence during Harmful Algal Blooms in Two South German Lakes. Front Microbiol 2017; 8:2387. [PMID: 29255452 PMCID: PMC5722842 DOI: 10.3389/fmicb.2017.02387] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/20/2017] [Indexed: 02/01/2023] Open
Abstract
Bacterioplankton plays an essential role in aquatic ecosystems, and cyanobacteria are an influential part of the microbiome in many water bodies. In freshwaters used for recreational activities or drinking water, toxic cyanobacteria cause concerns due to the risk of intoxication with cyanotoxins, such as microcystins. In this study, we aimed to unmask relationships between toxicity, cyanobacterial community composition, and environmental factors. At the same time, we assessed the correlation of a genetic marker with microcystin concentration and aimed to identify the main microcystin producer. We used Illumina MiSeq sequencing to study the bacterioplankton in two recreational lakes in South Germany. We quantified a microcystin biosynthesis gene (mcyB) using qPCR and linked this information with microcystin concentration to assess toxicity. Microcystin biosynthesis gene (mcyE)-clone libraries were used to determine the origin of microcystin biosynthesis genes. Bloom toxicity did not alter the bacterial community composition, which was highly dynamic at the lowest taxonomic level for some phyla such as Cyanobacteria. At the OTU level, we found distinctly different degrees of temporal variation between major bacteria phyla. Cyanobacteria and Bacteroidetes showed drastic temporal changes in their community compositions, while the composition of Actinobacteria remained rather stable in both lakes. The bacterial community composition of Alpha- and Beta-proteobacteria remained stable over time in Lake Klostersee, but it showed temporal variations in Lake Bergknappweiher. The presence of potential microcystin degraders and potential algicidal bacteria amongst prevalent Bacteroidetes and Alphaproteobacteria implied a role of those co-occurring heterotrophic bacteria in cyanobacterial bloom dynamics. Comparison of both lakes studied revealed a large shared microbiome, which was shaped toward the lake specific community composition by environmental factors. Microcystin variants detected were microcystin-LR, -RR, and -YR. The maximum microcystin concentrations measured was 6.7 μg/L, a value still acceptable for recreational waters but not drinking water. Microcystin concentration correlated positively with total phosphorus and mcyB copy number. We identified low abundant Microcystis sp. as the only microcystin producer in both lakes. Therefore, risk assessment efforts need to take into account the fact that non-dominant species may cause toxicity of the blooms observed.
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Affiliation(s)
- Pia I Scherer
- Limnological Research Station Iffeldorf, Aquatic Systems Biology Unit, Department of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Andrew D Millard
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Andreas Miller
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Renate Schoen
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Uta Raeder
- Limnological Research Station Iffeldorf, Aquatic Systems Biology Unit, Department of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Juergen Geist
- Limnological Research Station Iffeldorf, Aquatic Systems Biology Unit, Department of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Katrin Zwirglmaier
- Limnological Research Station Iffeldorf, Aquatic Systems Biology Unit, Department of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
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