Genomics-Based Characterization of the Microbial Community and Plasmidome of the Regina Wastewater Treatment Facility and the Surrounding Aquatic Environment PDF Download
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Author: Claire Nicole Freeman
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
Wastewater produced from human activity contains high concentrations of contaminants like ammonia, pathogens, and organic compounds with high biological oxygen demand; all of which must be remediated with proper wastewater treatment prior to discharge into the environment. Most large-scale wastewater treatment plants (WWTPs) remove contaminants from wastewater using the activated sludge process, wherein wastewater is mixed with a flocculent slurry of microorganisms that use these contaminants for the production of energy or increasing microbial biomass. The activated sludge environment is a complex microbial ecosystem, containing stable populations of organisms adapted to activated sludge, as well as transient environmental and human gutassociated organisms. These microbial communities are subject to various selective pressures, including predation, fluctuating temperatures, sub-therapeutic levels of antibiotics, and heavy metals. Although microbial activity plays a large role in the functionality of these systems, there is limited information about the resident microbial communities within. In general, the bacteria in these systems are monitored through microscopy, staining, and culturing. While these tools are useful, they provide limited information about the microbial communities as a whole. Thus, this work aims to use higher resolution tools like high-throughput metagenomic sequencing and quantitative PCR to gain more information about the microbial communities in a wastewater treatment environment. This thesis focuses on three aspects of the microbial communities in the Regina WWTP: (1) the composition of the activated sludge microbial community and how it changes in response to seasonality (2) mobile genetic elements in untreated wastewater and activated sludge, and (3) the antimicrobial resistance (AMR) genes that are released into Wascana creek in the treated wastewater effluent. Samples of WWTP effluent, untreated wastewater, and activated sludge were collected from the Regina WWTP. DNA was extracted from all samples and used in high throughput sequencing to determine information about microbial community composition and mobile genetic elements, or quantitative PCR to quantify the AMR genes leaving the WWTP in the effluent. The results indicated that the Regina WWTP activated sludge system is primarily composed of the bacterial phyla, Proteobacteria and Actinobacteria. Although the composition of this microbial community varied seasonally at the genus level, the performance of the WWTP remained stable, suggesting that the functionality of this system is robust to some change within the microbial community. Quantification of functional genes revealed that denitrification genes were abundant, while nitrification genes were not, likely due to nitrifying organisms accounting for a very low proportion of the overall microbial biomass. In the recovered collection of mobile genetic elements, plasmids providing resistance to metals and antibiotics were abundant, which likely contribute to microbial adaptation to these environments. Additionally, quantification of antibiotic resistance genes in the treated effluent revealed that some of these genes are surviving the wastewater treatment process, suggesting that WWTPs may be contributing to the dissemination of antibiotic resistance in the environment.
Author: Claire Nicole Freeman
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
Wastewater produced from human activity contains high concentrations of contaminants like ammonia, pathogens, and organic compounds with high biological oxygen demand; all of which must be remediated with proper wastewater treatment prior to discharge into the environment. Most large-scale wastewater treatment plants (WWTPs) remove contaminants from wastewater using the activated sludge process, wherein wastewater is mixed with a flocculent slurry of microorganisms that use these contaminants for the production of energy or increasing microbial biomass. The activated sludge environment is a complex microbial ecosystem, containing stable populations of organisms adapted to activated sludge, as well as transient environmental and human gutassociated organisms. These microbial communities are subject to various selective pressures, including predation, fluctuating temperatures, sub-therapeutic levels of antibiotics, and heavy metals. Although microbial activity plays a large role in the functionality of these systems, there is limited information about the resident microbial communities within. In general, the bacteria in these systems are monitored through microscopy, staining, and culturing. While these tools are useful, they provide limited information about the microbial communities as a whole. Thus, this work aims to use higher resolution tools like high-throughput metagenomic sequencing and quantitative PCR to gain more information about the microbial communities in a wastewater treatment environment. This thesis focuses on three aspects of the microbial communities in the Regina WWTP: (1) the composition of the activated sludge microbial community and how it changes in response to seasonality (2) mobile genetic elements in untreated wastewater and activated sludge, and (3) the antimicrobial resistance (AMR) genes that are released into Wascana creek in the treated wastewater effluent. Samples of WWTP effluent, untreated wastewater, and activated sludge were collected from the Regina WWTP. DNA was extracted from all samples and used in high throughput sequencing to determine information about microbial community composition and mobile genetic elements, or quantitative PCR to quantify the AMR genes leaving the WWTP in the effluent. The results indicated that the Regina WWTP activated sludge system is primarily composed of the bacterial phyla, Proteobacteria and Actinobacteria. Although the composition of this microbial community varied seasonally at the genus level, the performance of the WWTP remained stable, suggesting that the functionality of this system is robust to some change within the microbial community. Quantification of functional genes revealed that denitrification genes were abundant, while nitrification genes were not, likely due to nitrifying organisms accounting for a very low proportion of the overall microbial biomass. In the recovered collection of mobile genetic elements, plasmids providing resistance to metals and antibiotics were abundant, which likely contribute to microbial adaptation to these environments. Additionally, quantification of antibiotic resistance genes in the treated effluent revealed that some of these genes are surviving the wastewater treatment process, suggesting that WWTPs may be contributing to the dissemination of antibiotic resistance in the environment.
Author: Maulin P. Shah
Publisher: Springer Nature
ISBN: 3031446186
Category : Science
Languages : en
Pages : 129
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Book Description
This book discusses the key problems and solutions with various applicable approaches to combat antibiotic-resistant genes in industrial waste water. Several genes are selected within the chapters to illustrate the past and future roles of molecular ecophysiology and genomics in the development of wastewater microbiology as an important subdiscipline of microbial ecology. As we have very limited knowledge of composition, dynamics and stability of microbial communities, various processes in wastewater treatment have been generally considered to be "black box." In recent years, with the development of several new high throughput sequencing platforms, metagenome sequencing strategies and bioinformatics toolboxes, the analysis of the genome of complex communities has become much more accessible and means easier. The opening of the biological wastewater treatment “black box” is not the unpleasant experience it was before. The viable, but not cultural, ceases to be the inconsequential, uncharacterizable enigma that existed today. Metagenomics leads the way for more specific studies in related fields. Finally, genomic studies of wastewater treatment microbes, in addition to their biotechnological applications, are also an excellent testing ground for variety of other ecological and environmental burns questions. Wastewater treatment plants are considered hotspots for the environmental dissemination of antimicrobial-resistant determinants. Comparative genomics of antibiotic resistant genes isolated from conventional activated sludge and biological aerated filter wastewater treatment plants is discussed.
Author: Francis Martin
Publisher: Springer Nature
ISBN: 1071628712
Category : Science
Languages : en
Pages : 370
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Book Description
This volume guides researchers on how to characterize, image rare, and hitherto unknown taxa and their interactions, to identify new functions and biomolecules and to understand how environmental changes condition the activity and the response of the organisms living with us and in our environment. Chapters cover different organism types (i.e., archaea, bacteria, fungi, protest, microfauna and microeukaryotes) and propose detailed protocols to produce high quality DNA, to analyse active microbial communities directly involved in complex interactions or processes through stable isotope probing, to identify and characterize of new functional genes, to image in situ interactions and to apply bioinformatics analysis tools to complex metagenomic or RNAseq sequence data. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Microbial Environmental Genomics (MEG): Methods and Protocols, Second Edition aims to serve as a primary research reference for researchers in microbiology working to in the expanding field of molecular ecology and environmental genomics.
Author: Institute of Medicine
Publisher: National Academies Press
ISBN: 0309268192
Category : Science
Languages : en
Pages : 429
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Book Description
Over the past several decades, new scientific tools and approaches for detecting microbial species have dramatically enhanced our appreciation of the diversity and abundance of the microbiota and its dynamic interactions with the environments within which these microorganisms reside. The first bacterial genome was sequenced in 1995 and took more than 13 months of work to complete. Today, a microorganism's entire genome can be sequenced in a few days. Much as our view of the cosmos was forever altered in the 17th century with the invention of the telescope, these genomic technologies, and the observations derived from them, have fundamentally transformed our appreciation of the microbial world around us. On June 12 and 13, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to discuss the scientific tools and approaches being used for detecting and characterizing microbial species, and the roles of microbial genomics and metagenomics to better understand the culturable and unculturable microbial world around us. Through invited presentations and discussions, participants examined the use of microbial genomics to explore the diversity, evolution, and adaptation of microorganisms in a wide variety of environments; the molecular mechanisms of disease emergence and epidemiology; and the ways that genomic technologies are being applied to disease outbreak trace back and microbial surveillance. Points that were emphasized by many participants included the need to develop robust standardized sampling protocols, the importance of having the appropriate metadata, data analysis and data management challenges, and information sharing in real time. The Science and Applications of Microbial Genomics summarizes this workshop.
Author: Lu Yang (Researcher in environmental engineering)
Publisher:
ISBN:
Category : Bacterial pollution of water
Languages : en
Pages : 0
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Book Description
Microorganisms are involved in various important environmental processes. While current understanding of these microbial processes is shaped to a large extent by studies of individual populations, increasing efforts have been made to understanding the roles of microbial communities as a whole in environmental processes, which is made possible with the development of high-throughput sequencing technologies. In this dissertation, the microbial communities in anaerobic waste treatment processes and stream waters influenced by anthropogenic activities were investigated as models of engineered and natural systems using microbial community-based analyses. In the anaerobic waste treatment processes, metagenomics analyses revealed the persistence of antibiotic resistant genes (ARGs) and association with specific microbial hosts, providing insight into potential targets for mitigating the spread of ARGs. Further, community-based analysis identified legacy effect as an important mechanism contributing to the assembly of microbial communities, shedding light on potential strategies for the control of important populations underlying waste treatment. In the investigation of stream waters impacted by anthropogenic activities, microbial community-based analyses enabled the successful identification of primary anthropogenic sources contributing to the microbial contamination in stream water, which has long been confounded using traditional indicator-based approaches. Results from this study provide an innovative technique for microbial source tracking not otherwise possible with individual population-based approaches. Community-based analyses, as demonstrated in this dissertation, are capable of identifying interactions between microbial populations which are essential for the survival, persistence, and function of microorganisms in the environment. Furthermore, community-based analyses are capable of utilizing all information embedded in microbial communities, which enables more precise and accurate quantification of microbial community composition and function, paving the way for the development of more effective data analytics techniques for the characterization and modeling of microbial communities.
Author:
Publisher: Academic Press
ISBN: 012407927X
Category : Science
Languages : en
Pages : 683
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Book Description
This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers microbial metagenomics, metatranscriptomics, and metaproteomics, and includes chapters on such topics as in-solution FISH for single cell genome preparation, preparation of BAC libraries from marine microbial community DNA, and preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton. - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers microbial metagenomics, metatranscriptomics, and metaproteomics - Contains chapters on such topics as in-solution fluorescence in situ hybridization (FISH) for single cell genome preparation, preparation of BAC libraries from marine microbial community DNA, and preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton
Author: Diana Elizabeth Marco
Publisher: Frontiers Media SA
ISBN: 2889458148
Category :
Languages : en
Pages : 674
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Book Description
Most ecosystem services and goods human populations use and consume are provided by microbial populations and communities. Indeed, numerous provisioning services (e.g. food and enzymes for industrial processes), regulating services (e.g. water quality, contamination alleviation and biological processes such as plant-microbial symbioses), and supporting services (e.g. nutrient cycling, agricultural production and biodiversity) are mediated by microbes. The fast development of metagenomics and other meta-omics technologies is expanding our understanding of microbial diversity, ecology, evolution and functioning. This enhanced knowledge directly translates into the emergence of new applications in an unlimited variety of areas across all microbial ecosystem services and goods. The varied topics addressed in this Research Topic include the development of innovative industrial processes, the discovery of novel natural products, the advancement of new agricultural methods, the amelioration of negative effects of productive or natural microbiological processes, as well as food security and human health, and archeological conservation. The articles compiled provide an updated, high-quality overview of current work in the field. This body of research makes a valuable contribution to the understanding of microbial ecosystem services, and expands the horizon for finding and developing new and more efficient biotechnological applications.
Author: Cassandra Helt
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
The ubiquitous nature of antibiotic resistance and antibiotic resistance genes (ARGs) among environmental pathogens from a variety of wastewater effluents, suggests that the aquatic environment, and specifically alternative wastewater treatment systems, may act as reservoirs for drug resistant bacteria and ARGs, thereby contributing to the widespread dissemination of antibiotic resistance. More research is necessary to contribute to our understanding of the occurrence, fate, and mobility of antibiotic resistance and ARGs among bacterial indicators of faecal contamination as well as pathogenic bacteria within Canadian wastewater treatment systems. The primary objective of this research was to determine the prevalence, fate, and potential transfer of bacterial resistance and ARGs among selected environmental pathogens exposed to alternative wastewater treatment systems, while considering the impact of treatment strategies on the expression of antibiotic resistance. A detailed analysis was initially conducted with respect to the characterization and quantification of microbial populations (including antibiotic resistant bacteria) in a variety of treatment systems and waste effluent sources. Traditional culture-based screening techniques in combination with molecular characterization (through colony or multiplex PCR), and molecular quantification using real-time quantitative PCR were utilized in order to help establish a preliminary environmental assessment of selected pathogens (Escherichia coli, Enterococcus spp., Salmonella spp.) and ARGs (tetA, blaSHV, & ampC) within a variety of wastewater treatment systems (lab-scale mesocosms, constructed wetland, constructed lagoon system, and pilot-scale biological nutrient removal (BNR) system). Overall, the level of multiple antibiotic resistance (MAR) among culturable indicator (E. coli & Enterococcus spp.) and environmental bacteria was high (reaching 100% in several instances) within different types of wastewater treatment systems and effluent sources (poultry waste effluent, municipal wastewater, aquaculture wastewater). Common antibiotic resistance profiles among E. coli isolates included simultaneous resistance to between three and five antimicrobials, whereas common MAR profiles among Enterococcus spp. isolates showed resistance to ten or more antibiotics. Real time quantitative PCR was used to determine the concentration of three bacterial pathogens; E. coli, Enterococcus faecalis, and Salmonella spp., and three ARGs; tetA, ampC, and blaSHV, within a variety of wastewater samples. Based on the results, it was concluded that high concentrations of ARGs were present in the treated effluent (104- 106 target gene copies/100 mL), regardless of system type (i.e. constructed lagoon, pilot-scale BNR, or constructed wetland), which may ultimately serve as a potential route for entry of ARGs and antibiotic resistant bacteria into the natural environment. Water is considered an important medium for transfer of resistance genes and resistant bacteria to the broader environment. Few studies have examined the transferability via conjugation of ARGs in E. coli and Salmonella spp. isolated from wastewater. Identification of three resistance determinants (tetA, strA, strB) conferring resistance to tetracycline and streptomycin was performed on selected multi-drug resistant Salmonella spp. and E. coli isolates. The potential for transfer of tetracycline and streptomycin resistance genes was demonstrated through broth conjugation experiments using multi-drug resistant Salmonella spp. and E. coli isolates as donors, and E. coli K12 as the recipient. Conjugation was successfully observed in 75% (9/12) of donor isolates, occurring in both Salmonella spp. and E. coli isolates. Six strains (50%) were capable of transferring their tetA, strA, and strB genes to the recipient strain, resulting in 58.5% (38/65) of total transconjugant strains acquiring all three resistance determinants. The results confirm the role of environmental bacteria (isolated from wastewater treatment utilities) as a reservoir of antibiotic resistance and ARGs, containing mobile genetic elements, which are capable of disseminating and transferring ARGs. As concerns about water quality and environmental contamination by human and agricultural effluents have increased, it has become increasingly more important to consider the prevalence and transferability of ARGs to opportunistic and human pathogens. As observed in this research, the ubiquitous nature of multi-drug resistant bacteria in water and wastewater effluents, the presence of diverse ARGs of human and veterinary health significance, as well as the transfer of resistance determinants through conjugative plasmids to recipient bacteria, suggests that environmental exposure through contact or consumption with contaminated water is probable. However, a lack of critical information still exists regarding the movement of resistance genes within and between microbial populations in the environment. In addition, the extent of human exposure to ARGs and antibiotic resistant bacteria is still not well understood, and future studies on human exposure to these resistant contaminants are necessary.
Author: Jenna Morgan Lang
Publisher:
ISBN: 9781267758101
Category :
Languages : en
Pages :
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Book Description
The work presented here represents examples of three approaches to the study of microbial diversity, including 16S PCR survey, metagenomics, and comparative genomics. Environmental 16S sequencing is used to address the role that microbes play in the biology of a model organism, Drosophila. In this case the environment examined is the gut of several species of fruit fly, including the laboratory workhorse, Drosophila melanogaster, as well as several species collected from a variety of food sources. In particular, I ask what role microbes might have in the evolution of dietary specialization in natural populations of Drosophila and whether the microbial communities present in flies that have been bred in the lab might serve as useful models for the microbial communities that are present in natural populations of Drosophila species. I also present an effort to benchmark current methods used in metagenomics to characterize microbial communities. Metagenomics allows us to use DNA sequencing to ask what kinds of microbes are in a given environment, what are their relative abundances, and what sort of metabolic capabilities do they possess. Here, I address the first two of these questions by creating an artificial microbial community, with known members at known relative abundances, and then using metagenomic techniques to recover that community composition. Finally, I take advantage of the large numbers and phylogenetic diversity of published microbial genomes to 1) create a picture of how all of those organisms are related to each other by building a phylogenetic tree and 2) to use that phylogenetic tree as a framework within which to study microbial genome evolution. In particular, I explore the environmental factors that are correlated with the incidence of horizontal gene transfer within each genome. Horizontal gene transfer is an important force driving the evolution of microbial species, allowing them to adapt rapidly to new environmental conditions, and invade new niches. Horizontal gene transfer has practical applications in the consideration of introducing genetically modified organisms into the environment, in the acquisition of antibiotic resistance, and in the transition of species from harmless to pathogenic. Here, I ask what types of physical environments promote horizontal gene transfer.
Author: Liping Ma
Publisher:
ISBN: 9781361039021
Category :
Languages : en
Pages :
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Book Description
This dissertation, "Antibiotic Resistance Genes Carried by Microbial Communities in Drinking Water Systems" by Liping, Ma, 馬黎萍, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: The overuse and misuse of antibiotics not only for human therapy but also for livestock breeding have led to the emergence and prosperity of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) and attracted great concerns worldwide. Drinking water distribution system (DWDS) considered as important means to remove pathogens for drinking water supply has been discovered as reservoir of ARGs. However, the comprehensive profiles of ARGs distributed in DWDS or the elimination efficiency of ARGs by drinking water treatment process or the hosts of ARGs distributed in DWDS has not been well studied yet. Thus, the major objectives of this study were (1) to reveal the wide-spectrum profiles of ARGs in DWDS; (2) to investigate the elimination efficiency of ARGs using traditional drinking water treatment process; (3) to develop a metagenomic assembly based method for identification of ARG-carrying genomes; (4) to explore the impacts of chlorination treatment on the shift of ARGs among microbial community. To scan for the occurrence, abundance and diversity of ARGs in DWDS, the metagenomic sequencing approach combined with structured ARG database was established. ARGs were found enriched by 81%-109% after traditional drinking water treatment processes, while the diversity of ARGs greatly decreased by 28%-51%. Acridine, chloramphenicol, and polymyxin related ARGs were fully removed during drinking water treatment. A metagenomic assembly based method for identifying ARG-carrying genomes in environmental samples was developed, could be applied to 1) identify host of ARGs, 2) to quantify their abundance in samples based on coverage, 3) to explore the antibiotic resistome shared among bacteria, and 4) to determine the correlations of ARGs with associated genetic elements. Moreover, the broad-spectrum profiles of ARGs were detected in tap water samples collected from six countries or regions, including mainland China, Hong Kong, Macau, Taiwan, South Africa, Singapore and United States, respectively. Totally, 16 ARG types and 183 ARG subtypes were detected. The most dominant ARG types were bacitracin, multidrug and aminoglycoside resistance genes. 8 subtypes were generalists which existed in all samples, including bacitracin undecaprenyl diphosphatase, bacitracin undecaprenol kinase, multidrug efflux protein, multidrug HAE1-family protein, multidrug mexF, beta-lactam TEM-2, macrolide macB, and beta-lactam TEM-15. The culture-based isolation approach combined with antimicrobial susceptibility test and high-throughput sequencing technique revealed that 66.8% ARG subtypes decreased after chlorination treatments, while, only 4.5% ARG subtypes were enriched after chlorination. Tetracycline resistance genes were effectively removed by chlorination treatment (>78%). This study is the first application of high-throughput sequencing technique combined with traditional culture-based isolation approach to detect ARGs of viable microorganisms after chlorination process. The established class 1 integrase database and the assembly of gene cassettes carried by integrons were applied to investigate the abundance of intI1 in diverse environments and the arrangement of gene cassettes. Class 1 integrase intI1 genes were detected at abundance of 0 -1.3 〖10〗 DEGREES(-1)copy of intI1/cellin drinking water samples. Aminoglycoside resistance genes were most frequently
