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Imran M, Sun Z, Abo-Elyousr KAM, Ali H, Aldayel MF, Li C. One stone two birds: Endophytes alleviating trace elements accumulation and suppressing soilborne pathogen by stimulating plant growth, photosynthetic potential and defense related gene expression. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135084. [PMID: 38991649 DOI: 10.1016/j.jhazmat.2024.135084] [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: 03/18/2024] [Revised: 06/24/2024] [Accepted: 06/30/2024] [Indexed: 07/13/2024]
Abstract
In the present investigation, we utilized zinc nanoparticles (Zn-NPs) and bacterial endophytes to address the dual challenge of heavy metal (HM) toxicity in soil and Rhizoctonia solani causing root rot disease of tomato. The biocontrol potential of Bacillus subtilis and Bacillus amyloliquefaciens was harnessed, resulting in profound inhibition of R. solani mycelial growth and efficient detoxification of HM through strong production of various hydrolytic enzymes and metabolites. Surprisingly, Zn-NPs exhibited notable efficacy in suppressing mycelial growth and enhancing the seed germination (%) while Gas chromatography-mass spectrometry (GC-MS) analysis unveiled key volatile compounds (VOCs) crucial for the inhibition of pathogen. Greenhouse trials underscored significant reduction in the disease severity (%) and augmented biomass in biocontrol-mediated plants by improving photosynthesis-related attributes. Interestingly, Zn-NPs and biocontrol treatments enhanced the antioxidant enzymes and mitigate oxidative stress indicator by increasing H2O2 concentration. Field experiments corroborated these findings, with biocontrol-treated plants, particularly those receiving consortia-mediated treatments, displayed significant reduction in disease severity (%) and enhanced the fruit yield under field conditions. Root analysis confirmed the effective detoxification of HM, highlighting the eco-friendly potential of these endophytes and Zn-NPs as fungicide alternative for sustainable production that foster soil structure, biodiversity and promote plant health.
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Affiliation(s)
- Muhammad Imran
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China.
| | - Zhongke Sun
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China.
| | - Kamal A M Abo-Elyousr
- Department of Plant Pathology, Faculty of Agriculture, University of Assiut, Assiut 71526, Egypt; Department of Agriculture, Faculty of Environmental Sciences, King Abdulaziz University, 80208 Jeddah, Saudi Arabia.
| | - Haider Ali
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom.
| | - Munirah F Aldayel
- Department of Biological Sciences, College of Science, King Faisal University, 31982 Al-Ahsa, Saudi Arabia.
| | - Chengwei Li
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China; College of Life Science, Henan Agriculture University, Zhengzhou, 450046, China.
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2
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Maksimović O, Bačnik K, Rivarez MPS, Vučurović A, Mehle N, Ravnikar M, Gutiérrez-Aguirre I, Kutnjak D. Virome analysis of irrigation water sources provides extensive insights into the diversity and distribution of plant viruses in agroecosystems. WATER RESEARCH 2024; 249:120712. [PMID: 38134622 DOI: 10.1016/j.watres.2023.120712] [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: 07/05/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 12/24/2023]
Abstract
Plant viruses pose a significant threat to agriculture. Several are stable outside their hosts, can enter water bodies and remain infective for prolonged periods of time. Even though the quality of irrigation water is of increasing importance in the context of plant health, the presence of plant viruses in irrigation waters is understudied. In this study, we conducted a large-scale high-throughput sequencing (HTS)-based virome analysis of irrigation and surface water sources to obtain complete information about the abundance and diversity of plant viruses in such waters. We detected nucleic acids of plant viruses from 20 families, discovered several novel plant viruses from economically important taxa, like Tobamovirus and observed the influence of the water source on the present virome. By comparing viromes of water and surrounding plants, we observed presence of plant viruses in both compartments, especially in cases of large-scale outbreaks, such as that of tomato mosaic virus. Moreover, we demonstrated that water virome data can extensively inform us about the distribution and diversity of plant viruses for which only limited information is available from plants. Overall, the results of the study provided extensive insights into the virome of irrigation waters from the perspective of plant health. It also suggested that an HTS-based water virome surveillance system could be used to detect potential plant disease outbreaks and to survey the distribution and diversity of plant viruses in the ecosystem.
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Affiliation(s)
- Olivera Maksimović
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia; Jožef Stefan International Postgraduate School, Slovenia
| | - Katarina Bačnik
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia
| | - Mark Paul Selda Rivarez
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia; Department of Entomology and Plant Pathology, North Carolina State University, USA; College of Agriculture and Agri-Industries, Caraga State University, Philippines
| | - Ana Vučurović
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia
| | - Nataša Mehle
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia; School for Viticulture and Enology, University of Nova Gorica, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia
| | | | - Denis Kutnjak
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia.
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3
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Zhang Y, Kitazumi A, Liao YT, de Los Reyes BG, Wu VCH. Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem. Microbiol Spectr 2023; 11:e0022623. [PMID: 37754684 PMCID: PMC10581182 DOI: 10.1128/spectrum.00226-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/10/2023] [Indexed: 09/28/2023] Open
Abstract
IMPORTANCE Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.
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Affiliation(s)
- Yujie Zhang
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center , Albany, California, USA
| | - Ai Kitazumi
- Department of Plant and Soil Science, Texas Tech University , Lubbock, Texas, USA
| | - Yen-Te Liao
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center , Albany, California, USA
| | | | - Vivian C H Wu
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center , Albany, California, USA
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4
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Ma D, Chen H, Feng Q, Zhang X, Wu D, Feng J, Cheng S, Wang D, Liu Z, Zhong Q, Wei J, Liu G. Dissemination of antibiotic resistance genes through fecal sewage treatment facilities to the ecosystem in rural area. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 333:117439. [PMID: 36758406 DOI: 10.1016/j.jenvman.2023.117439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Infection of antibiotic-resistant pathogens mostly occurs in rural areas. In this paper, the dissemination of antibiotic resistance genes (ARGs) through fecal sewage treatment facilities to the ecosystem in a typical rural area is investigated. Household three-chamber septic tanks (TCs), household biogas digesters (BDs), wastewater treatment plants (WWTPs), vegetable plots, water ponds, etc. Are taken into account. The relative abundance of ARGs in fecal sewage can be reduced by BDs and WWTPs by 80% and 60%, respectively. While TCs show no reduction ability for ARGs. Fast expectation-maximization microbial source tracking (FEAST) analysis revealed that TCs and BDs contribute a considerable percentage (15-22%) of ARGs to the surface water bodies (water ponds) in the rural area. Most ARGs tend to precipitate in the sediments of water bodies and stop moving downstream. Meanwhile, the immigration of microorganisms is more active than that of ARGs. The results provide scientific basic data for the management of fecal sewage and the controlling of ARGs in rural areas.
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Affiliation(s)
- Dachao Ma
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Hongcheng Chen
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Qingge Feng
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China.
| | - Xuan Zhang
- College of Civil Engineering and Architecture, Guangxi University, Nanning 530004, China
| | - Deli Wu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, People's Republic of China
| | - Jinghang Feng
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Shikun Cheng
- School of Energy and Environmental Engineering, Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing , 100083, China
| | - Dongbo Wang
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Zheng Liu
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Qisong Zhong
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Jinye Wei
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Guozi Liu
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
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5
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Anju VT, Busi S, Mohan MS, Salim SA, Ar S, Imchen M, Kumavath R, Dyavaiah M, Prasad R. Surveillance and mitigation of soil pollution through metagenomic approaches. Biotechnol Genet Eng Rev 2023:1-34. [PMID: 36881114 DOI: 10.1080/02648725.2023.2186330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.
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Affiliation(s)
- V T Anju
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Mahima S Mohan
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Simi Asma Salim
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Sabna Ar
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ranjith Kumavath
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ram Prasad
- Department of Botany, School of Life Sciences, Mahatma Gandhi Central University, Bihar, India
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6
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Malayil L, Ramachandran P, Chattopadhyay S, Allard SM, Bui A, Butron J, Callahan MT, Craddock HA, Murray R, East C, Sharma M, Kniel K, Micallef S, Hashem F, Gerba CP, Ravishankar S, Parveen S, May E, Handy E, Kulkarni P, Anderson-Coughlin B, Craighead S, Gartley S, Vanore A, Duncan R, Foust D, Haymaker J, Betancourt W, Zhu L, Mongodin EF, Sapkota A, Pop M, Sapkota AR. Variations in Bacterial Communities and Antibiotic Resistance Genes Across Diverse Recycled and Surface Water Irrigation Sources in the Mid-Atlantic and Southwest United States: A CONSERVE Two-Year Field Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15019-15033. [PMID: 36194536 PMCID: PMC9632240 DOI: 10.1021/acs.est.2c02281] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 05/30/2023]
Abstract
Reduced availability of agricultural water has spurred increased interest in using recycled irrigation water for U.S. food crop production. However, there are significant knowledge gaps concerning the microbiological quality of these water sources. To address these gaps, we used 16S rRNA gene and metagenomic sequencing to characterize taxonomic and functional variations (e.g., antimicrobial resistance) in bacterial communities across diverse recycled and surface water irrigation sources. We collected 1 L water samples (n = 410) between 2016 and 2018 from the Mid-Atlantic (12 sites) and Southwest (10 sites) U.S. Samples were filtered, and DNA was extracted. The V3-V4 regions of the 16S rRNA gene were then PCR amplified and sequenced. Metagenomic sequencing was also performed to characterize antibiotic, metal, and biocide resistance genes. Bacterial alpha and beta diversities were significantly different (p < 0.001) across water types and seasons. Pathogenic bacteria, such as Salmonella enterica, Staphylococcus aureus, and Aeromonas hydrophilia were observed across sample types. The most common antibiotic resistance genes identified coded against macrolides/lincosamides/streptogramins, aminoglycosides, rifampin and elfamycins, and their read counts fluctuated across seasons. We also observed multi-metal and multi-biocide resistance across all water types. To our knowledge, this is the most comprehensive longitudinal study to date of U.S. recycled water and surface water used for irrigation. Our findings improve understanding of the potential differences in the risk of exposure to bacterial pathogens and antibiotic resistance genes originating from diverse irrigation water sources across seasons and U.S. regions.
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Affiliation(s)
- Leena Malayil
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Padmini Ramachandran
- Office
of Regulatory Science, Division of Microbiology, United States Food and Drug Administration, HFS-712, 5001 Campus Drive, College Park, Maryland 20740, United States
| | - Suhana Chattopadhyay
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Sarah M. Allard
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Anthony Bui
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Jicell Butron
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Mary Theresa Callahan
- Department
of Plant Science and Landscape Agriculture, University of Maryland, College
Park, Maryland 20740, United States
| | - Hillary A. Craddock
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Rianna Murray
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Cheryl East
- Northeast
Area, Beltsville Agriculture Research Center, Environmental Microbiology
and Food Safety Laboratory, Agriculture
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, United States
| | - Manan Sharma
- Northeast
Area, Beltsville Agriculture Research Center, Environmental Microbiology
and Food Safety Laboratory, Agriculture
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, United States
| | - Kalmia Kniel
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Shirley Micallef
- Department
of Plant Science and Landscape Agriculture, University of Maryland, College
Park, Maryland 20740, United States
| | - Fawzy Hashem
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Charles P. Gerba
- Department
of Environmental Science, University of
Arizona, Tucson, Arizona 85719, United States
| | - Sadhana Ravishankar
- School
of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, United States
| | - Salina Parveen
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Eric May
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Eric Handy
- Northeast
Area, Beltsville Agriculture Research Center, Environmental Microbiology
and Food Safety Laboratory, Agriculture
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, United States
| | - Prachi Kulkarni
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Brienna Anderson-Coughlin
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Shani Craighead
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Samantha Gartley
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Adam Vanore
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Rico Duncan
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Derek Foust
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Joseph Haymaker
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Walter Betancourt
- Department
of Environmental Science, University of
Arizona, Tucson, Arizona 85719, United States
| | - Libin Zhu
- School
of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, United States
| | - Emmanuel F. Mongodin
- Institute
for Genome Sciences, University of Maryland
School of Medicine, Baltimore, Maryland 21201, United States
| | - Amir Sapkota
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Mihai Pop
- Department
of Computer Science and Center for Bioinformatics and Computational
Biology, University of Maryland, College Park, Maryland 20742, United States
| | - Amy R. Sapkota
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
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7
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Liu H, Li Z, Qiang Z, Karanfil T, Yang M, Liu C. The elimination of cell-associated and non-cell-associated antibiotic resistance genes during membrane filtration processes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155250. [PMID: 35427607 DOI: 10.1016/j.scitotenv.2022.155250] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/29/2022] [Accepted: 04/09/2022] [Indexed: 05/09/2023]
Abstract
With increasing water reuse as a sustainable water management strategy, antibiotic resistance genes (ARGs) which have been identified as emerging contaminants in wastewater are attracting global attentions. Given that wastewater treatment plants are now well-established as a sink and source of ARGs in both cell-associated and non-cell-associated forms, a need is acknowledged to reduce their proliferation and protect public health. Due to their different characteristics, cell-associated and non-cell-associated ARGs may have distinct responses to membrane filtration processes which are widely used as advanced treatment to the secondary effluent. This review improves the understanding of the abundance of cell-associated and non-cell-associated ARGs in wastewaters and the secondary effluents and compares the elimination of ARGs in cell-associated and non-cell-associated forms by low-pressure and high-pressure membrane filtration processes. The former process reduces the concentration of cell-associated ARGs by more than 2-logs on average. An increase of the retention efficiency of non-cell-associated ARGs is observed with decreasing molecular weight cut-offs in ultrafiltration. The high-pressure membrane filtration (i.e., nanofiltration and reverse osmosis) can effectively eliminate both cell-associated and non-cell-associated ARGs, with averagely more than 4.6-log reduction. In general, the two forms of ARGs can be removed from water by the membrane filtration processes via the effects of size exclusion, adsorption, and electrostatic repulsion. The size and conformation of cell-associated and non-cell-associated ARGs, characteristics of membranes, coexisting substances, and biofilm formation influence ARG retention. Accumulation and potential proliferation of cell-associated and non-cell-associated ARGs in foulants and concentrate and corresponding control strategies warrant future research.
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Affiliation(s)
- Hang Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ziqi Li
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhimin Qiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tanju Karanfil
- Department of Environmental Engineering and Earth Sciences, Clemson University, Anderson, SC 29625, USA
| | - Min Yang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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8
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Liang P, Jingan X, Liying S. The effects of reclaimed water irrigation on the soil characteristics and microbial populations of plant rhizosphere. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:17570-17579. [PMID: 34669129 DOI: 10.1007/s11356-021-16983-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
In this paper, the effects of irrigation with different water qualities on the soil characteristics of 8 kinds of garden plants were analyzed. The results showed that soil pH (ranging at 7.76-8.73) had no significant difference in different soils compared with the contrast treatment. Under the reclaimed water irrigation, the content of soil total salinity, chloride ions, and water soluble sodium in soil of most plants was averagely 160.3%, 83.3%, and 67.5% higher than that of tap water, respectively. The influences of reclaimed water irrigation on soil nutrients were changed with the types of plants. The content of soil organic matter and the available potassium showed no significant differences in most plants. Compared with the tap water irrigation, the content of alkaline nitrogen in 5 plants increased (averagely 25.8%) after 5-year irrigation with reclaimed water. In terms of soil microorganism, the increase of soil microbial population, including bacteria, fungus and actinomycetes, has been promoted by different levels of reclaimed water irrigation, which is closely related with soil nutrients.
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Affiliation(s)
- Pei Liang
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiao Jingan
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Sun Liying
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
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9
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Hou Q, Pucci F, Pan F, Xue F, Rooman M, Feng Q. Using metagenomic data to boost protein structure prediction and discovery. Comput Struct Biotechnol J 2022; 20:434-442. [PMID: 35070166 PMCID: PMC8760478 DOI: 10.1016/j.csbj.2021.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 11/19/2022] Open
Abstract
Over the past decade, metagenomic sequencing approaches have been providing an ever-increasing amount of protein sequence data at an astonishing rate. These constitute an invaluable source of information which has been exploited in various research fields such as the study of the role of the gut microbiota in human diseases and aging. However, only a small fraction of all metagenomic sequences collected have been functionally or structurally characterized, leaving much of them completely unexplored. Here, we review how this information has been used in protein structure prediction and protein discovery. We begin by presenting some widely used metagenomic databases and analyze in detail how metagenomic data has contributed to the impressive improvement in the accuracy of structure prediction methods in recent years. We then examine how metagenomic information can be exploited to annotate protein sequences. More specifically, we focus on the role of metagenomes in the discovery of enzymes and new CRISPR-Cas systems, and in the identification of antibiotic resistance genes. With this review, we provide an overview of how metagenomic data is currently revolutionizing our understanding of protein science.
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Affiliation(s)
- Qingzhen Hou
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong 250012, China
- National Institute of Health Data Science of China, Shandong University, Shandong 250002, China
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Fengming Pan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong 250012, China
- National Institute of Health Data Science of China, Shandong University, Shandong 250002, China
| | - Fuzhong Xue
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong 250012, China
- National Institute of Health Data Science of China, Shandong University, Shandong 250002, China
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Qiang Feng
- Shandong Provincial Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Department of Human Microbiome, School of Stomatology, Shandong University, Jinan, Shandong Province 250012, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong Province 266237, China
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10
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Garner E, Organiscak M, Dieter L, Shingleton C, Haddix M, Joshi S, Pruden A, Ashbolt NJ, Medema G, Hamilton KA. Towards risk assessment for antibiotic resistant pathogens in recycled water: a systematic review and summary of research needs. Environ Microbiol 2021; 23:7355-7372. [PMID: 34632683 DOI: 10.1111/1462-2920.15804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 11/26/2022]
Abstract
Risk assessment is critical for identifying target concentrations of antibiotic resistant pathogens necessary for mitigating potential harmful exposures associated with water reuse. However, there is currently limited available data characterizing the concentrations of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in recycled water to support robust efforts at risk assessment. The objective of this systematic review was to identify and synthesize the existing literature documenting the presence and abundance of ARB and ARGs in recycled water. In addition, this review identifies best practices and explores monitoring targets for studying ARB and ARGs in recycled water to guide future work and identifies key research needs aimed at better supporting quantitative microbial risk assessment focused on recycled water and antibiotic resistance. Future efforts to collect data about ARB and ARG prevalence in recycled water should report concentration data per unit volume. Sample metadata should also be provided, including a description of treatment approach, a description of planned water uses (e.g., potable, irrigation), methods for conveyance to the point of use, and available physicochemical water quality data. Additional research is needed aimed at identifying recommended ARB and ARG monitoring targets and for developing approaches to incorporate metagenomic data into risk assessment.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, Morgantown, WV, 26506, USA
| | - Marisa Organiscak
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, Morgantown, WV, 26506, USA
| | - Lucien Dieter
- School of Sustainable Engineering and the Built Environment, Arizona State University, 660 S College Ave, Tempe, AZ, 85281, USA.,The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85281, USA
| | - Carley Shingleton
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, Morgantown, WV, 26506, USA
| | - Madison Haddix
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, Morgantown, WV, 26506, USA
| | - Sayalee Joshi
- School of Sustainable Engineering and the Built Environment, Arizona State University, 660 S College Ave, Tempe, AZ, 85281, USA.,The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85281, USA
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Nicholas J Ashbolt
- Faculty of Science and Engineering, Southern Cross University, Lismore, Australia
| | - Gertjan Medema
- KWR Water Research Institute, 7 3433PE, Nieuwegein, The Netherlands.,Sanitary Engineering, Delft University of Technology, Stevinweg 1 2628 CN Delft, Nieuwegein, The Netherlands
| | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment, Arizona State University, 660 S College Ave, Tempe, AZ, 85281, USA.,The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85281, USA
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11
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Zero-Valent Iron Filtration Reduces Microbial Contaminants in Irrigation Water and Transfer to Raw Agricultural Commodities. Microorganisms 2021; 9:microorganisms9102009. [PMID: 34683330 PMCID: PMC8541138 DOI: 10.3390/microorganisms9102009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
Groundwater depletion is a critical agricultural irrigation issue, which can be mitigated by supplementation with water of higher microbiological risk, including surface and reclaimed waters, to support irrigation needs in the United States. Zero-valent iron (ZVI) filtration may be an affordable and effective treatment for reducing pathogen contamination during crop irrigation. This study was performed to determine the effects of ZVI filtration on the removal and persistence of Escherichia coli, and pepper mild mottle virus (PMMoV) in irrigation water. Water was inoculated with E. coli TVS 353, filtered through a ZVI filtration unit, and used to irrigate cucurbit and cruciferous crops. Water (n = 168), leaf (n = 40), and soil (n = 24) samples were collected, the E. coli were enumerated, and die-off intervals were calculated for bacteria in irrigation water. Variable reduction of PMMoV was observed, however E. coli levels were consistently and significantly (p < 0.05) reduced in the filtered (9.59 lnMPN/mL), compared to unfiltered (13.13 lnMPN/mL) water. The die-off intervals of the remaining bacteria were significantly shorter in the filtered (−1.50 lnMPN/day), as compared to the unfiltered (−0.48 lnMPN/day) water. E. coli transfer to crop leaves and soils was significantly reduced (p < 0.05), as expected. The reduction of E. coli in irrigation water and its transfer to crops, by ZVI filtration is indicative of its potential to reduce pathogens in produce pre-harvest environments.
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12
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Zhang Y, Cheng D, Zhang Y, Xie J, Xiong H, Wan Y, Zhang Y, Chen X, Shi X. Soil type shapes the antibiotic resistome profiles of long-term manured soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147361. [PMID: 33971610 DOI: 10.1016/j.scitotenv.2021.147361] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Animal manure fertilization facilitates the proliferation and dissemination of antibiotic resistance genes (ARGs) in soil, posing high risks to humans and ecosystem health. Although studies suggest that soil types could shape the ARG profiles in greenhouse soil, there is still a lack of comparative studies on the fate of ARGs in different types of manured soils under field trials. Thus, a metagenomic approach was used to decipher the fate of ARGs in 12-year long-term fertilized (inorganic fertilizer, compost manure and a mix of them) acidic, near-neutral and alkaline soils. A total of 408 unique ARG subtypes with multidrug, glycopeptide, beta-lactam and aminoglycoside resistance genes were identified as the most universal ARG types in all soil samples. Genes conferred to beta-lactam was the predominant ARG type in all the manure-amended soils. Genomic and statistical analyses showed that manure application caused the enrichment of 98 and 91 ARG subtypes in acidic and near-neutral soils, respectively, and 8 ARG subtypes in alkaline soil. The abundances of Proteobacteria (acidic and near-neutral soils) and Actinobacteria (alkaline soil), which are the potential hosts of ARGs, were clearly increased in manured soils. Random forest modelling and Pearson correlation analysis revealed that the soil properties (pH and bio-available Zn) and mobile genetic elements had considerable impacts on the transmission of ARGs. A structural equation model further indicated that soil types shaped the ARG profiles by significantly (P < 0.01) influencing the soil properties, bacterial abundance and bacterial diversity, where bacterial abundance was the major factor influencing the ARG profiles. This study systematically explored the mechanisms shaping the ARG profiles of long-term manured soils, and this information could support strategies to manage the dissemination of ARGs in different soil types.
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Affiliation(s)
- Yu Zhang
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Dengmiao Cheng
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan 523808, China
| | - Yuting Zhang
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Jun Xie
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Huaye Xiong
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Yu Wan
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| | - Yueqiang Zhang
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Xinping Chen
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing 400716, China.
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13
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Zhao J, Li B, Lv P, Hou J, Qiu Y, Huang X. Distribution of antibiotic resistance genes and their association with bacteria and viruses in decentralized sewage treatment facilities. FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING 2021; 16:35. [PMID: 34249401 PMCID: PMC8255336 DOI: 10.1007/s11783-021-1469-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 05/24/2023]
Abstract
The distribution of antibiotic resistance genes (ARGs) has been intensively studied in large-scale wastewater treatment plants and livestock sources. However, small-scale decentralized sewage treatment facilities must also be explored due to their possible direct exposure to residents. In this study, six wastewater treatment facilities in developed rural areas in eastern China were investigated to understand their risks of spreading ARGs. Using metagenomics and network analysis tools, ARGs and bacterial and viral communities were identified in the influent (INF) and effluent (EFF) samples. The dominant ARGs belonged to the bacitracin class, which are different from most of municipal wastewater treatment plants (WWTPs). The dominant hosts of ARGs are Acidovorax in bacterial communities and Prymnesiovirus in viral communities. Furthermore, a positive relationship was found between ARGs and phages. The ARGs significantly correlated with phages were all hosted by specific genera of bacteria, indicating that phages had contributed to the ARG's proliferation in sewage treatment facilities. Paying significant concern on the possible enhanced risks caused by bacteria, viruses and their related ARGs in decentralized sewage treatment facilities is necessary. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material is available in the online version of this article at 10.1007/s11783-021-1469-4 and is accessible for authorized users.
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Affiliation(s)
- Jiaheng Zhao
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083 China
| | - Bing Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083 China
| | - Pin Lv
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083 China
| | - Jiahui Hou
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083 China
| | - Yong Qiu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084 China
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084 China
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14
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Zhu NJ, Ghosh S, Edwards MA, Pruden A. Interplay of Biologically Active Carbon Filtration and Chlorine-Based Disinfection in Mitigating the Dissemination of Antibiotic Resistance Genes in Water Reuse Distribution Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8329-8340. [PMID: 34080846 DOI: 10.1021/acs.est.1c01199] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Appropriate management approaches are needed to minimize the proliferation of antibiotic resistance genes (ARGs) in reclaimed water distribution systems (RWDSs). Six laboratory-scale RWDSs were operated over 3 years receiving influent with or without biologically active carbon (BAC) filtration + chlorination, chloramination, or no disinfectant residual. Shotgun metagenomic sequencing was applied toward comprehensive characterization of resistomes, focusing on total ARGs, ARG mobility, and specific ARGs of clinical concern. ARGs such as aadA, bacA, blaOXA, mphE, msrE, sul1, and sul2 were found to be particularly sensitive to varying RWDS conditions. BAC filtration with chlorination most effectively achieved and maintained the lowest levels of nearly all metagenomically derived antibiotic resistance indicators. However, BAC filtration or addition of residual disinfectants alone tended to increase these indicators. Biofilm and sediment compartments harbored ARGs in disinfected systems, presenting a concern for their release to bulk water. Relative and absolute abundances of most ARGs tended to decrease with water age (up to 5 days), with notable exceptions in BAC-filtered chloraminated and no residual systems. Superchlorination of unfiltered water especially raised concerns in terms of elevation of clinically relevant and mobile ARGs. This study revealed that BAC filtration and disinfection must be carefully coordinated in order to effectively mitigate ARG dissemination via RWDSs.
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Affiliation(s)
- Ni Joyce Zhu
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Sudeshna Ghosh
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Marc A Edwards
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
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15
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Summerlin HN, Pola CC, McLamore ES, Gentry T, Karthikeyan R, Gomes CL. Prevalence of Escherichia coli and Antibiotic-Resistant Bacteria During Fresh Produce Production (Romaine Lettuce) Using Municipal Wastewater Effluents. Front Microbiol 2021; 12:660047. [PMID: 34093474 PMCID: PMC8172605 DOI: 10.3389/fmicb.2021.660047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
High demand for food and water encourages the exploration of new water reuse programs, including treated municipal wastewater usage. However, these sources could contain high contaminant levels posing risks to public health. The objective of this study was to grow and irrigate a leafy green (romaine lettuce) with treated wastewater from a municipal wastewater treatment plant to track Escherichia coli and antibiotic-resistant microorganisms through cultivation and post-harvest storage to assess their fate and prevalence. Contamination levels found in the foliage, leachate, and soil were directly (p < 0.05) related to E. coli concentrations in the irrigation water. Wastewater concentrations from 177 to 423 CFU ml-1 resulted in 15-25% retention in the foliage. Leachate and soil presented means of 231 and 116% retention, respectively. E. coli accumulation on the foliage was observed (p < 0.05) and increased by over 400% during 14-day storage (4°C). From randomly selected E. coli colonies, in all four biomass types, 81 and 34% showed resistance to ampicillin and cephalothin, respectively. Reclaimed wastewater usage for leafy greens cultivation could pose potential health risks, especially considering the bacteria found have a high probability of being antibiotic resistance. Successful reuse of wastewater in agriculture will depend on appropriate mitigation and management strategies to guarantee an inexpensive, efficient, and safe water supply.
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Affiliation(s)
- Harvey N Summerlin
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX, United States
| | - Cícero C Pola
- Department of Mechanical Engineering, Iowa State University, Ames, IA, United States
| | - Eric S McLamore
- Department of Agricultural Sciences, Clemson University, Clemson, SC, United States
| | - Terry Gentry
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | | | - Carmen L Gomes
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX, United States.,Department of Mechanical Engineering, Iowa State University, Ames, IA, United States
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16
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Yu Z, Schwarz C, Zhu L, Chen L, Shen Y, Yu P. Hitchhiking Behavior in Bacteriophages Facilitates Phage Infection and Enhances Carrier Bacteria Colonization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2462-2472. [PMID: 33381966 DOI: 10.1021/acs.est.0c06969] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Interactions between bacteriophages (phages) and biofilms remain poorly understood despite the broad implications for microbial ecology, water quality, and microbiome engineering. Here, we demonstrate that lytic coliphage PHH01 can hitchhike on carrier bacteria Bacillus cereus to facilitate its infection of host bacteria, Escherichia coli, in biofilms. Specifically, PHH01 could adsorb onto the flagella of B. cereus, and thus phage motility was increased, resulting in 4.36-fold more effective infection of E. coli in biofilm relative to free PHH01 alone. Moreover, phage infection mitigated interspecies competition and enhanced B. cereus colonization; the fraction of B. cereus in the final biofilm increased from 9% without phages to 43% with phages. The mutualistic relationship between the coliphage and carrier bacteria was substantiated by migration tests on an E. coli lawn: the conjugation of PHH01 and B. cereus enhanced B. cereus colonization by 6.54-fold compared to B. cereus alone (6.15 vs 0.94 cm2 in 24 h) and PHH01 migration by 5.15-fold compared to PHH01 alone (10.3 vs 2.0 mm in 24 h). Metagenomic and electron microscopic analysis revealed that the phages of diverse taxonomies and different morphologies could be adsorbed by the flagella of B. cereus, suggesting hitchhiking on flagellated bacteria might be a widespread strategy in aquatic phage populations. Overall, our study highlights that hitchhiking behavior in phages can facilitate phage infection of biofilm bacteria, promote carrier bacteria colonization, and thus significantly influence biofilm composition, which holds promise for mediating biofilm functions and moderating associated risks.
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Affiliation(s)
- Zhuodong Yu
- School of Environment and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Liang Zhu
- School of Environment and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Linlin Chen
- School of Environment and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yun Shen
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
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17
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Malayil L, Ramachandran P, Chattopadhyay S, Cagle R, Hittle L, Ottesen A, Mongodin EF, Sapkota AR. Metabolically-active bacteria in reclaimed water and ponds revealed using bromodeoxyuridine DNA labeling coupled with 16S rRNA and shotgun sequencing. WATER RESEARCH 2020; 184:116185. [PMID: 32726735 DOI: 10.1016/j.watres.2020.116185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Understanding the complex microbiota of agricultural irrigation water is vital to multiple sectors of sustainable agriculture and public health. To date, microbiome characterization methods have provided comprehensive profiles of aquatic microbiotas, but have not described which taxa are likely metabolically-active. Here, we combined 5‑bromo‑2'-deoxyuridine (BrdU) labeling with 16S rRNA and shotgun sequencing to identify metabolically-active bacteria in reclaimed and agricultural pond water samples (n = 28) recovered from the Mid-Atlantic United States between March 2017 and January 2018. BrdU-treated samples were significantly less diverse (alpha diversity) compared to non-BrdU-treated samples. The most abundant taxa in the metabolically-active fraction of water samples (BrdU-treated samples) were unclassified Actinobacteria, Flavobacterium spp., Pseudomonas spp. and Aeromonas spp. Interestingly, we also observed that antimicrobial resistance and virulence gene profiles seemed to be more diverse and more abundant in non-BrdU-treated water samples compared to BrdU-treated samples. These findings raise the possibility that these genes may be associated more with relic (inactive) DNA present in the tested water types rather than viable, metabolically-active microorganisms. Our study demonstrates that the coupled use of BrdU labeling and sequencing can enhance understanding of the metabolically-active fraction of bacterial communities in alternative irrigation water sources. Agricultural pond and reclaimed waters are vital to the future of sustainable agriculture, and thus, the full understanding of the pathogenic potential of these waters is important to guide mitigation strategies that ensure appropriate water quality for intended purposes.
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Affiliation(s)
- Leena Malayil
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States
| | - Padmini Ramachandran
- Food and Drug Administration, Office of Regulatory Science, Division of Microbiology, HFS-712, 5001 Campus Drive, College Park, MD20740, United States
| | - Suhana Chattopadhyay
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States
| | - Robin Cagle
- Food and Drug Administration, Office of Regulatory Science, Division of Microbiology, HFS-712, 5001 Campus Drive, College Park, MD20740, United States
| | - Lauren Hittle
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201United States
| | - Andrea Ottesen
- Food and Drug Administration, Office of Regulatory Science, Division of Microbiology, HFS-712, 5001 Campus Drive, College Park, MD20740, United States
| | - Emmanuel F Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201United States
| | - Amy R Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States.
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18
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Abstract
Many biological contaminants are disseminated through water, and their occurrence has potential detrimental impacts on public and environmental health. Conventional monitoring tools rely on cultivation and are not robust in addressing modern water quality concerns. This review proposes metagenomics as a means to provide a rapid, nontargeted assessment of biological contaminants in water. When further coupled with appropriate methods (e.g., quantitative PCR and flow cytometry) and bioinformatic tools, metagenomics can provide information concerning both the abundance and diversity of biological contaminants in reclaimed waters. Further correlation between the metagenomic-derived data of selected contaminants and the measurable parameters of water quality can also aid in devising strategies to alleviate undesirable water quality. Here, we review metagenomic approaches (i.e., both sequencing platforms and bioinformatic tools) and studies that demonstrated their use for reclaimed-water quality monitoring. We also provide recommendations on areas of improvement that will allow metagenomics to significantly impact how the water industry performs reclaimed-water quality monitoring in the future.
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Affiliation(s)
- Pei-Ying Hong
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - David Mantilla-Calderon
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Changzhi Wang
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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