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Yuan Y, Zhang G, Fang H, Peng S, Xia Y, Wang F. The ecology of the sewer systems: Microbial composition, function, assembly, and network in different spatial locations. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 359:121107. [PMID: 38728984 DOI: 10.1016/j.jenvman.2024.121107] [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: 11/22/2023] [Revised: 02/04/2024] [Accepted: 05/05/2024] [Indexed: 05/12/2024]
Abstract
Microbial induced concrete corrosion (MICC) is the primary deterioration affecting global sewers. Disentangling ecological mechanisms in the sewer system is meaningful for implementing policies to protect sewer pipes using trenchless technology. It is necessary to understand microbial compositions, interaction networks, functions, alongside assembly processes in sewer microbial communities. In this study, sewer wastewater samples and microbial samples from the upper part (UP), middle part (MP) and bottom part (BP) of different pipes were collected for 16S rRNA gene amplicon analysis. It was found that BP harbored distinct microbial communities and the largest proportion of unique species (1141) compared to UP and MP. The community in BP tended to be more clustered. Furthermore, significant differences in microbial functions existed in different spatial locations, including the carbon cycle, nitrogen cycle and sulfur cycle. Active microbial sulfur cycling indicated the corrosion risk of MICC. Among the environmental factors, the oxidation‒reduction potential drove changes in BP, while sulfate managed changes in UP and BP. Stochasticity dominated community assembly in the sewer system. Additionally, the sewer microbial community exhibited numerous positive links. BP possessed a more complex, modular network with higher modularity. These deep insights into microbial ecology in the sewer system may guide engineering safety and disaster prevention in sewer infrastructure.
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Affiliation(s)
- Yiming Yuan
- School of Water Conservancy and Transportation, Zhengzhou University. Zhengzhou 450001, China; Yellow River Laboratory, Zhengzhou University. Zhengzhou 450001, China; National Local Joint Engineering Laboratory of Major Infrastructure Testing and Rehabilitation Technology, Zhengzhou 450001, China; Collaborative Innovation Center of Water Conservancy and Transportation Infrastructure Safety, Henan Province, Zhengzhou 450001, China
| | - Guangyi Zhang
- School of Water Conservancy and Transportation, Zhengzhou University. Zhengzhou 450001, China.
| | - Hongyuan Fang
- School of Water Conservancy and Transportation, Zhengzhou University. Zhengzhou 450001, China; Yellow River Laboratory, Zhengzhou University. Zhengzhou 450001, China; National Local Joint Engineering Laboratory of Major Infrastructure Testing and Rehabilitation Technology, Zhengzhou 450001, China; Collaborative Innovation Center of Water Conservancy and Transportation Infrastructure Safety, Henan Province, Zhengzhou 450001, China.
| | - Siwei Peng
- School of Water Conservancy and Transportation, Zhengzhou University. Zhengzhou 450001, China
| | - Yangyang Xia
- School of Water Conservancy and Transportation, Zhengzhou University. Zhengzhou 450001, China; Yellow River Laboratory, Zhengzhou University. Zhengzhou 450001, China; National Local Joint Engineering Laboratory of Major Infrastructure Testing and Rehabilitation Technology, Zhengzhou 450001, China; Collaborative Innovation Center of Water Conservancy and Transportation Infrastructure Safety, Henan Province, Zhengzhou 450001, China
| | - Fuming Wang
- School of Water Conservancy and Transportation, Zhengzhou University. Zhengzhou 450001, China; Yellow River Laboratory, Zhengzhou University. Zhengzhou 450001, China; National Local Joint Engineering Laboratory of Major Infrastructure Testing and Rehabilitation Technology, Zhengzhou 450001, China; Collaborative Innovation Center of Water Conservancy and Transportation Infrastructure Safety, Henan Province, Zhengzhou 450001, China
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Yuan Y, Zhang G, Fang H, Guo H, Li Y, Li Z, Peng S, Wang F. Diversity, composition, metabolic characteristics, and assembly process of the microbial community in sewer system at the early stage. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:13075-13088. [PMID: 38240967 DOI: 10.1007/s11356-024-31941-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
Sewer systems play vital roles in wastewater treatment facilities, and the microbial communities contribute significantly to the transformation of domestic wastewater. Therefore, this study conducted a 180-day experiment on a sewer system and utilized the high-throughput sequencing technology to characterize the microbial communities. Additionally, community assembly analysis was performed to understand the early-stage dynamics within the sewer system. The results demonstrated that the overall diversity of microbial communities exhibited fluctuations as the system progressed. The dominant phyla observed were Chloroflexi, Bacteroidetes, Firmicutes, and Proteobacteria, accounting for over 85.4% of the total relative abundances. At the genus level, bacteria associated with fermentation displayed a high relative abundance, particularly during days 75 to 180. A random-forest machine-learning model identified a group of microbes that confirmed the substantial contribution of fermentation. During the process of fermentation, microorganisms predominantly utilized propionate formation as the main pathway for acidogenesis, followed by acetate and butyrate formation. In terms of nitrogen and sulfur cycles, dissimilatory nitrate reduction and assimilatory sulfate reduction played significant roles. Furthermore, stochastic ecological processes had a dominant effect during the experiment. Dispersal limitation primarily governed the assembly process almost the entire experimental period, indicating the strong adaptability and metabolic plasticity of microorganisms in response to environmental variations. This experiment provides valuable insights into the metabolic mechanisms and microbial assembly associated with sewer systems.
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Affiliation(s)
- Yiming Yuan
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
- Yellow River Laboratory, Zhengzhou University, Zhengzhou, 450001, China
- National Local Joint Engineering Laboratory of Major Infrastructure Testing and Rehabilitation Technology, Zhengzhou, 450001, China
- Collaborative Innovation Center of Water Conservancy and Transportation Infrastructure Safety, Zhengzhou, 450001, Henan Province, China
| | - Guangyi Zhang
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China.
| | - Hongyuan Fang
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
- Yellow River Laboratory, Zhengzhou University, Zhengzhou, 450001, China
- National Local Joint Engineering Laboratory of Major Infrastructure Testing and Rehabilitation Technology, Zhengzhou, 450001, China
- Collaborative Innovation Center of Water Conservancy and Transportation Infrastructure Safety, Zhengzhou, 450001, Henan Province, China
| | - Haifeng Guo
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
| | - Yongkang Li
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
| | - Zezhuang Li
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
| | - Siwei Peng
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
| | - Fuming Wang
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
- Yellow River Laboratory, Zhengzhou University, Zhengzhou, 450001, China
- National Local Joint Engineering Laboratory of Major Infrastructure Testing and Rehabilitation Technology, Zhengzhou, 450001, China
- Collaborative Innovation Center of Water Conservancy and Transportation Infrastructure Safety, Zhengzhou, 450001, Henan Province, China
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3
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Shi X, Zhang R, Sand W, Mathivanan K, Zhang Y, Wang N, Duan J, Hou B. Comprehensive Review on the Use of Biocides in Microbiologically Influenced Corrosion. Microorganisms 2023; 11:2194. [PMID: 37764038 PMCID: PMC10535546 DOI: 10.3390/microorganisms11092194] [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: 07/13/2023] [Revised: 08/04/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
A microbiologically influenced corrosion (MIC) causes huge economic losses and serious environmental damage every year. The prevention and control measures for MIC mainly include physical, chemical, and biological methods. Among them, biocide application is the most cost-effective method. Although various biocides have their own advantages in preventing and treating MIC, most biocides have the problem of polluting the environment and increasing microorganism resistance. Therefore, it has stimulated the exploration of continuously developing new environmentally friendly and efficient biocides. In this review, the application advantages and research progress of various biocides used to prevent and control MIC are discussed. Also, this review provides a resource for the research and rational use of biocides regarding MIC mitigation and prevention.
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Affiliation(s)
- Xin Shi
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.S.); (W.S.); (K.M.); (Y.Z.); (N.W.); (J.D.); (B.H.)
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Open Studio for Marine Corrosion and Protection, Laoshan Laboratory, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruiyong Zhang
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.S.); (W.S.); (K.M.); (Y.Z.); (N.W.); (J.D.); (B.H.)
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Open Studio for Marine Corrosion and Protection, Laoshan Laboratory, Qingdao 266237, China
- Institute of Marine Corrosion Protection, Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning 530007, China
| | - Wolfgang Sand
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.S.); (W.S.); (K.M.); (Y.Z.); (N.W.); (J.D.); (B.H.)
- Aquatic Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany
- Institute of Biosciences, University of Mining and Technology, 09599 Freiberg, Germany
| | - Krishnamurthy Mathivanan
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.S.); (W.S.); (K.M.); (Y.Z.); (N.W.); (J.D.); (B.H.)
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yimeng Zhang
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.S.); (W.S.); (K.M.); (Y.Z.); (N.W.); (J.D.); (B.H.)
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Open Studio for Marine Corrosion and Protection, Laoshan Laboratory, Qingdao 266237, China
| | - Nan Wang
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.S.); (W.S.); (K.M.); (Y.Z.); (N.W.); (J.D.); (B.H.)
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Open Studio for Marine Corrosion and Protection, Laoshan Laboratory, Qingdao 266237, China
| | - Jizhou Duan
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.S.); (W.S.); (K.M.); (Y.Z.); (N.W.); (J.D.); (B.H.)
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Open Studio for Marine Corrosion and Protection, Laoshan Laboratory, Qingdao 266237, China
- Institute of Marine Corrosion Protection, Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning 530007, China
| | - Baorong Hou
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.S.); (W.S.); (K.M.); (Y.Z.); (N.W.); (J.D.); (B.H.)
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Open Studio for Marine Corrosion and Protection, Laoshan Laboratory, Qingdao 266237, China
- Institute of Marine Corrosion Protection, Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning 530007, China
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Kiledal EA, Shaw M, Polson SW, Maresca JA. Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea. Microbiol Spectr 2023; 11:e0511222. [PMID: 37404173 PMCID: PMC10434110 DOI: 10.1128/spectrum.05112-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/15/2023] [Indexed: 07/06/2023] Open
Abstract
Concrete hosts a small but diverse microbiome that changes over time. Shotgun metagenomic sequencing would enable assessment of both the diversity and function of the microbial community in concrete, but a number of unique challenges make this difficult for concrete samples. The high concentration of divalent cations in concrete interferes with nucleic acid extraction, and the extremely low biomass in concrete means that DNA from laboratory contamination may be a large fraction of the sequence data. Here, we develop an improved method for DNA extraction from concrete, with higher yield and lower laboratory contamination. To show that this method provides DNA of sufficient quality and quantity to do shotgun metagenomic sequencing, DNA was extracted from a sample of concrete obtained from a road bridge and sequenced with an Illumina MiSeq system. This microbial community was dominated by halophilic Bacteria and Archaea, with enriched functional pathways related to osmotic stress responses. Although this was a pilot-scale effort, we demonstrate that metagenomic sequencing can be used to characterize microbial communities in concrete and that older concrete structures may host different microbes than recently poured concrete. IMPORTANCE Prior work on the microbial communities of concrete focused on the surfaces of concrete structures such as sewage pipes or bridge pilings, where thick biofilms were easy to observe and sample. Because the biomass inside concrete is so low, more recent analyses of the microbial communities inside concrete used amplicon sequencing methods to describe those communities. However, to understand the activity and physiology of microbes in concrete, or to develop living infrastructure, we must develop more direct methods of community analysis. The method developed here for DNA extraction and metagenomic sequencing can be used for analysis of microbial communities inside concrete and can likely be adapted for other cementitious materials.
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Affiliation(s)
- E. Anders Kiledal
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Mark Shaw
- Sequencing and Genotyping Center, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Julia A. Maresca
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
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Gomez-Alvarez V, Siponen S, Kauppinen A, Hokajärvi AM, Tiwari A, Sarekoski A, Miettinen IT, Torvinen E, Pitkänen T. A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland. WATER RESEARCH 2023; 229:119495. [PMID: 37155494 PMCID: PMC10125003 DOI: 10.1016/j.watres.2022.119495] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The emergence and development of next-generation sequencing technologies (NGS) has made the analysis of the water microbiome in drinking water distribution systems (DWDSs) more accessible and opened new perspectives in microbial ecology studies. The current study focused on the characterization of the water microbiome employing a gene- and genome-centric metagenomic approach to five waterworks in Finland with different raw water sources, treatment methods, and disinfectant. The microbial communities exhibit a distribution pattern of a few dominant taxa and a large representation of low-abundance bacterial species. Changes in the community structure may correspond to the presence or absence and type of disinfectant residual which indicates that these conditions exert selective pressure on the microbial community. The Archaea domain represented a small fraction (up to 2.5%) and seemed to be effectively controlled by the disinfection of water. Their role particularly in non-disinfected DWDS may be more important than previously considered. In general, non-disinfected DWDSs harbor higher microbial richness and maintaining disinfectant residual is significantly important for ensuring low microbial numbers and diversity. Metagenomic binning recovered 139 (138 bacterial and 1 archaeal) metagenome-assembled genomes (MAGs) that had a >50% completeness and <10% contamination consisting of 20 class representatives in 12 phyla. The presence and occurrence of nitrite-oxidizing bacteria (NOB)-like microorganisms have significant implications for nitrogen biotransformation in drinking water systems. The metabolic and functional complexity of the microbiome is evident in DWDSs ecosystems. A comparative analysis found a set of differentially abundant taxonomic groups and functional traits in the active community. The broader set of transcribed genes may indicate an active and diverse community regardless of the treatment methods applied to water. The results indicate a highly dynamic and diverse microbial community and confirm that every DWDS is unique, and the community reflects the selection pressures exerted at the community structure, but also at the levels of functional properties and metabolic potential.
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Affiliation(s)
- Vicente Gomez-Alvarez
- Office of Research and Development, U.S. Environmental Protection Agency, 26W. Martin Luther King Dr., Cincinnati, OH 45268, United States
- Corresponding author. (V. Gomez-Alvarez)
| | - Sallamaari Siponen
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
- Department of Environmental and Biological Sciences, Kuopio 70211, Finland
| | - Ari Kauppinen
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
| | - Anna-Maria Hokajärvi
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
| | - Ananda Tiwari
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
- Faculty of Veterinary Medicine, Department Food Hygiene and Environmental Health, University of Helsinki, Helsinki 00790, Finland
| | - Anniina Sarekoski
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
- Faculty of Veterinary Medicine, Department Food Hygiene and Environmental Health, University of Helsinki, Helsinki 00790, Finland
| | - Ilkka T. Miettinen
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
| | - Eila Torvinen
- Department of Environmental and Biological Sciences, Kuopio 70211, Finland
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland
- Faculty of Veterinary Medicine, Department Food Hygiene and Environmental Health, University of Helsinki, Helsinki 00790, Finland
- Corresponding author at: Finnish Institute for Health and Welfare, Department of Health Security, Kuopio 70701, Finland. (T. Pitkänen)
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Pible O, Petit P, Steinmetz G, Rivasseau C, Armengaud J. Taxonomical composition and functional analysis of biofilms sampled from a nuclear storage pool. Front Microbiol 2023; 14:1148976. [PMID: 37125163 PMCID: PMC10133526 DOI: 10.3389/fmicb.2023.1148976] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Sampling small amounts of biofilm from harsh environments such as the biofilm present on the walls of a radioactive material storage pool offers few analytical options if taxonomic characterization and estimation of the different biomass contributions are the objectives. Although 16S/18S rRNA amplification on extracted DNA and sequencing is the most widely applied method, its reliability in terms of quantitation has been questioned as yields can be species-dependent. Here, we propose a tandem-mass spectrometry proteotyping approach consisting of acquiring peptide data and interpreting then against a generalist database without any a priori. The peptide sequence information is transformed into useful taxonomical information that allows to obtain the different biomass contributions at different taxonomical ranks. This new methodology is applied for the first time to analyze the composition of biofilms from minute quantities of material collected from a pool used to store radioactive sources in a nuclear facility. For these biofilms, we report the identification of three genera, namely Sphingomonas, Caulobacter, and Acidovorax, and their functional characterization by metaproteomics which shows that these organisms are metabolic active. Differential expression of Gene Ontology GOslim terms between the two main microorganisms highlights their metabolic specialization.
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Affiliation(s)
- Olivier Pible
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Pauline Petit
- Université Grenoble Alpes, CEA, CNRS, IRIG, Grenoble, France
| | - Gérard Steinmetz
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Corinne Rivasseau
- Université Grenoble Alpes, CEA, CNRS, IRIG, Grenoble, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
- *Correspondence: Jean Armengaud,
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7
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Metagenomic insights into taxonomic, functional diversity and inhibitors of microbial biofilms. Microbiol Res 2022; 265:127207. [DOI: 10.1016/j.micres.2022.127207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/17/2022] [Accepted: 09/18/2022] [Indexed: 11/21/2022]
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Ji Y, Zhang Z, Zhuang Y, Liao R, Zhou Z, Chen S. Molecular-level variation of dissolved organic matter and microbial structure of produced water during its early storage in Fuling shale gas field, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:38361-38373. [PMID: 33733405 DOI: 10.1007/s11356-021-13228-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Shale gas-produced water (PW), the waste fluid generated during gas production, contains a large number of organic contaminants and high salinity matrix. Previous studies generally focused on the end-of-pipe treatment of the PW and ignored the early collection process. In this study, the transformation of the molecular composition and microbial community structure of the PW in the transportation and storage process (i.e., from the gas-liquid separator to the storage tank) were investigated. As the PW was transported from the gas-liquid separator to the portable storage tank, the dissolved organic matter (DOM) showed greater saturation, less oxidation, and lower polarity. DOMs with high O/C and low H/C ratios (numbers of oxygen and hydrogen divided by numbers of carbon) were eliminated, which may be due to precipitation or adsorption by the solids suspended in the PW. The values of double-bond equivalent (DBE), DBE/C (DBE divided by the number of carbon), and aromatic index (AI) decreased, likely because of the microbial degradation of aromatic compounds. The PW in the gas-liquid separator presented a lower biodiversity than that in the storage tank. The microbial community in the storage tank showed the coexistence of anaerobes and aerobes. Genera related to biocorrosion and souring were detected in the two facilities, thus indicating the necessity of more efficient anticorrosion strategies. This study helps to enhance the understanding of the environmental behavior of PW during shale gas collection and provides a scientific reference for the design and formulation of efficient transportation and storage strategies to prevent and control the environmental risk of shale gas-derived PW.
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Affiliation(s)
- Yufei Ji
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaoji Zhang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Yiling Zhuang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rugang Liao
- Sinopec Chongqing Fuling Shale Gas Exploration & Development Co. Ltd., Chongqing, 408014, China
| | - Zejun Zhou
- Sinopec Chongqing Fuling Shale Gas Exploration & Development Co. Ltd., Chongqing, 408014, China
| | - Shaohua Chen
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
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Dalby FR, Hafner SD, Petersen SO, Vanderzaag A, Habtewold J, Dunfield K, Chantigny MH, Sommer SG. A mechanistic model of methane emission from animal slurry with a focus on microbial groups. PLoS One 2021; 16:e0252881. [PMID: 34111183 PMCID: PMC8191904 DOI: 10.1371/journal.pone.0252881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 05/25/2021] [Indexed: 11/19/2022] Open
Abstract
Liquid manure (slurry) from livestock releases methane (CH4) that contributes significantly to global warming. Existing models for slurry CH4 production-used for mitigation and inventories-include effects of organic matter loading, temperature, and retention time but cannot predict important effects of management, or adequately capture essential temperature-driven dynamics. Here we present a new model that includes multiple methanogenic groups whose relative abundance shifts in response to changes in temperature or other environmental conditions. By default, the temperature responses of five groups correspond to those of four methanogenic species and one uncultured methanogen, although any number of groups could be defined. We argue that this simple mechanistic approach is able to describe both short- and long-term responses to temperature where other existing approaches fall short. The model is available in the open-source R package ABM (https://github.com/sashahafner/ABM) as a single flexible function that can include effects of slurry management (e.g., removal frequency and treatment methods) and changes in environmental conditions over time. Model simulations suggest that the reduction of CH4 emission by frequent emptying of slurry pits is due to washout of active methanogens. Application of the model to represent a full-scale slurry storage tank showed it can reproduce important trends, including a delayed response to temperature changes. However, the magnitude of predicted emission is uncertain, primarily as a result of sensitivity to the hydrolysis rate constant, due to a wide range in reported values. Results indicated that with additional work-particularly on the magnitude of hydrolysis rate-the model could be a tool for estimation of CH4 emissions for inventories.
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Affiliation(s)
- Frederik R. Dalby
- Department of Biotechnology and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Aarhus, Denmark
- * E-mail: (SDH); (FRD); (SGS)
| | - Sasha D. Hafner
- Department of Biotechnology and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Aarhus, Denmark
- Hafner Consulting LLC, Reston, Virginia, United States of America
- * E-mail: (SDH); (FRD); (SGS)
| | | | - Andrew Vanderzaag
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Jemaneh Habtewold
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Kari Dunfield
- School of Environmental Science, University of Guelph, Guelph, Canada
| | - Martin H. Chantigny
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec, Canada
| | - Sven G. Sommer
- Department of Biotechnology and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Aarhus, Denmark
- * E-mail: (SDH); (FRD); (SGS)
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10
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Abstract
Concrete is an extreme but common environment and is home to microbial communities adapted to alkaline, saline, and oligotrophic conditions. Microbes inside the concrete that makes up buildings or roads have received little attention despite their ubiquity and capacity to interact with the concrete. Because concrete is a composite of materials which have their own microbial communities, we hypothesized that the microbial communities of concrete reflect those of the concrete components and that these communities change as the concrete ages. Here, we used a 16S amplicon study to show how microbial communities change over 2 years of outdoor weathering in two sets of concrete cylinders, one prone to the concrete-degrading alkali-silica reaction (ASR) and the other having the risk of the ASR mitigated. After identifying and removing taxa that were likely laboratory or reagent contaminants, we found that precursor materials, particularly the large aggregate (gravel), were the probable source of ∼50 to 60% of the bacteria observed in the first cylinders from each series. Overall, community diversity decreased over 2 years, with temporarily increased diversity in warmer summer months. We found that most of the concrete microbiome was composed of Proteobacteria, Firmicutes, and Actinobacteria, although community composition changed seasonally and over multiyear time scales and was likely influenced by environmental deposition. Although the community composition between the two series was not significantly different overall, several taxa, including Arcobacter, Modestobacter, Salinicoccus, Rheinheimera, Lawsonella, and Bryobacter, appear to be associated with ASR. IMPORTANCE Concrete is the most-used building material in the world and a biologically extreme environment, with a microbiome composed of bacteria that likely come from concrete precursor materials, aerosols, and environmental deposition. These microbes, though seeded from a variety of materials, are all subject to desiccation, heating, starvation, high salinity, and very high pH. Microbes that survive and even thrive under these conditions can potentially either degrade concrete or contribute to its repair. Thus, understanding which microbes survive in concrete, under what conditions, and for how long has potential implications for biorepair of concrete. Further, methodological pipelines for analyzing concrete microbial communities can be applied to concrete from a variety of structures or with different types of damage to identify bioindicator species that can be used for structural health monitoring and service life prediction.
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11
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Garner E, Davis BC, Milligan E, Blair MF, Keenum I, Maile-Moskowitz A, Pan J, Gnegy M, Liguori K, Gupta S, Prussin AJ, Marr LC, Heath LS, Vikesland PJ, Zhang L, Pruden A. Next generation sequencing approaches to evaluate water and wastewater quality. WATER RESEARCH 2021; 194:116907. [PMID: 33610927 DOI: 10.1016/j.watres.2021.116907] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 05/24/2023]
Abstract
The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, 1306 Evansdale Drive, Morgantown, WV 26505, United States.
| | - Benjamin C Davis
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Erin Milligan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Matthew Forrest Blair
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ishi Keenum
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ayella Maile-Moskowitz
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Jin Pan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Mariah Gnegy
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Krista Liguori
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Suraj Gupta
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States
| | - Aaron J Prussin
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Linsey C Marr
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States.
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12
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Zan F, Guo G, Zheng T, Chen G. Biofilm development in a pilot-scale gravity sewer: Physical characteristics, microstructure, and microbial communities. ENVIRONMENTAL RESEARCH 2021; 195:110838. [PMID: 33581085 DOI: 10.1016/j.envres.2021.110838] [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: 08/18/2020] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
The existence of abundant biofilms on sewer pipeline walls can lead to negative environmental impacts, such as poisonous gas release and pipe corrosions through transforming various pollutants. Investigating the formation process of sewer biofilms is of importance in advancing knowledge of sewer operation and maintenance. In this study, the changes in physical characteristics, microstructure, and microbial communities of sewer biofilm were analyzed in-depth in a pilot-scale gravity sewer during a 45-day operation. The results show that a high specific surface area at the early stage could channel the substrates for stimulating the primary colonizers (e.g., Cytophagia, Sphingobacteriia, Alpha-, and Betaproteobacteria), which could excrete an extracellular matrix to facilitate biofilm growth. The sewer biofilms were gradually formed with 62 g VS/m2 organic content, 1.2 mm biofilm thickness, and 89 mg/cm3 dry density after 45 days operation. Moreover, the biofilm growth promoted the emergence of facultative bacteria and anaerobes (affiliated with Flavobacteriia, Gemmatimonadetes, Deltaproteobacteria, and Epsilonproteobacteria). Microelectrode analysis further verified that an anaerobic zone existed in mature biofilm with a negative oxidation-reduction potential (-105 mV), where approximately 0.1 μmol/L of sulfide was produced. Our results suggest that the migration of the microbial community correlated with the changes in the evolved physical characteristics and microstructure of sewer biofilm, and this can contribute to the strategies for sulfide control for improving sewer maintenance.
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Affiliation(s)
- Feixiang Zan
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, China; Department of Civil and Environmental Engineering, Water Technology Center, Hong Kong Branch of Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong
| | - Gang Guo
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, China.
| | - Tianlong Zheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guanghao Chen
- Department of Civil and Environmental Engineering, Water Technology Center, Hong Kong Branch of Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong.
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13
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Reis MDP, de Paula RS, Reis ALM, Souza CCE, Júnior RBDO, Ferreira JA, Mota HR, de Carvalho MD, Jorge EC, Cardoso AV, Nascimento AMA. Microbial composition of a hydropower cooling water system reveals thermophilic bacteria with a possible role in primary biofilm formation. BIOFOULING 2021; 37:246-256. [PMID: 33730946 DOI: 10.1080/08927014.2021.1897790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Microfouling, ie biofilm formation on surfaces, can have an economic impact and requires costly maintenance in water-powered energy generation systems. In this study, the microbiota of a cooling system (filter and heat exchanger) in the Irapé hydroelectric power plant in Brazil was examined. The goal was to identify bacteria that could be targeted to more efficiently reduce biofilm formation. Two sampling campaigns were made corresponding to two well-defined seasons of the Brazilian Cerrado biome: the dry (campaign 1) and the wet (campaign 2). Microfouling communities varied considerably over time in samples obtained at different times after the last clearance of the heat exchanger. The thermophilic bacteria Meiothermus, Thermomonas and Symbiobacterium were exclusive and abundant in the microfouling of the heat exchanger in campaign 2, while methanotrophs and iron-reducing bacteria were abundant only in filter sediments. These findings could help to guide strategies for ecofriendly measures to reduce biofilm fouling in hydroelectric power plants, minimizing environmental and economic losses.
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Affiliation(s)
- Mariana de Paula Reis
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rayan Silva de Paula
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Clara Carvalho E Souza
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Renato Brito de Oliveira Júnior
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Jacqueline Alves Ferreira
- Departamento de Estatística, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Helen Regina Mota
- Companhia Energética de Minas Gerais S.A., Belo Horizonte, MG, Brazil
| | | | - Erika Cristina Jorge
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Andréa Maria Amaral Nascimento
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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14
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Yang Z, Zhu DZ, Yu T, Edwini-Bonsu S, Shypanski A, Liu Y. Case study of H 2S release and transport in a trunk sewer with drops. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2020; 82:2271-2281. [PMID: 33339783 DOI: 10.2166/wst.2020.475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Field work was performed to investigate the release of hydrogen sulphide (H2S) and its transport in the sewer trunk with drops in the Bonnie Doon area in Edmonton, Alberta, Canada, in order to develop a proper odor control strategy. The liquid sulfide concentration in the upstream trunk was low (less than 1.0 mg/L), and no H2S gas was detected in the head space under this low concentration. However, high H2S gas concentration was detected in the middle reach of the trunk due to the stripping effect of the three drops (2.7 m, 5.2 m and 2.0 m) along the trunk. The released H2S at drops was then transported in the sewer system and emitted at various locations and caused odor concerns. These drops played an important role in H2S release, and the overall H2S mass transfer coefficient at drops was much higher than that in normal gravity sewers. The overall oxygen and H2S mass transfer coefficient (KLa) was estimated to be around 200 h-1 and 300 h-1 at the first two drops, respectively. Field sampling of biofilm indicates that Desulfomicrobium was identified as the sulfate-reducing bacteria (SRB) responsible for sulfide generation in sewer wall biofilm and Thiobacillus was the only predominant member in manhole wall biofilm contributing to sewer manhole corrosion.
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Affiliation(s)
- Zhi Yang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 2W2, Canada E-mail:
| | - David Z Zhu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 2W2, Canada E-mail:
| | - Tong Yu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 2W2, Canada E-mail:
| | | | - Adam Shypanski
- Drainage Planning, EPCOR Drainage Services, Edmonton, AB T5 J 3A3, Canada
| | - Yanchen Liu
- International Joint Laboratory on Low Carbon Clean Energy Innovation, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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15
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Xia Y. Correlation and association analyses in microbiome study integrating multiomics in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:309-491. [PMID: 32475527 DOI: 10.1016/bs.pmbts.2020.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Correlation and association analyses are one of the most widely used statistical methods in research fields, including microbiome and integrative multiomics studies. Correlation and association have two implications: dependence and co-occurrence. Microbiome data are structured as phylogenetic tree and have several unique characteristics, including high dimensionality, compositionality, sparsity with excess zeros, and heterogeneity. These unique characteristics cause several statistical issues when analyzing microbiome data and integrating multiomics data, such as large p and small n, dependency, overdispersion, and zero-inflation. In microbiome research, on the one hand, classic correlation and association methods are still applied in real studies and used for the development of new methods; on the other hand, new methods have been developed to target statistical issues arising from unique characteristics of microbiome data. Here, we first provide a comprehensive view of classic and newly developed univariate correlation and association-based methods. We discuss the appropriateness and limitations of using classic methods and demonstrate how the newly developed methods mitigate the issues of microbiome data. Second, we emphasize that concepts of correlation and association analyses have been shifted by introducing network analysis, microbe-metabolite interactions, functional analysis, etc. Third, we introduce multivariate correlation and association-based methods, which are organized by the categories of exploratory, interpretive, and discriminatory analyses and classification methods. Fourth, we focus on the hypothesis testing of univariate and multivariate regression-based association methods, including alpha and beta diversities-based, count-based, and relative abundance (or compositional)-based association analyses. We demonstrate the characteristics and limitations of each approaches. Fifth, we introduce two specific microbiome-based methods: phylogenetic tree-based association analysis and testing for survival outcomes. Sixth, we provide an overall view of longitudinal methods in analysis of microbiome and omics data, which cover standard, static, regression-based time series methods, principal trend analysis, and newly developed univariate overdispersed and zero-inflated as well as multivariate distance/kernel-based longitudinal models. Finally, we comment on current association analysis and future direction of association analysis in microbiome and multiomics studies.
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Affiliation(s)
- Yinglin Xia
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States.
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16
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A microbiological survey of handwashing sinks in the hospital built environment reveals differences in patient room and healthcare personnel sinks. Sci Rep 2020; 10:8234. [PMID: 32427892 PMCID: PMC7237474 DOI: 10.1038/s41598-020-65052-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/24/2020] [Indexed: 01/22/2023] Open
Abstract
Handwashing sinks and their associated premise plumbing are an ideal environment for pathogen-harboring biofilms to grow and spread throughout facilities due to the connected system of wastewater plumbing. This study was designed to understand the distribution of pathogens and antibiotic resistant organisms (ARO) within and among handwashing sinks in healthcare settings, using culture-dependent methods to quantify Pseudomonas aeruginosa, opportunistic pathogens capable of growth on a cefotaxime-containing medium (OPP-C), and carbapenem-resistant Enterobacteriaceae (CRE). Isolates from each medium identified as P. aeruginosa or Enterobacteriaceae were tested for susceptibility to aztreonam, ceftazidime, and meropenem; Enterobacteriaceae were also tested against ertapenem and cefotaxime. Isolates exhibiting resistance or intermediate resistance were designated ARO. Pathogens were quantified at different locations within handwashing sinks and compared in quantity and distribution between healthcare personnel (HCP) and patient room (PR) sinks. ARO were compared between samples within a sink (biofilm vs planktonic samples) and between sink types (HCP vs. PR). The drain cover was identified as a reservoir within multiple sinks that was often colonized by pathogens despite daily sink cleaning. P. aeruginosa and OPP-C mean log10 CFU/cm2 counts were higher in p-trap and tail pipe biofilm samples from HCP compared to PR sinks (2.77 ± 2.39 vs. 1.23 ± 1.62 and 5.27 ± 1.10 vs. 4.74 ± 1.06) for P. aeruginosa and OPP-C, respectively. P. aeruginosa and OPP-C mean log10 CFU/ml counts were also higher (p < 0.05) in HCP compared to PR sinks p-trap water (2.21 ± 1.52 vs. 0.89 ± 1.44 and 3.87 ± 0.78 vs. 3.21 ± 1.11) for P. aeruginosa and OPP-C, respectively. However, a greater percentage of ARO were recovered from PR sinks compared to HCP sinks (p < 0.05) for Enterobacteriaceae (76.4 vs. 32.9%) and P. aeruginosa (25.6 vs. 0.3%). This study supports previous work citing that handwashing sinks are reservoirs for pathogens and ARO and identifies differences in pathogen and ARO quantities between HCP and PR sinks, despite the interconnected premise plumbing.
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Li X, Bond PL, O'Moore L, Wilkie S, Hanzic L, Johnson I, Mueller K, Yuan Z, Jiang G. Increased Resistance of Nitrite-Admixed Concrete to Microbially Induced Corrosion in Real Sewers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2323-2333. [PMID: 31977201 DOI: 10.1021/acs.est.9b06680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Microbially induced concrete corrosion is a major deterioration process in sewers, causing a huge economic burden, and improved mitigating technologies are required. This study reports a novel and promising effective solution to attenuate the corrosion in sewers using calcium nitrite-admixed concrete. This strategy aims to suppress the development and activity of corrosion-inducing microorganisms with the antimicrobial free nitrous acid, which is generated in situ from calcium nitrite that is added to the concrete. Concrete coupons with calcium nitrite as an admixture were exposed in a sewer manhole, together with control coupons that had no nitrite admixture, for 18 months. The corrosion process was monitored by measuring the surface pH, corrosion product composition, concrete corrosion loss, and the microbial community on the corrosion layer. During the exposure, the corrosion loss of the admixed concrete coupons was 30% lower than that of the control coupons. The sulfide uptake rate of the admixed concrete was also 30% lower, leading to a higher surface pH (0.5-0.6 unit), in comparison to that of the control coupons. A negative correlation between the calcium nitrite admixture in concrete and the abundance of sulfide-oxidizing microorganisms was determined by DNA sequencing. The results obtained in this field study demonstrated that this novel use of calcium nitrite as an admixture in concrete is a promising strategy to mitigate the microbially induced corrosion in sewers.
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Affiliation(s)
- Xuan Li
- Advanced Water Management Centre , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Philip L Bond
- Advanced Water Management Centre , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Liza O'Moore
- School of Civil Engineering , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Simeon Wilkie
- Advanced Water Management Centre , The University of Queensland , Brisbane , QLD 4072 , Australia
- Getty Conservation Institute , Los Angeles , California 90049 , United States
| | - Lucija Hanzic
- School of Civil Engineering , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Ian Johnson
- Council of the City of Gold Coast , Gold Coast , QLD 4211 , Australia
| | - Kara Mueller
- Council of the City of Gold Coast , Gold Coast , QLD 4211 , Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Guangming Jiang
- Advanced Water Management Centre , The University of Queensland , Brisbane , QLD 4072 , Australia
- School of Civil, Mining and Environmental Engineering , University of Wollongong , Wollongong , NSW 2522 , Australia
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18
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Bastaraud A, Cecchi P, Handschumacher P, Altmann M, Jambou R. Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17020480. [PMID: 31940838 PMCID: PMC7013806 DOI: 10.3390/ijerph17020480] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 11/29/2022]
Abstract
A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could be specifically the case within biofilms that develop on the surface of the myriads of floating macroplastics increasingly polluting urban tropical surface waters. Moreover, as uncultivable bacterial strains could be involved, analyses of the microbial communities in their whole have to be performed. This means that new-omic technologies must be routinely implemented in low- and middle-income countries to detect the appearance of resistance genes in microbial ecosystems, especially when considering the new ‘plastic context.’ We summarize the related current knowledge in this short review paper to anticipate new strategies for monitoring and surveying microbial communities.
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Affiliation(s)
- Alexandra Bastaraud
- Laboratoire d’Hygiène des Aliments et de l’Environnement, Institut Pasteur de Madagascar, BP 1274, Antananarivo 101, Madagascar;
| | - Philippe Cecchi
- MARBEC (IRD, IFREMER, UM2 and CNRS), University Montpellier, 34095 Montpellier, France;
- Centre de Recherche Océanologique (CRO), Abidjan BPV 18, Ivory Coast
| | - Pascal Handschumacher
- IRD UMR 912 SESSTIM, INSERM-IRD-Université de Marseille II, 13000 Marseille, France;
| | - Mathias Altmann
- ISPED Université Victor Segalen Bordeaux II, 146 rue Leo Saignat, 33076 Bordeaux cedex, France;
| | - Ronan Jambou
- Département de Parasitologie et des insectes vecteurs, Institut Pasteur Paris, 75015 Paris, France
- Correspondence: ; Tel.: +33-622-10-72-96
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19
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Mathews ER, Wood JL, Phillips D, Billington N, Barnett D, Franks AE. Town-scale microbial sewer community and H 2S emissions response to common chemical and biological dosing treatments. J Environ Sci (China) 2020; 87:133-148. [PMID: 31791487 DOI: 10.1016/j.jes.2019.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/15/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Controlling hydrogen sulfide (H2S) odors and emissions using a single, effective treatment across a town-scale sewer network is a challenge faced by many water utilities. Implementation of a sewer diversion provided the opportunity to compare the effectiveness of magnesium hydroxide (Mg(OH)2) and two biological dosing compounds (Bioproducts A and B), with different modes of action (MOA), in a field-test across a large sewer network. Mg(OH)2 increases sewer pH allowing suppression of H2S release into the sewer environment while Bioproduct A acts to disrupt microbial communication through quorum sensing (QS), reducing biofilm integrity. Bioproduct B reduces H2S odors by scouring the sewer of fats, oils and grease (FOGs), which provide adhesion points for the microbial biofilm. Results revealed that only Mg(OH)2 altered the microbial community structure and reduced H2S emissions in a live sewer system, whilst Bioproducts A and B did not reduce H2S emissions or have an observable effect on the composition of the microbial community at the dosed site. Study results recommend in situ testing of dosing treatments before implementation across an operational system.
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Affiliation(s)
- Elizabeth R Mathews
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Australia
| | - Jennifer L Wood
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Australia; Centre for Future Landscapes, La Trobe University, Melbourne, Australia; Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Australia
| | | | | | | | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Australia; Centre for Future Landscapes, La Trobe University, Melbourne, Australia.
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20
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Li W, Zheng T, Ma Y, Liu J. Current status and future prospects of sewer biofilms: Their structure, influencing factors, and substance transformations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 695:133815. [PMID: 31416035 DOI: 10.1016/j.scitotenv.2019.133815] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
With rapid urbanization, sewer systems are extensively being constructed for the collection and transportation of sewage to minimize the severe environmental and health issues, especially relating to the spread diseases. The existence of abundant biofilms on the inner walls of sewers could lead to potential risks such as sewer explosions, poisonous gas leaks, and pipe corrosions with the transformations of various kinds of pollutants. Therefore, it is urgent to clarify their inner mechanisms to safely govern sewer systems. In this study, the characteristics of sewer biofilms including their structure, influencing factors, and substance transformations were analyzed in-depth. The results reveal that sewer biofilms (1.0 mm depth approximately) consist of large quantities of inorganic and some organic substances, while the abundant functional genus of the bacteria and archaea are summarized. Sewer biofilms influencing factors were determined to be sewer operation mode, sewage characteristics, and shear stress. Further, the transformation of organics, sulfur, and nitrogen as well as emerging micropollutants (such as, biomarkers, antibiotic resistance genes, and engineered nanoparticles) was investigated to guarantee sewer security and public health. Therefore, the current review could be considered as guidance for researchers and decision-makers.
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Affiliation(s)
- Wenkai Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, 19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China.
| | - Tianlong Zheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, 19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China.
| | - Yingqun Ma
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore.
| | - Junxin Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, 19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China.
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21
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Yao Y, Habimana O. Biofilm research within irrigation water distribution systems: Trends, knowledge gaps, and future perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 673:254-265. [PMID: 30991317 DOI: 10.1016/j.scitotenv.2019.03.464] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/25/2019] [Accepted: 03/30/2019] [Indexed: 06/09/2023]
Abstract
Biofilms in irrigation water distribution systems (IWDSs) play an essential role in spreading pathogens, chemical pollutants, and environmental pollutants into downstream irrigated crops and thus should be considered a potential threat to food safety. Although the role of biofilms in drinking water distribution systems has been extensively studied in the last decade, the research on IWDS biofilms in this period has been limited. This review identifies research gaps in the field of IWDS biofilms, provides perspectives on experimental designs for investigating IWDS biofilms, and suggests potential strategies worth pursuing in IWDS management. The current state of the art of IWDS biofilms is discussed, and an analysis of the challenges in IWDS biofilm research is presented. Furthermore, this review proposes useful advanced technologies that allow a practical, in-depth fundamental understanding of IWDS biofilms. In a nutshell, this article provides future directions and insights into detailed experimental designs on a relatively under-reported research topic: "IWDS biofilms."
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Affiliation(s)
- Yuan Yao
- The School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Olivier Habimana
- The School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; The University of Hong Kong Shenzhen Institute of Research and Innovation (HKU-SIRI), Shenzhen, Guangdong Province, People's Republic of China.
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Vishwakarma V, Anandkumar B. Molecular biological tools in concrete biodeterioration - a mini review. ENVIRONMENTAL TECHNOLOGY 2019; 40:i-xi. [PMID: 30112961 DOI: 10.1080/09593330.2018.1513082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 08/12/2018] [Indexed: 06/08/2023]
Abstract
Concrete structures develop biofilms when exposed to various environments. At a certain stage, the microbial films destroy the concrete structures leading to significant deterioration. Culture-dependent techniques give an incomplete picture of the microbial communities on the concrete surface. Culture-independent techniques or molecular biological tools pave a new way to analyse microbial communities involved in concrete biodeterioration. This study highlights the need to 'build' a database, for Microbiologically Influenced Concrete Corrosion (MICC) involving microbial groups that are being identified using culture-dependent and independent techniques. The role of molecular tools such as 16S rRNA sequencing, denaturing gradient gel electrophoresis (DGGE), Fluorescent in situ hybridization (FISH), Real-time Polymerase Chain Reaction (RT-PCR), microarray analysis, 2-Dimensional gel electrophoresis (2-DE) in analysing microbial communities on the concrete structures have been reviewed in this paper.
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Affiliation(s)
- Vinita Vishwakarma
- Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai, India
| | - Balakrishnan Anandkumar
- Corrosion Science and Technology Division, Indira Gandhi Centre for Atomic Research, Kalpakkam, India
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Karačić S, Wilén BM, Suarez C, Hagelia P, Persson F. Subsea tunnel reinforced sprayed concrete subjected to deterioration harbours distinct microbial communities. BIOFOULING 2018; 34:1161-1174. [PMID: 30740996 DOI: 10.1080/08927014.2018.1556259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/29/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
Deterioration of concrete is a large societal cost. In the Oslofjord subsea tunnel (Norway), deterioration of sprayed concrete and corrosion of reinforcing steel fibres occur under biofilm formed at sites with intrusion of saline groundwater. In this study, the microbial community structure, in situ environmental gradients and chemical composition of the biofilms were examined at three tunnel sites. Ammonia- and nitrite-oxidising microorganisms, in particular Nitrosopumilus sp., and iron-oxidising bacteria within Mariprofundus sp., were omnipresent, together with a diversity of presumably heterotrophic bacteria. Alpha- and beta diversity measures showed significant differences in richness and community structure between the sites as well as over time and null-models suggested that deterministic factors were important for the community assembly. The superficial flow of water over the biofilm had a strong effect on oxygen penetration in the biofilm and was identified as one major environmental gradient that varied between the sites, likely being important for shaping the microbial communities.
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Affiliation(s)
- Sabina Karačić
- a Department of Architecture and Civil Engineering , Chalmers University of Technology , Göteborg , Göteborg , Sweden
| | - Britt-Marie Wilén
- a Department of Architecture and Civil Engineering , Chalmers University of Technology , Göteborg , Göteborg , Sweden
| | - Carolina Suarez
- b Department of Chemistry and Molecular Biology , University of Gothenburg , Göteborg , Göteborg , Sweden
| | - Per Hagelia
- c Tunnel and Concrete Division , The Norwegian Public Roads Administration , Oslo , Norway
| | - Frank Persson
- a Department of Architecture and Civil Engineering , Chalmers University of Technology , Göteborg , Göteborg , Sweden
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López-Leal G, Cornejo-Granados F, Hurtado-Ramírez JM, Mendoza-Vargas A, Ochoa-Leyva A. Functional and taxonomic classification of a greenhouse water drain metagenome. Stand Genomic Sci 2018; 13:20. [PMID: 30323887 PMCID: PMC6173933 DOI: 10.1186/s40793-018-0326-y] [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: 09/14/2017] [Accepted: 09/24/2018] [Indexed: 02/07/2023] Open
Abstract
Microbiome sequencing has become the standard procedure in the study of new ecological and human-constructed niches. To our knowledge, this is the first report of a metagenome from the water of a greenhouse drain. We found that the greenhouse is not a diverse niche, mainly dominated by Rhizobiales and Rodobacterales. The analysis of the functions encoded in the metagenome showed enrichment of characteristic features of soil and root-associated bacteria such as ABC-transporters and hydrolase enzymes. Additionally, we found antibiotic resistances genes principally for spectinomycin, tetracycline, and aminoglycosides. This study aimed to identify the bacteria and functional gene composition of a greenhouse water drain sample and also provide a genomic resource to search novel proteins from a previously unexplored niche. All the metagenome proteins and their annotations are available to the scientific community via http://microbiomics.ibt.unam.mx/tools/metagreenhouse/.
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Affiliation(s)
- Gamaliel López-Leal
- 1Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, 62210 Morelos Mexico
| | - Fernanda Cornejo-Granados
- 1Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, 62210 Morelos Mexico
| | - Juan Manuel Hurtado-Ramírez
- 1Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, 62210 Morelos Mexico
| | - Alfredo Mendoza-Vargas
- 2Instituto Nacional de Medicina Genómica, Secretaría de Salud, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, 14610 Ciudad de México, Mexico
| | - Adrian Ochoa-Leyva
- 1Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, 62210 Morelos Mexico
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Zhang K, Gu J, Wang X, Yin Y, Zhang X, Zhang R, Tuo X, Zhang L. Variations in the denitrifying microbial community and functional genes during mesophilic and thermophilic anaerobic digestion of cattle manure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 634:501-508. [PMID: 29631139 DOI: 10.1016/j.scitotenv.2018.03.377] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/27/2018] [Accepted: 03/30/2018] [Indexed: 06/08/2023]
Abstract
In this study, the anaerobic digestion (AD) of cattle manure was conducted at two temperatures (mesophilic: 35 °C; thermophilic: 55 °C) to analyze the dynamics of the denitrifying functional microbial community and functional genes. The cumulative N2O production under thermophilic conditions was 130.3% higher than that under mesophilic conditions. Thermophilic AD decreased the abundance of nosZ, which was more functional than other denitrifying genes. Firmicutes, Proteobacteria, and Bacteroidetes were the main phyla, and they were also related to denitrification during AD. Redundancy analysis indicated that pH, temperature, and NH4+-N mainly affected the functional bacterial community. Temperature altered the co-occurrence patterns of the bacterial community and the keystone genera in AD. Desulfovibrio in mesophilic AD and Thiobacillus in thermophilic AD were closely related to nitrogen transformation among the keystone genera. The variations in the abundances of members of the denitrifying microbial community and functional genes during AD suggest that thermophilic AD may have caused greater nitrogen losses.
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Affiliation(s)
- Kaiyu Zhang
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Gu
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojuan Wang
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanan Yin
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xin Zhang
- College of Science, Northwest A&F University, Yangling 712100, China
| | - Ranran Zhang
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaxia Tuo
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Zhang
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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Pal S, Qureshi A, Purohit HJ. Intercepting signalling mechanism to control environmental biofouling. 3 Biotech 2018; 8:364. [PMID: 30105189 DOI: 10.1007/s13205-018-1383-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 07/29/2018] [Indexed: 12/29/2022] Open
Abstract
Biofouling in environmental systems employs bacterial quorum sensing signals (autoinducers) and extracellular polymeric substances to onset the event. The present review has highlighted on the fundamental mechanisms behind biofilm formation over broad spectrum environmental niches especially membrane biofouling in water systems and consequent chances of pathogenic contamination leading to global economic loss. It has broadly discussed on bioelectrical signal (via, potassium gradient) and molecular signal (via, AHLs) mediated quorum sensing which help to propagate biofilm formation. The review has illustrated the potential of genomic intervention towards biofouled membrane microbial community and has uncovered possible features of biofilm microenvironment like quorum quenching bacteria, bioelectrical waves capture, siderophores arrest and surface modifications. Based on information, the concept of interception of quorum signals (AHLs) and bioelectrical signals (K+) by employing electro-modified (negative charges) membrane surface have been hypothesized in the present review to favour anti-biofouling.
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Affiliation(s)
- Smita Pal
- 1Academy of Scientific and Innovative Research (AcSIR), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, Maharashtra 440020 India
- 2CSIR-Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, Maharashtra 440020 India
| | - Asifa Qureshi
- 1Academy of Scientific and Innovative Research (AcSIR), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, Maharashtra 440020 India
- 2CSIR-Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, Maharashtra 440020 India
| | - Hemant J Purohit
- 2CSIR-Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, Maharashtra 440020 India
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27
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Grengg C, Mittermayr F, Ukrainczyk N, Koraimann G, Kienesberger S, Dietzel M. Advances in concrete materials for sewer systems affected by microbial induced concrete corrosion: A review. WATER RESEARCH 2018; 134:341-352. [PMID: 29453009 DOI: 10.1016/j.watres.2018.01.043] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/17/2018] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
Microbial induced concrete corrosion (MICC) is recognized as one of the main degradation mechanisms of subsurface infrastructure worldwide, raising the demand for sustainable construction materials in corrosive environments. This review aims to summarize the key research progress acquired during the last decade regarding the understanding of MICC reaction mechanisms and the development of durable materials from an interdisciplinary perspective. Special focus was laid on aspects governing concrete - micoorganisms interaction since being the central process steering biogenic acid corrosion. The insufficient knowledge regarding the latter is proposed as a central reason for insufficient progress in tailored material development for aggressive wastewater systems. To date no cement-based material exists, suitable to withstand the aggressive conditions related to MICC over its entire service life. Research is in particular needed on the impact of physiochemical material parameters on microbial community structure, growth characteristics and limitations within individual concrete speciation. Herein an interdisciplinary approach is presented by combining results from material sciences, microbiology, mineralogy and hydrochemistry to stimulate the development of novel and sustainable materials and mitigation strategies for MICC. For instance, the application of antibacteriostatic agents is introduced as an effective instrument to limit microbial growth on concrete surfaces in aggressive sewer environments. Additionally, geopolymer concretes are introduced as highly resistent in acid environments, thus representing a possible green alternative to conventional cement-based construction materials.
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Affiliation(s)
- Cyrill Grengg
- Institute of Applied Geosciences, Graz University of Technology, Rechbauerstraße 12, 8010, Graz, Austria.
| | - Florian Mittermayr
- Institute of Technology and Testing of Building Materials, Graz University of Technology, Inffeldgasse 24, 8010, Graz, Austria
| | - Neven Ukrainczyk
- Institute of Construction and Building Materials, Technische Universität Darmstadt, Franziska-Braun-Straße 3, 64287, Darmstadt, Germany
| | - Günther Koraimann
- Institute of Molecular Biosciences, University of Graz, Humboldstraße 50, 8010, Graz, Austria
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, Humboldstraße 50, 8010, Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010, Graz, Austria
| | - Martin Dietzel
- Institute of Applied Geosciences, Graz University of Technology, Rechbauerstraße 12, 8010, Graz, Austria
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Microbiome analysis and -omics studies of microbial denitrification processes in wastewater treatment: recent advances. SCIENCE CHINA-LIFE SCIENCES 2018; 61:753-761. [DOI: 10.1007/s11427-017-9228-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/22/2017] [Indexed: 10/18/2022]
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Cayford BI, Jiang G, Keller J, Tyson G, Bond PL. Comparison of microbial communities across sections of a corroding sewer pipe and the effects of wastewater flooding. BIOFOULING 2017; 33:780-792. [PMID: 28956470 DOI: 10.1080/08927014.2017.1369050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/11/2017] [Indexed: 06/07/2023]
Abstract
This study investigated the variation in microbially induced concrete corrosion communities at different circumferential locations of a real sewer pipe and the effects of a wastewater flooding event on the community. Three distinct microbial community groups were found in different corrosion samples. The physico-chemical properties of the corrosion layers and the microbial communities were distinct for the cross-sectional positions within the pipe, ie ceiling, wall and tidal zones. The microbial communities detected from the same positions in the pipe were consistent over the length of the pipe, as well as being consistent between the replicate pipes. The dominating ceiling communities were members of the bacterial orders Rhodospirillales, Acidithiobacillales, Actinomycetales, Xanthomonadales and Acidobacteriales. The wall communities were composed of members of the Xanthomonadales, Hydrogenophilales, Chromatiales and Sphingobacteriales. The tidal zones were dominated by eight bacterial and one archaeal order, with the common physiological trait of anaerobic metabolism. Sewage flooding within the sewer system did not change the tidal and wall communities, although the corrosion communities in ceiling samples were notably different, becoming more similar to the wall and tidal samples. This suggests that sewage flooding has a significant impact on the corrosion community in sewers.
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Affiliation(s)
- Barry I Cayford
- a Advanced Water Management Centre , The University of Queensland , St Lucia , Australia
| | - Guangming Jiang
- a Advanced Water Management Centre , The University of Queensland , St Lucia , Australia
| | - Jurg Keller
- a Advanced Water Management Centre , The University of Queensland , St Lucia , Australia
| | - Gene Tyson
- b Australian Centre for Ecogenomics , The University of Queensland , St Lucia , Australia
| | - Philip L Bond
- a Advanced Water Management Centre , The University of Queensland , St Lucia , Australia
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Li X, Kappler U, Jiang G, Bond PL. The Ecology of Acidophilic Microorganisms in the Corroding Concrete Sewer Environment. Front Microbiol 2017; 8:683. [PMID: 28473816 PMCID: PMC5397505 DOI: 10.3389/fmicb.2017.00683] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/04/2017] [Indexed: 12/19/2022] Open
Abstract
Concrete corrosion is one of the most significant problems affecting valuable sewer infrastructure on a global scale. This problem occurs in the aerobic zone of the sewer, where a layer of surface corrosion develops on the exposed concrete and the surface pH is typically lowered from around 11–10 (pristine concrete) to pH 2–4. Acidophilic microorganisms become established as biofilms within the concrete corrosion layer and enhance the loss of concrete mass. Until recently, the acidophilic community was considered to comprise relatively few species of microorganisms, however, the biodiversity of the corrosion community is now recognized as being extensive and varying from different sewer environmental conditions. The diversity of acidophiles in the corrosion communities includes chemolithoautotrophs, chemolithoheterotrophs, and chemoorganoheterotrophs. The activity of these microorganisms is strongly affected by H2S levels in the sewer gas phase, although CO2, organic matter, and iron in the corrosion layer influence this acidic ecosystem. This paper briefly presents the conditions within the sewer that lead to the development of concrete corrosion in that environment. The review focuses on the acidophilic microorganisms detected in sewer corrosion environments, and then summarizes their proposed functions and physiology, especially in relation to the corrosion process. To our knowledge, this is the first review of acidophilic corrosion microbial communities, in which, the ecology and the environmental conditions (when available) are considered. Ecological studies of sewer corrosion are limited, however, where possible, we summarize the important metabolic functions of the different acidophilic species detected in sewer concrete corrosion layers. It is evident that microbial functions in the acidic sewer corrosion environment can be linked to those occurring in the analogous acidic environments of acid mine drainage and bioleaching.
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Affiliation(s)
- Xuan Li
- Advanced Water Management Centre, The University of Queensland, BrisbaneQLD, Australia
| | - Ulrike Kappler
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, BrisbaneQLD, Australia
| | - Guangming Jiang
- Advanced Water Management Centre, The University of Queensland, BrisbaneQLD, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, BrisbaneQLD, Australia
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31
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Dong Q, Shi H, Liu Y. Microbial Character Related Sulfur Cycle under Dynamic Environmental Factors Based on the Microbial Population Analysis in Sewerage System. Front Microbiol 2017; 8:64. [PMID: 28261160 PMCID: PMC5306501 DOI: 10.3389/fmicb.2017.00064] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/10/2017] [Indexed: 11/22/2022] Open
Abstract
The undesired sulfur cycle derived by microbial population can ultimately causes the serious problems of sewerage systems. However, the microbial community characters under dynamic environment factors in actual sewerage system is still not enough. This current study aimed to character the distributions and compositions of microbial communities that participate in the sulfur cycle under the dynamic environmental conditions in a local sewerage system. To accomplish this, microbial community compositions were assessed using 454 high-throughput sequencing (16S rDNA) combined with dsrB gene-based denaturing gradient gel electrophoresis. The results indicated that a higher diversity of microbial species was present at locations in sewers with high concentrations of H2S. Actinobacteria and Proteobacteria were dominant in the sewerage system, while Actinobacteria alone were dominant in regions with high concentrations of H2S. Specifically, the unique operational taxonomic units could aid to characterize the distinct microbial communities within a sewerage manhole. The proportion of sulfate-reducing bacteria, each sulfur-oxidizing bacteria (SOB) were strongly correlated with the liquid parameters (DO, ORP, COD, Sulfide, NH3-N), while the Mycobacterium and Acidophilic SOB (M&A) was strongly correlated with gaseous factors within the sewer, such as H2S, CH4, and CO. Identifying the distributions and proportions of critical microbial communities within sewerage systems could provide insights into how the microbial sulfur cycle is affected by the dynamic environmental conditions that exist in sewers and might be useful for explaining the potential sewerage problems.
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Affiliation(s)
- Qian Dong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University Beijing, China
| | - Hanchang Shi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University Beijing, China
| | - Yanchen Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University Beijing, China
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Sul WJ, Kim IS, Ekpeghere KI, Song B, Kim BS, Kim HG, Kim JT, Koh SC. Metagenomic insight of nitrogen metabolism in a tannery wastewater treatment plant bioaugmented with the microbial consortium BM-S-1. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2016; 51:1164-1172. [PMID: 27471001 DOI: 10.1080/10934529.2016.1206387] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nitrogen (N) removal in a tannery wastewater treatment plant was significantly enhanced by the bioaugmentation of the novel consortium BM-S-1. In order to identify dominant taxa responsible for N metabolisms in the different stages of the treatment process, Illumina MiSeq Sequencer was used to conduct metagenome sequencing of the microbial communities in the different stages of treatment system, including influent (I), buffering (B), primary aeration (PA), secondary aeration (SA) and sludge digestion (SD). Based on MG-RAST analysis, the dominant phyla were Proteobacteria, Bacteroidetes and Firmicutes in B, PA, SA and SD, whereas Firmicutes was the most dominant in I before augmentation. The augmentation increased the abundance of the denitrification genes found in the genera such as Ralstonia (nirS, norB and nosZ), Pseudomonas (narG, nirS and norB) and Escherichia (narG) in B and PA. In addition, Bacteroides, Geobacter, Porphyromonasand Wolinella carrying nrfA gene encoding dissimilatory nitrate reduction to ammonium were abundantly present in B and PA. This was corroborated with the higher total N removal in these two stages. Thus, metagenomic analysis was able to identify the dominant taxa responsible for dissimilatory N metabolisms in the tannery wastewater treatment system undergoing bioaugmentation. This metagenomic insight into the nitrogen metabolism will contribute to a successful monitoring and operation of the eco-friendly tannery wastewater treatment system.
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Affiliation(s)
- Woo-Jun Sul
- a Department of Systems Biotechnology , Chung-Ang University , Anseong , South Korea
| | - In-Soo Kim
- b Department of Environmental Engineering , Korea Maritime and Ocean University , Busan , South Korea
| | - Kalu I Ekpeghere
- b Department of Environmental Engineering , Korea Maritime and Ocean University , Busan , South Korea
| | - Bongkeun Song
- c Department of Biological Sciences , Viginia Institute of Marine Science , Gloucester Point , Virginia , USA
- d Department of Life Science , Dongguk University-Seoul , Junggu , Seoul , South Korea
| | - Bong-Soo Kim
- e Department of Life Science , Hallym University , Chuncheon , South Korea
| | | | | | - Sung-Cheol Koh
- b Department of Environmental Engineering , Korea Maritime and Ocean University , Busan , South Korea
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Purohit HJ, Kapley A, Khardenavis A, Qureshi A, Dafale NA. Insights in Waste Management Bioprocesses Using Genomic Tools. ADVANCES IN APPLIED MICROBIOLOGY 2016; 97:121-170. [PMID: 27926430 DOI: 10.1016/bs.aambs.2016.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.
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Affiliation(s)
- H J Purohit
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Kapley
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Khardenavis
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Qureshi
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - N A Dafale
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
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Vikram A, Lipus D, Bibby K. Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale. MICROBIAL ECOLOGY 2016; 72:571-581. [PMID: 27457653 DOI: 10.1007/s00248-016-0811-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 06/29/2016] [Indexed: 06/06/2023]
Abstract
Controlling microbial activity is a primary concern during the management of the large volumes of wastewater (produced water) generated during high-volume hydraulic fracturing. In this study we analyzed the transcriptional activity (metatranscriptomes) of three produced water samples from the Marcellus Shale. The goal of this study was to describe active metabolic pathways of industrial concern for produced water management and reuse, and to improve understanding of produced water microbial activity. Metatranscriptome analysis revealed active biofilm formation, sulfide production, and stress management mechanisms of the produced water microbial communities. Biofilm-formation and sulfate-reduction pathways were identified in all samples. Genes related to a diverse array of stress response mechanisms were also identified with implications for biocide efficacy. Additionally, active expression of a methanogenesis pathway was identified in a sample of produced water collected prior to holding pond storage. The active microbial community identified by metatranscriptome analysis was markedly different than the community composition as identified by 16S rRNA sequencing, highlighting the value of evaluating the active microbial fraction during assessments of produced water biofouling potential and evaluation of biocide application strategies. These results indicate biofouling and corrosive microbial processes are active in produced water and should be taken into consideration while designing produced water reuse strategies.
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Affiliation(s)
- Amit Vikram
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Daniel Lipus
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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Huber B, Herzog B, Drewes JE, Koch K, Müller E. Characterization of sulfur oxidizing bacteria related to biogenic sulfuric acid corrosion in sludge digesters. BMC Microbiol 2016; 16:153. [PMID: 27430211 PMCID: PMC4950637 DOI: 10.1186/s12866-016-0767-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 07/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biogenic sulfuric acid (BSA) corrosion damages sewerage and wastewater treatment facilities but is not well investigated in sludge digesters. Sulfur/sulfide oxidizing bacteria (SOB) oxidize sulfur compounds to sulfuric acid, inducing BSA corrosion. To obtain more information on BSA corrosion in sludge digesters, microbial communities from six different, BSA-damaged, digesters were analyzed using culture dependent methods and subsequent polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE). BSA production was determined in laboratory scale systems with mixed and pure cultures, and in-situ with concrete specimens from the digester headspace and sludge zones. RESULTS The SOB Acidithiobacillus thiooxidans, Thiomonas intermedia, and Thiomonas perometabolis were cultivated and compared to PCR-DGGE results, revealing the presence of additional acidophilic and neutrophilic SOB. Sulfate concentrations of 10-87 mmol/L after 6-21 days of incubation (final pH 1.0-2.0) in mixed cultures, and up to 433 mmol/L after 42 days (final pH <1.0) in pure A. thiooxidans cultures showed huge sulfuric acid production potentials. Additionally, elevated sulfate concentrations in the corroded concrete of the digester headspace in contrast to the concrete of the sludge zone indicated biological sulfur/sulfide oxidation. CONCLUSIONS The presence of SOB and confirmation of their sulfuric acid production under laboratory conditions reveal that these organisms might contribute to BSA corrosion within sludge digesters. Elevated sulfate concentrations on the corroded concrete wall in the digester headspace (compared to the sludge zone) further indicate biological sulfur/sulfide oxidation in-situ. For the first time, SOB presence and activity is directly relatable to BSA corrosion in sludge digesters.
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Affiliation(s)
- Bettina Huber
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748, Garching, Germany
| | - Bastian Herzog
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748, Garching, Germany
| | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748, Garching, Germany.
| | - Konrad Koch
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748, Garching, Germany
| | - Elisabeth Müller
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748, Garching, Germany
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Benedek T, Táncsics A, Szabó I, Farkas M, Szoboszlay S, Fábián K, Maróti G, Kriszt B. Polyphasic analysis of an Azoarcus-Leptothrix-dominated bacterial biofilm developed on stainless steel surface in a gasoline-contaminated hypoxic groundwater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:9019-9035. [PMID: 26825521 DOI: 10.1007/s11356-016-6128-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/18/2016] [Indexed: 06/05/2023]
Abstract
Pump and treat systems are widely used for hydrocarbon-contaminated groundwater remediation. Although biofouling (formation of clogging biofilms on pump surfaces) is a common problem in these systems, scarce information is available regarding the phylogenetic and functional complexity of such biofilms. Extensive information about the taxa and species as well as metabolic potential of a bacterial biofilm developed on the stainless steel surface of a pump submerged in a gasoline-contaminated hypoxic groundwater is presented. Results shed light on a complex network of interconnected hydrocarbon-degrading chemoorganotrophic and chemolitotrophic bacteria. It was found that besides the well-known hydrocarbon-degrading aerobic/facultative anaerobic biofilm-forming organisms (e.g., Azoarcus, Leptothrix, Acidovorax, Thauera, Pseudomonas, etc.), representatives of Fe(2+)-and Mn(2+)-oxidizing (Thiobacillus, Sideroxydans, Gallionella, Rhodopseudomonas, etc.) as well as of Fe(3+)- and Mn(4+)-respiring (Rhodoferax, Geobacter, Magnetospirillum, Sulfurimonas, etc.) bacteria were present in the biofilm. The predominance of β-Proteobacteria within the biofilm bacterial community in phylogenetic and functional point of view was revealed. Investigation of meta-cleavage dioxygenase and benzylsuccinate synthase (bssA) genes indicated that within the biofilm, Azoarcus, Leptothrix, Zoogloea, and Thauera species are most probably involved in intrinsic biodegradation of aromatic hydrocarbons. Polyphasic analysis of the biofilm shed light on the fact that subsurface microbial accretions might be reservoirs of novel putatively hydrocarbon-degrading bacterial species. Moreover, clogging biofilms besides their detrimental effects might supplement the efficiency of pump and treat systems.
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Affiliation(s)
- Tibor Benedek
- Regional University Center of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, 2100, Hungary
| | - András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, 2100, Hungary.
| | - István Szabó
- Department of Environmental Safety and Ecotoxicology, Szent István University, Páter K. u. 1, Gödöllő, 2100, Hungary
| | - Milán Farkas
- Department of Environmental Safety and Ecotoxicology, Szent István University, Páter K. u. 1, Gödöllő, 2100, Hungary
| | - Sándor Szoboszlay
- Department of Environmental Safety and Ecotoxicology, Szent István University, Páter K. u. 1, Gödöllő, 2100, Hungary
| | - Krisztina Fábián
- Department of Environmental Safety and Ecotoxicology, Szent István University, Páter K. u. 1, Gödöllő, 2100, Hungary
| | - Gergely Maróti
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62., Szeged, 6726, Hungary
| | - Balázs Kriszt
- Department of Environmental Safety and Ecotoxicology, Szent István University, Páter K. u. 1, Gödöllő, 2100, Hungary
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Brereton NJB, Gonzalez E, Marleau J, Nissim WG, Labrecque M, Joly S, Pitre FE. Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants. PLANT PHYSIOLOGY 2016; 171:3-24. [PMID: 27002060 PMCID: PMC4854704 DOI: 10.1104/pp.16.00090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/20/2016] [Indexed: 05/09/2023]
Abstract
Metatranscriptomic study of nonmodel organisms requires strategies that retain the highly resolved genetic information generated from model organisms while allowing for identification of the unexpected. A real-world biological application of phytoremediation, the field growth of 10 Salix cultivars on polluted soils, was used as an exemplar nonmodel and multifaceted crop response well-disposed to the study of gene expression. Sequence reads were assembled de novo to create 10 independent transcriptomes, a global transcriptome, and were mapped against the Salix purpurea 94006 reference genome. Annotation of assembled contigs was performed without a priori assumption of the originating organism. Global transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotated from 1588 species, often common in all 10 cultivars. Comparisons between transcriptomic and metatranscriptomic methodologies provide clear evidence that nonnative RNA can mistakenly map to reference genomes, especially to conserved regions of common housekeeping genes, such as actin, α/β-tubulin, and elongation factor 1-α. In Salix, Rubisco activase transcripts were down-regulated in contaminated trees across all 10 cultivars, whereas thiamine thizole synthase and CP12, a Calvin Cycle master regulator, were uniformly up-regulated. De novo assembly approaches, with unconstrained annotation, can improve data quality; care should be taken when exploring such plant genetics to reduce de facto data exclusion by mapping to a single reference genome alone. Salix gene expression patterns strongly suggest cultivar-wide alteration of specific photosynthetic apparatus and protection of the antenna complexes from oxidation damage in contaminated trees, providing an insight into common stress tolerance strategies in a real-world phytoremediation system.
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Affiliation(s)
- Nicholas J B Brereton
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Emmanuel Gonzalez
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Julie Marleau
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Werther Guidi Nissim
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Michel Labrecque
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Simon Joly
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Frederic E Pitre
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
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Cheng L, House MW, Weiss WJ, Banks MK. Monitoring sulfide-oxidizing biofilm activity on cement surfaces using non-invasive self-referencing microsensors. WATER RESEARCH 2016; 89:321-329. [PMID: 26707733 DOI: 10.1016/j.watres.2015.11.066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/15/2015] [Accepted: 11/28/2015] [Indexed: 06/05/2023]
Abstract
Microbially influenced corrosion (MIC) in concrete results in significant cost for infrastructure maintenance. Prior studies have employed molecular techniques to identify microbial community species in corroded concrete, but failed to explore bacterial activity and functionality during deterioration. In this study, biofilms of different sulfur-oxidizing bacteria compositions were developed on the surface of cement paste samples to simulate the natural ecological succession of microbial communities during MIC processes. Noninvasive, self-referencing (SR) microsensors were used to quantify real time changes of oxygen, hydrogen ion and calcium ion flux for the biofilm to provide more information about bacterial behavior during deterioration. Results showed higher transport rates in oxygen consumption, and hydrogen ion at 4 weeks than 2 weeks, indicating increased bacterial activity over time. Samples with five species biofilm had the highest hydrogen ion and calcium ion transport rates, confirming attribution of acidophilic sulfur-oxidizing microorganisms (ASOM). Differences in transport rates between three species samples and two species samples confirmed the diversity between Thiomonas intermedia and Starkeya novella. The limitations of SR sensors in corrosion application could be improved in future studies when combined with molecular techniques to identify the roles of major bacterial species in the deterioration process.
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Affiliation(s)
- Liqiu Cheng
- Zachry Department of Civil Engineering, Texas A&M University, 3136 TAMU, College Station, TX 77843-3136, USA.
| | - Mitch W House
- Lyles School of Civil Engineering, Purdue University, 550 Stadium Mall Drive, West Lafayette, IN 47907-2051, USA
| | - W Jason Weiss
- Lyles School of Civil Engineering, Purdue University, 550 Stadium Mall Drive, West Lafayette, IN 47907-2051, USA; Bindley Bioscience Center, Physiological Sensing Facility, Discovery Park, Purdue University, 1203 W. State Street, West Lafayette, IN 47907-2057, USA
| | - M Katherine Banks
- Zachry Department of Civil Engineering, Texas A&M University, 3136 TAMU, College Station, TX 77843-3136, USA
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Blaustein RA, Shelton DR, Van Kessel JAS, Karns JS, Stocker MD, Pachepsky YA. Irrigation waters and pipe-based biofilms as sources for antibiotic-resistant bacteria. ENVIRONMENTAL MONITORING AND ASSESSMENT 2016; 188:56. [PMID: 26703979 DOI: 10.1007/s10661-015-5067-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/16/2015] [Indexed: 06/05/2023]
Abstract
The presence of antibiotic-resistant bacteria in environmental surface waters has gained recent attention. Wastewater and drinking water distribution systems are known to disseminate antibiotic-resistant bacteria, with the biofilms that form on the inner-surfaces of the pipeline as a hot spot for proliferation and gene exchange. Pipe-based irrigation systems that utilize surface waters may contribute to the dissemination of antibiotic-resistant bacteria in a similar manner. We conducted irrigation events at a perennial stream on a weekly basis for 1 month, and the concentrations of total heterotrophic bacteria, total coliforms, and fecal coliforms, as well as the concentrations of these bacterial groups that were resistant to ampicillin and tetracycline, were monitored at the intake water. Prior to each of the latter three events, residual pipe water was sampled and 6-in. sections of pipeline (coupons) were detached from the system, and biofilm from the inner-wall was removed and analyzed for total protein content and the above bacteria. Isolates of biofilm-associated bacteria were screened for resistance to a panel of seven antibiotics, representing five antibiotic classes. All of the monitored bacteria grew substantially in the residual water between irrigation events, and the biomass of the biofilm steadily increased from week to week. The percentages of biofilm-associated isolates that were resistant to antibiotics on the panel sometimes increased between events. Multiple-drug resistance was observed for all bacterial groups, most often for fecal coliforms, and the distributions of the numbers of antibiotics that the total coliforms and fecal coliforms were resistant to were subject to change from week to week. Results from this study highlight irrigation waters as a potential source for antibiotic-resistant bacteria, which can subsequently become incorporated into and proliferate within irrigation pipe-based biofilms.
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Affiliation(s)
- Ryan A Blaustein
- USDA-ARS Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Ave. Bldg. 173, Beltsville, MD, 20705, USA
- Department of Environmental Science and Technology, University of Maryland, College Park, MD, USA
- Soil and Water Science Department, University of Florida, Gainesville, FL, USA
| | - Daniel R Shelton
- USDA-ARS Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Ave. Bldg. 173, Beltsville, MD, 20705, USA
| | - Jo Ann S Van Kessel
- USDA-ARS Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Ave. Bldg. 173, Beltsville, MD, 20705, USA
| | - Jeffrey S Karns
- USDA-ARS Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Ave. Bldg. 173, Beltsville, MD, 20705, USA
| | - Matthew D Stocker
- USDA-ARS Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Ave. Bldg. 173, Beltsville, MD, 20705, USA
| | - Yakov A Pachepsky
- USDA-ARS Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Ave. Bldg. 173, Beltsville, MD, 20705, USA.
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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Jiang G, Sun J, Sharma KR, Yuan Z. Corrosion and odor management in sewer systems. Curr Opin Biotechnol 2015; 33:192-7. [DOI: 10.1016/j.copbio.2015.03.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 03/06/2015] [Accepted: 03/11/2015] [Indexed: 10/23/2022]
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Ling AL, Robertson CE, Harris JK, Frank DN, Kotter CV, Stevens MJ, Pace NR, Hernandez MT. High-resolution microbial community succession of microbially induced concrete corrosion in working sanitary manholes. PLoS One 2015; 10:e0116400. [PMID: 25748024 PMCID: PMC4352008 DOI: 10.1371/journal.pone.0116400] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 12/09/2014] [Indexed: 12/19/2022] Open
Abstract
Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low α-diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high α-diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers.
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Affiliation(s)
- Alison L. Ling
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, United States of America
| | - Charles E. Robertson
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, United States of America
| | - J. Kirk Harris
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, United States of America
| | - Daniel N. Frank
- Department of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, 80045, United States of America
| | - Cassandra V. Kotter
- Department of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, 80045, United States of America
| | - Mark J. Stevens
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, United States of America
| | - Norman R. Pace
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, United States of America
| | - Mark T. Hernandez
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, United States of America
- * E-mail:
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Gomez-Alvarez V, Humrighouse BW, Revetta RP, Santo Domingo JW. Bacterial composition in a metropolitan drinking water distribution system utilizing different source waters. JOURNAL OF WATER AND HEALTH 2015; 13:140-151. [PMID: 25719474 DOI: 10.2166/wh.2014.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We investigated the bacterial composition of water samples from two service areas within a drinking water distribution system (DWDS), each associated with a different primary source of water (groundwater, GW; surface water, SW) and different treatment process. Community analysis based on 16S rRNA gene clone libraries indicated that Actinobacteria (Mycobacterium spp.) and α-Proteobacteria represented nearly 43 and 38% of the total sequences, respectively. Sequences closely related to Legionella, Pseudomonas, and Vibrio spp. were also identified. In spite of the high number of sequences (71%) shared in both areas, multivariable analysis revealed significant differences between the GW and SW areas. While the dominant phylotypes where not significantly contributing in the ordination of samples, the populations associated with the core of phylotypes (1-10% in each sample) significantly contributed to the differences between both service areas. Diversity indices indicate that the microbial community inhabiting the SW area is more diverse and contains more distantly related species coexisting with local assemblages as compared with the GW area. The bacterial community structure of SW and GW service areas were dissimilar, suggesting that their respective source water and/or water quality parameters shaped by the treatment processes may contribute to the differences in community structure observed.
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Affiliation(s)
| | - Ben W Humrighouse
- Department of Civil and Environmental Engineering, University of Cincinnati, Cincinnati, Ohio, USA and US Centers for Disease Control and Prevention, 1600 Clifton Road, Mail Stop D11, Atlanta, GA 30333, USA
| | - Randy P Revetta
- United States Environmental Protection Agency, Cincinnati, Ohio, USA E-mail:
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Luo J, Zhang J, Tan X, McDougald D, Zhuang G, Fane AG, Kjelleberg S, Cohen Y, Rice SA. Characterization of the archaeal community fouling a membrane bioreactor. J Environ Sci (China) 2015; 29:115-123. [PMID: 25766019 DOI: 10.1016/j.jes.2014.07.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 07/14/2014] [Accepted: 07/19/2014] [Indexed: 06/04/2023]
Abstract
Biofilm formation, one of the primary causes of biofouling, results in reduced membrane flux or increased transmembrane pressure and thus represents a major impediment to the wider implementation of membrane bioreactor (MBR) technologies for water purification. Most studies have focused on the role of bacteria in membrane fouling as they are the most dominant and best studied organisms present in the MBR. In contrast, there is limited information on the role of the archaeal community in biofilm formation in MBRs. This study investigated the composition of the archaeal community during the process of biofouling in an MBR. The archaeal community was observed to have lower richness and diversity in the biofilm than the sludge during the establishment of biofilms at low transmembrane pressure (TMP). Clustering of the communities based on the Bray-Curtis similarity matrix indicated that a subset of the sludge archaeal community formed the initial biofilms. The archaeal community in the biofilm was mainly composed of Thermoprotei, Thermoplasmata, Thermococci, Methanopyri, Methanomicrobia and Halobacteria. Among them, the Thermoprotei and Thermoplasmata were present at higher relative proportions in the biofilms than they were in the sludge. Additionally, the Thermoprotei, Thermoplasmata and Thermococci were the dominant organisms detected in the initial biofilms at low TMP, while as the TMP increased, the Methanopyri, Methanomicrobia, Aciduliprofundum and Halobacteria were present at higher abundances in the biofilms at high TMP.
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Affiliation(s)
- Jinxue Luo
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore; Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 639798, Singapore.
| | - Jinsong Zhang
- Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 639798, Singapore
| | - Xiaohui Tan
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 639798, Singapore
| | - Diane McDougald
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore; Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 639798, Singapore
| | - Guoqiang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Anthony G Fane
- Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 639798, Singapore
| | - Staffan Kjelleberg
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore; Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 639798, Singapore
| | - Yehuda Cohen
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 639798, Singapore
| | - Scott A Rice
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore; Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 639798, Singapore.
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Characterisation of the physical composition and microbial community structure of biofilms within a model full-scale drinking water distribution system. PLoS One 2015; 10:e0115824. [PMID: 25706303 PMCID: PMC4338064 DOI: 10.1371/journal.pone.0115824] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/02/2014] [Indexed: 11/19/2022] Open
Abstract
Within drinking water distribution systems (DWDS), microorganisms form multi-species biofilms on internal pipe surfaces. A matrix of extracellular polymeric substances (EPS) is produced by the attached community and provides structure and stability for the biofilm. If the EPS adhesive strength deteriorates or is overcome by external shear forces, biofilm is mobilised into the water potentially leading to degradation of water quality. However, little is known about the EPS within DWDS biofilms or how this is influenced by community composition or environmental parameters, because of the complications in obtaining biofilm samples and the difficulties in analysing EPS. Additionally, although biofilms may contain various microbial groups, research commonly focuses solely upon bacteria. This research applies an EPS analysis method based upon fluorescent confocal laser scanning microscopy (CLSM) in combination with digital image analysis (DIA), to concurrently characterize cells and EPS (carbohydrates and proteins) within drinking water biofilms from a full-scale DWDS experimental pipe loop facility with representative hydraulic conditions. Application of the EPS analysis method, alongside DNA fingerprinting of bacterial, archaeal and fungal communities, was demonstrated for biofilms sampled from different positions around the pipeline, after 28 days growth within the DWDS experimental facility. The volume of EPS was 4.9 times greater than that of the cells within biofilms, with carbohydrates present as the dominant component. Additionally, the greatest proportion of EPS was located above that of the cells. Fungi and archaea were established as important components of the biofilm community, although bacteria were more diverse. Moreover, biofilms from different positions were similar with respect to community structure and the quantity, composition and three-dimensional distribution of cells and EPS, indicating that active colonisation of the pipe wall is an important driver in material accumulation within the DWDS.
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46
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Kip N, van Veen JA. The dual role of microbes in corrosion. ISME JOURNAL 2014; 9:542-51. [PMID: 25259571 DOI: 10.1038/ismej.2014.169] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/11/2014] [Indexed: 12/16/2022]
Abstract
Corrosion is the result of a series of chemical, physical and (micro) biological processes leading to the deterioration of materials such as steel and stone. It is a world-wide problem with great societal and economic consequences. Current corrosion control strategies based on chemically produced products are under increasing pressure of stringent environmental regulations. Furthermore, they are rather inefficient. Therefore, there is an urgent need for environmentally friendly and sustainable corrosion control strategies. The mechanisms of microbially influenced corrosion and microbially influenced corrosion inhibition are not completely understood, because they cannot be linked to a single biochemical reaction or specific microbial species or groups. Corrosion is influenced by the complex processes of different microorganisms performing different electrochemical reactions and secreting proteins and metabolites that can have secondary effects. Information on the identity and role of microbial communities that are related to corrosion and corrosion inhibition in different materials and in different environments is scarce. As some microorganisms are able to both cause and inhibit corrosion, we pay particular interest to their potential role as corrosion-controlling agents. We show interesting interfaces in which scientists from different disciplines such as microbiology, engineering and art conservation can collaborate to find solutions to the problems caused by corrosion.
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Affiliation(s)
- Nardy Kip
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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47
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Zhang H, Chen X, Braithwaite D, He Z. Phylogenetic and metagenomic analyses of substrate-dependent bacterial temporal dynamics in microbial fuel cells. PLoS One 2014; 9:e107460. [PMID: 25202990 PMCID: PMC4159341 DOI: 10.1371/journal.pone.0107460] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/12/2014] [Indexed: 12/25/2022] Open
Abstract
Understanding the microbial community structure and genetic potential of anode biofilms is key to improve extracellular electron transfers in microbial fuel cells. We investigated effect of substrate and temporal dynamics of anodic biofilm communities using phylogenetic and metagenomic approaches in parallel with electrochemical characterizations. The startup non-steady state anodic bacterial structures were compared for a simple substrate, acetate, and for a complex substrate, landfill leachate, using a single-chamber air-cathode microbial fuel cell. Principal coordinate analysis showed that distinct community structures were formed with each substrate type. The bacterial diversity measured as Shannon index decreased with time in acetate cycles, and was restored with the introduction of leachate. The change of diversity was accompanied by an opposite trend in the relative abundance of Geobacter-affiliated phylotypes, which were acclimated to over 40% of total Bacteria at the end of acetate-fed conditions then declined in the leachate cycles. The transition from acetate to leachate caused a decrease in output power density from 243±13 mW/m2 to 140±11 mW/m2, accompanied by a decrease in Coulombic electron recovery from 18±3% to 9±3%. The leachate cycles selected protein-degrading phylotypes within phylum Synergistetes. Metagenomic shotgun sequencing showed that leachate-fed communities had higher cell motility genes including bacterial chemotaxis and flagellar assembly, and increased gene abundance related to metal resistance, antibiotic resistance, and quorum sensing. These differentially represented genes suggested an altered anodic biofilm community in response to additional substrates and stress from the complex landfill leachate.
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Affiliation(s)
- Husen Zhang
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Florida, United States of America
- * E-mail:
| | - Xi Chen
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Florida, United States of America
| | - Daniel Braithwaite
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Chicago, Illinois, United States of America
| | - Zhen He
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
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48
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Ling AL, Robertson CE, Harris JK, Frank DN, Kotter CV, Stevens MJ, Pace NR, Hernandez MT. Carbon dioxide and hydrogen sulfide associations with regional bacterial diversity patterns in microbially induced concrete corrosion. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:7357-7364. [PMID: 24842376 DOI: 10.1021/es500763e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The microbial communities associated with deteriorating concrete corrosion fronts were characterized in 35 samples taken from wastewater collection and treatment systems in ten utilities. Bacterial communities were described using Illumina MiSeq sequencing of the V1V2 region of the small subunit ribosomal ribonucleic acid (SSU-rRNA) gene recovered from fresh corrosion products. Headspace gas concentrations (hydrogen sulfide, carbon dioxide, and methane), pore water pH, moisture content, and select mineralogy were tested for correlation to community outcomes and corrosion extent using pairwise linear regressions and canonical correspondence analysis. Corroding concrete was most commonly characterized by moisture contents greater than 10%, pore water pH below one, and limited richness (<10 taxa). Bacterial community composition was not correlated to geographic location when considered independently from other environmental factors. Corrosion was most severe in sites with high levels of hydrogen sulfide (>100 ppm) and carbon dioxide (>1%) gases, conditions which also were associated with low diversity biofilms dominated by members of the acidophilic sulfur-oxidizer genus Acidithiobacillus.
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Affiliation(s)
- Alison L Ling
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder , Boulder, Colorado 80309, United States
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49
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Yu P, Shaw CA. An efficient algorithm for accurate computation of the Dirichlet-multinomial log-likelihood function. Bioinformatics 2014; 30:1547-54. [PMID: 24519380 PMCID: PMC4081639 DOI: 10.1093/bioinformatics/btu079] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/10/2013] [Accepted: 01/31/2014] [Indexed: 11/13/2022] Open
Abstract
The Dirichlet-multinomial (DMN) distribution is a fundamental model for multicategory count data with overdispersion. This distribution has many uses in bioinformatics including applications to metagenomics data, transctriptomics and alternative splicing. The DMN distribution reduces to the multinomial distribution when the overdispersion parameter ψ is 0. Unfortunately, numerical computation of the DMN log-likelihood function by conventional methods results in instability in the neighborhood of [Formula: see text]. An alternative formulation circumvents this instability, but it leads to long runtimes that make it impractical for large count data common in bioinformatics. We have developed a new method for computation of the DMN log-likelihood to solve the instability problem without incurring long runtimes. The new approach is composed of a novel formula and an algorithm to extend its applicability. Our numerical experiments show that this new method both improves the accuracy of log-likelihood evaluation and the runtime by several orders of magnitude, especially in high-count data situations that are common in deep sequencing data. Using real metagenomic data, our method achieves manyfold runtime improvement. Our method increases the feasibility of using the DMN distribution to model many high-throughput problems in bioinformatics. We have included in our work an R package giving access to this method and a vingette applying this approach to metagenomic data.
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Affiliation(s)
- Peng Yu
- Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering (CBGSE), Texas A&M University, College Station, TX 77843, USA and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad A Shaw
- Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering (CBGSE), Texas A&M University, College Station, TX 77843, USA and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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50
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Biofilm-growing bacteria involved in the corrosion of concrete wastewater pipes: protocols for comparative metagenomic analyses. Methods Mol Biol 2014; 1147:323-40. [PMID: 24664844 DOI: 10.1007/978-1-4939-0467-9_23] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advances in high-throughput next-generation sequencing (NGS) technology for direct sequencing of environmental DNA (i.e., shotgun metagenomics) are transforming the field of microbiology. NGS technologies are now regularly being applied in comparative metagenomic studies, which provide the data for functional annotations, taxonomic comparisons, community profile, and metabolic reconstructions. For example, comparative metagenomic analysis of corroded pipes unveiled novel insights on the bacterial populations associated with the sulfur and nitrogen cycle, which may be directly or indirectly implicated in concrete wastewater pipe corrosion. The objective of this chapter is to describe the steps involved in the taxonomic and functional analysis of metagenome datasets from biofilm involved in microbial-induced concrete corrosion (MICC).
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