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Zarrabian M, Sherif SM. Silence is not always golden: A closer look at potential environmental and ecotoxicological impacts of large-scale dsRNA application. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175311. [PMID: 39122031 DOI: 10.1016/j.scitotenv.2024.175311] [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: 06/05/2024] [Revised: 08/02/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
RNA interference (RNAi) technology has emerged as a pivotal strategy in sustainable pest management, offering a targeted approach that significantly mitigates the environmental and health risks associated with traditional insecticides. Originally implemented through genetically modified organisms (GMOs) to produce specific RNAi constructs, the technology has evolved in response to public and regulatory concerns over GMOs. This evolution has spurred the development of non-transgenic RNAi applications such as spray-induced gene silencing (SIGS), which employs double-stranded RNA (dsRNA) to silence pest genes directly without altering the plant's genetic makeup. Despite its advantages in specificity and reduced ecological footprint, SIGS faces significant obstacles, particularly the instability of dsRNA in field conditions, which limits its practical efficacy. To overcome these limitations, innovative delivery mechanisms have been developed. These include nanotechnology-based systems, minicells, and nanovesicles, which are designed to protect dsRNA from degradation and enhance its delivery to target organisms. While these advancements have improved the stability and application efficiency of dsRNA, comprehensive assessments of their environmental safety and the potential for increased exposure risks to non-target organisms remain incomplete. This comprehensive review aims to elucidate the environmental fate of dsRNA and evaluate the potential risks associated with its widespread application on non-target organisms, encompassing soil microorganisms, beneficial insects, host plants, and mammals. The objective is to establish a more refined framework for RNAi risk assessment within environmental and ecotoxicological contexts, thereby fostering the development of safer, non-transgenic RNAi-based pest control strategies.
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Affiliation(s)
- Mohammad Zarrabian
- Virginia Tech, School of Plant and Environmental Sciences, Alson H. Smith Jr. Agricultural Research, and Extension Center, Winchester, VA 22602, United States
| | - Sherif M Sherif
- Virginia Tech, School of Plant and Environmental Sciences, Alson H. Smith Jr. Agricultural Research, and Extension Center, Winchester, VA 22602, United States.
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2
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Deng J, Zhang W, Zhang L, Qin C, Wang H, Ling W. Micro-interfacial behavior of antibiotic-resistant bacteria and antibiotic resistance genes in the soil environment: A review. ENVIRONMENT INTERNATIONAL 2024; 191:108972. [PMID: 39180776 DOI: 10.1016/j.envint.2024.108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/11/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024]
Abstract
Overutilization and misuse of antibiotics in recent decades markedly intensified the rapid proliferation and diffusion of antibiotic resistance genes (ARGs) within the environment, thereby elevating ARGs to the status of a global public health crisis. Recognizing that soil acts as a critical reservoir for ARGs, environmental researchers have made great progress in exploring the sources, distribution, and spread of ARGs in soil. However, the microscopic state and micro-interfacial behavior of ARGs in soil remains inadequately understood. In this study, we reviewed the micro-interfacial behaviors of antibiotic-resistant bacteria (ARB) in soil and porous media, predominantly including migration-deposition, adsorption, and biofilm formation. Meanwhile, adsorption, proliferation, and degradation were identified as the primary micro-interfacial behaviors of ARGs in the soil, with component of soil serving as significant determinant. Our work contributes to the further comprehension of the microstates and processes of ARB and ARGs in the soil environments and offers a theoretical foundation for managing and mitigating the risks associated with ARG contamination.
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Affiliation(s)
- Jibao Deng
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenkang Zhang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lingyu Zhang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hefei Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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3
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Aldeias V, Stahlschmidt MC. Sediment DNA can revolutionize archaeology-if it is used the right way. Proc Natl Acad Sci U S A 2024; 121:e2317042121. [PMID: 38900796 PMCID: PMC11214044 DOI: 10.1073/pnas.2317042121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Affiliation(s)
- Vera Aldeias
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, Universidade do Algarve, Faro8005-139, Portugal
| | - Mareike C. Stahlschmidt
- Department of Evolutionary Anthropology, University of Vienna, Vienna1010, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna1010, Austria
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4
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You Z, Wang C, Yang X, Liu Z, Guan Y, Mu J, Shi H, Zhao Z. Effects of eutrophication on the horizontal transfer of antibiotic resistance genes in microalgal-bacterial symbiotic systems. ENVIRONMENTAL RESEARCH 2024; 251:118692. [PMID: 38493856 DOI: 10.1016/j.envres.2024.118692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
Overloading of nutrients such as nitrogen causes eutrophication of freshwater bodies. The spread of antibiotic resistance genes (ARGs) poses a threat to ecosystems. However, studies on the enrichment and spread of ARGs from increased nitrogen loading in algal-bacterial symbiotic systems are limited. In this study, the transfer of extracellular kanamycin resistance (KR) genes from large (RP4) small (pEASY-T1) plasmids into the intracellular and extracellular DNA (iDNA, eDNA) of the inter-algal environment of Chlorella pyrenoidosa was investigated, along with the community structure of free-living (FL) and particle-attached (PA) bacteria under different nitrogen source concentrations (0-2.5 g/L KNO3). The results showed that KR gene abundance in the eDNA adsorbed on solid particles (D-eDNA) increased initially and then decreased with increasing nitrogen concentration, while the opposite was true for the rest of the free eDNA (E-eDNA). Medium nitrogen concentrations promoted the transfer of extracellular KR genes into the iDNA attached to algal microorganisms (A-iDNA), eDNA attached to algae (B-eDNA), and the iDNA of free microorganisms (C-iDNA); high nitrogen contributed to the transfer of KR genes into C-iDNA. The highest percentage of KR genes was found in B-eDNA with RP4 plasmid treatment (66.2%) and in C-iDNA with pEASY-T1 plasmid treatment (86.88%). In addition, dissolved oxygen (DO) significantly affected the bacterial PA and FL community compositions. Nephelometric turbidity units (NTU) reflected the abundance of ARGs in algae. Proteobacteria, Cyanobacteria, Bacteroidota, and Actinobacteriota were the main potential hosts of ARGs. These findings provide new insights into the distribution and dispersal of ARGs in the phytoplankton inter-algal environment.
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Affiliation(s)
- Ziqi You
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China.
| | - Ce Wang
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Xiaobin Yang
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Zikuo Liu
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Yueqiang Guan
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Jiandong Mu
- Hebei Ocean and Fisheries Science Research Institute, Qinhuangdao, 066200, China
| | - Huijuan Shi
- Museum of Hebei University, Hebei University, Baoding, Hebei, China.
| | - Zhao Zhao
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China.
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5
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Müller ND, Kirtane A, Schefer RB, Mitrano DM. eDNA Adsorption onto Microplastics: Impacts of Water Chemistry and Polymer Physiochemical Properties. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7588-7599. [PMID: 38624040 DOI: 10.1021/acs.est.3c10825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Adsorption of biomacromolecules onto polymer surfaces, including microplastics (MPs), occurs in multiple environmental compartments, forming an ecocorona. Environmental DNA (eDNA), genetic material shed from organisms, can adsorb onto MPs which can potentially either (1) promote long-range transport of antibiotic resistant genes or (2) serve to gain insights into the transport pathways and origins of MPs by analyzing DNA sequences on MPs. However, little is known about the capacity of MPs to adsorb eDNA or the factors that influence sorption, such as polymer and water chemistries. Here we investigated the adsorption of extracellular linear DNA onto a variety of model MP fragments composed of three of the most environmentally prevalent polymers (polyethylene, polyethylene terephthalate, and polystyrene) in their pristine and photochemically weathered states. Batch adsorption experiments in a variety of water chemistries were complemented with nonlinear modeling to quantify the rate and extent of eDNA sorption. Ionic strength was shown to strongly impact DNA adsorption by reducing or inhibiting electrostatic repulsion. Polyethylene terephthalate exhibited the highest adsorption capacity when normalizing for MP specific surface area, likely due to the presence of ester groups. Kinetics experiments showed fast adsorption (majority adsorbed under 30 min) before eventually reaching equilibrium after 1-2 h. Overall, we demonstrated that DNA quickly binds to MPs, with pseudo-first- and -second-order models describing adsorption kinetics and the Freundlich model describing adsorption isotherms most accurately. These insights into DNA sorption onto MPs show that there is potential for MPs to act as vectors for genetic material of interest, especially considering that particle-bound DNA typically persists longer in the environment than dissolved DNA.
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Affiliation(s)
- Nicolas D Müller
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Anish Kirtane
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Roman B Schefer
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Denise M Mitrano
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
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Kleemann K, Bolduan P, Battagliarin G, Christl I, McNeill K, Sander M. Molecular Structure and Conformation of Biodegradable Water-Soluble Polymers Control Adsorption and Transport in Model Soil Mineral Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1274-1286. [PMID: 38164921 PMCID: PMC10795197 DOI: 10.1021/acs.est.3c05770] [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: 07/20/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 01/03/2024]
Abstract
Water-soluble polymers (WSPs) are used in diverse applications, including agricultural formulations, that can result in the release of WSPs to soils. WSP biodegradability in soils is desirable to prevent long-term accumulation and potential associated adverse effects. In this work, we assessed adsorption of five candidate biodegradable WSPs with varying chemistry, charge, and polarity characteristics (i.e., dextran, diethylaminoethyl dextran, carboxymethyl dextran, polyethylene glycol monomethyl ether, and poly-l-lysine) and of one nonbiodegradable WSP (poly(acrylic acid)) to sand and iron oxide-coated sand particles that represent important soil minerals. Combined adsorption studies using solution-depletion measurements, direct surface adsorption techniques, and column transport experiments over varying solution pH and ionic strengths revealed electrostatics dominating interactions of charged WSPs with the sorbents as well as WSP conformations and packing densities in the adsorbed states. Hydrogen bonding controls adsorption of noncharged WSPs. Under transport in columns, WSP adsorption exhibited fast and slow kinetic adsorption regimes with time scales of minutes to hours. Slow adsorption kinetics in soil may lead to enhanced transport but also shorter lifetimes of biodegradable WSPs, assuming more rapid biodegradation when dissolved than adsorbed. This work establishes a basis for understanding the coupled adsorption and biodegradation dynamics of biodegradable WSPs in agricultural soils.
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Affiliation(s)
- Kevin Kleemann
- Institute
of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Patrick Bolduan
- BASF
SE, Materials and Formulation Research, Carl-Bosch-Strasse 38, 67056 Ludwigshafen, Germany
| | - Glauco Battagliarin
- BASF
SE, Materials and Formulation Research, Carl-Bosch-Strasse 38, 67056 Ludwigshafen, Germany
| | - Iso Christl
- Institute
of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Kristopher McNeill
- Institute
of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Michael Sander
- Institute
of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
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7
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Wang X, Pu L, Sun Z, Fang G, Wang Y, Gu C, Gao J. Comparative study of the photooxidation of arsenite mediated by dissolved and mineral-associated humic acid under light irradiation. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132759. [PMID: 37832435 DOI: 10.1016/j.jhazmat.2023.132759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/18/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023]
Abstract
The photochemical processes of dissolved humic acid and its potential contribution to As(III) oxidation in natural water has received considerable attention. However, the role of mineral-humic complexes in As(III) conversion is rarely studied. Herein, two simulated mineral-humic complexes were prepared by coating humic acid on hydrous aluminum oxide, HA@HAO, or montmorillonite, HA@SWy, respectively, and batch experiments at circumneutral pH were performed under light irradiation. Our findings showed that the light-assisted oxidation of As(III) increased with increasing fractions of organic carbon in mineral-humic complexes, and As(III) photooxidation with HA@HAO or HA@SWy was up to 18.2 or 3.5-fold higher compared to that measured in the presence of equivalent amount of free HA, respectively. The reactive triplet state of HA and hydroxyl radicals in HA@HAO and HA@SWy system made a primary contribution to As(III) oxidation under irradiation. The results indicated that mineral-humic complexes have dual roles, an adsorbent and a photosensitizer, to promote As(III) access to reactive intermediates at the particle surfaces. This process was important for As(III) conversion in paddy water as colloidal particles, composed of both minerals and HA, could greatly promote As(III) oxidation and As(V) immobilization. This study provides a previously overlooked, important mechanism of As(III) phototransformation mediated by mineral-associated humic acid in natural environment.
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Affiliation(s)
- Xinghao Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Lirong Pu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhaoyue Sun
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Guodong Fang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yujun Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Cheng Gu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Juan Gao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Nanjing 211135, China.
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8
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Liu G, Guo L, Wang C, Liu J, Hu Z, Dahlke HE, Xie E, Zhao X, Huang G, Niu J, Fa K, Zhang C, Huo Z. Revealing the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167378. [PMID: 37758151 DOI: 10.1016/j.scitotenv.2023.167378] [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: 07/11/2023] [Revised: 08/31/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
It has been recently demonstrated that free DNA tracers have the potential in tracing water flow and contaminant transport through the vadose zone. However, whether the free DNA tracer can be used in flood irrigation area to track water flow and solute/contaminant transport is still unclear. To reveal the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation, we tested the fate and transport behavior of surface applied free DNA tracers through packed saturated sandy soil columns with a 10 cm water head mimicking flood irrigation. From the experimental breakthrough curves and by fitting a two-site kinetic sorption model (R2 = 0.83-0.91 and NSE = 0.79-0.89), adsorption/desorption rates could be obtained and tracer retention profiles could be simulated. Together these results revealed that 1) the adsorption of free DNA was dominantly to clay particles in the soil, which took up 1.96 % by volume, but took up >97.5 % by surface area and densely cover the surface of sand particles; and 2) at a pore water pH of 8.0, excluding the 4.9 % passing through and 3.1 % degradation amount, the main retention mechanisms in the experimental soil were ligand exchange (42.0 %), Van der Waals interactions (mainly hydrogen bonds), electrostatic forces and straining (together 44.7 %), and cation bridge (5.3 %). To our knowledge, this study is the first to quantify the contribution of each of the main retention mechanisms of free synthetic DNA tracers passing through soil. Our findings could facilitate the application of free DNA tracer to trace vadose zone water flow and solute/contaminant transport under flood irrigation and other infiltration conditions.
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Affiliation(s)
- Geng Liu
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Linxi Guo
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Chaozi Wang
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China.
| | - Jiarong Liu
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Zengjie Hu
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Helen E Dahlke
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, CA 95616, USA
| | - En Xie
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Xiao Zhao
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Guanhua Huang
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Jun Niu
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Keyu Fa
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Chenglong Zhang
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Zailin Huo
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
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Sodnikar K, Kaegi R, Christl I, Schroth MH, Sander M. Transport of double-stranded ribonucleic acids (dsRNA) and deoxyribonucleic acids (DNA) in sand and iron oxide-coated sand columns under varying solution chemistries. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2023; 25:2067-2080. [PMID: 37870439 DOI: 10.1039/d3em00294b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Assessing ecological risks associated with the use of genetically modified RNA interference crops demands an understanding of the fate of crop-released insecticidal double-stranded RNA (dsRNA) molecules in soils. We studied the adsorption of one dsRNA and two double-stranded DNA as model nucleic acids (NAs) during transport through sand- and iron oxide-coated sand (IOCS)-filled columns over a range of solution pH and ionic compositions. Consistent with NA-sand electrostatic repulsion, we observed only slight retention of NAs in sand columns. Conversely, pronounced NA retention in IOCS columns is consistent with strong and irreversible NA adsorption involving electrostatic attraction to and inner-sphere complex formation of NAs with iron oxide coatings. Adsorption of NAs to iron oxides revealed a fast and a slow kinetic adsorption regime, possibly caused by the excluded-area effect. Adsorption of NAs to sand and IOCS increased in the presence of dissolved Mg2+ and with increasing ionic strength, reflecting cation-bridging and screening of repulsive electrostatics, respectively. The co-solute phosphate and a pre-adsorbed dissolved organic matter isolate competitively suppressed dsRNA adsorption to IOCS. Similar adsorption characteristics of dsRNA and similarly sized DNA suggest that existing information on DNA adsorption to soil particles helps in predicting adsorption and fate of dsRNA molecules in soils.
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Affiliation(s)
- Katharina Sodnikar
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland.
| | - Ralf Kaegi
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Iso Christl
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland.
| | - Martin Herbert Schroth
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland.
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland.
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10
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Qin C, Zhang RH, Li Z, Zhao HM, Li YW, Feng NX, Li H, Cai QY, Hu X, Gao Y, Xiang L, Mo CH, Xing B. Insights into the enzymatic degradation of DNA expedited by typical perfluoroalkyl acids. ECO-ENVIRONMENT & HEALTH (ONLINE) 2023; 2:278-286. [PMID: 38435362 PMCID: PMC10902504 DOI: 10.1016/j.eehl.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/27/2023] [Accepted: 09/05/2023] [Indexed: 03/05/2024]
Abstract
Perfluoroalkyl acids (PFAAs) are considered forever chemicals, gaining increasing attention for their hazardous impacts. However, the ecological effects of PFAAs remain unclear. Environmental DNA (eDNA), as the environmental gene pool, is often collected for evaluating the ecotoxicological effects of pollutants. In this study, we found that all PFAAs investigated, including perfluorohexanoic acid, perfluorooctanoic acid, perfluorononanoic acid, and perfluorooctane sulfonate, even at low concentrations (0.02 and 0.05 mg/L), expedited the enzymatic degradation of DNA in a nonlinear dose-effect relationship, with DNA degradation fragment sizes being lower than 1,000 bp and 200 bp after 15 and 30 min of degradation, respectively. This phenomenon was attributed to the binding interaction between PFAAs and AT bases in DNA via groove binding. van der Waals force (especially dispersion force) and hydrogen bonding are the main binding forces. DNA binding with PFAAs led to decreased base stacking and right-handed helicity, resulting in loose DNA structure exposing more digestion sites for degrading enzymes, and accelerating the enzymatic degradation of DNA. The global ecological risk evaluation results indicated that PFAA contamination could cause medium and high molecular ecological risk in 497 samples from 11 contamination-hot countries (such as the USA, Canada, and China). The findings of this study show new insights into the influence of PFAAs on the environmental fates of biomacromolecules and reveal the hidden molecular ecological effects of PFAAs in the environment.
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Affiliation(s)
- Chao Qin
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Run-Hao Zhang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zekai Li
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Nai-Xian Feng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States
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11
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Chatterjee A, Zhang K, Parker KM. Binding of Dissolved Organic Matter to RNA and Protection from Nuclease-Mediated Degradation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16086-16096. [PMID: 37811805 DOI: 10.1021/acs.est.3c05019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The persistence of RNA in environmental systems is an important parameter for emerging applications, including ecological surveys, wastewater-based epidemiology, and RNA interference biopesticides. RNA persistence is controlled by its rate of biodegradation, particularly by extracellular enzymes, although the specific factors determining this rate have not been characterized. Due to prior work suggesting that nucleic acids-specifically DNA-interact with dissolved organic matter (DOM), we hypothesized that DOM may bind RNA and impede its biodegradation in natural systems. We first adapted a technique previously used to assess RNA-protein binding to differentiate RNA that is bound at all sites by DOM from RNA that is unbound or partially bound by DOM. Results from this technique suggested that humic acids bound RNA more extensively than fulvic acids. At concentrations of 8-10 mgC/L, humic acids were also found to be more effective than fulvic acids at suppressing enzymatic degradation of RNA. In surface water and soil extract containing DOM, RNA degradation was suppressed by 39-46% relative to pH-adjusted controls. Due to the ability of DOM to both bind and suppress the enzymatic degradation of RNA, RNA biodegradation may be slowed in environmental systems with high DOM concentrations, which may increase its persistence.
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Affiliation(s)
- Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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12
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Breadner PR, Dhiyebi HA, Fattahi A, Srikanthan N, Hayat S, Aucoin MG, Boegel SJ, Bragg LM, Craig PM, Xie Y, Giesy JP, Servos MR. A comparative analysis of the partitioning behaviour of SARS-CoV-2 RNA in liquid and solid fractions of wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165095. [PMID: 37355124 PMCID: PMC10287177 DOI: 10.1016/j.scitotenv.2023.165095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
As fragments of SARS-CoV-2 RNA can be quantified and measured temporally in wastewater, surveillance of concentrations of SARS-CoV-2 in wastewater has become a vital resource for tracking the spread of COVID-19 in and among communities. However, the absence of standardized methods has affected the interpretation of data for public health efforts. In particular, analyzing either the liquid or solid fraction has implications for the interpretation of how viral RNA is quantified. Characterizing how SARS-CoV-2 or its RNA fragments partition in wastewater is a central part of understanding fate and behaviour in wastewater. In this study, partitioning of SARS-CoV-2 was investigated by use of centrifugation with varied durations of spin and centrifugal force, polyethylene glycol (PEG) precipitation followed by centrifugation, and ultrafiltration of wastewater. Partitioning of the endogenous pepper mild mottled virus (PMMoV), used to normalize the SARS-CoV-2 signal for fecal load in trend analysis, was also examined. Additionally, two surrogates for coronavirus, human coronavirus 229E and murine hepatitis virus, were analyzed as process controls. Even though SARS-CoV-2 has an affinity for solids, the total RNA copies of SARS-CoV-2 per wastewater sample, after centrifugation (12,000 g, 1.5 h, no brake), were partitioned evenly between the liquid and solid fractions. Centrifugation at greater speeds for longer durations resulted in a shift in partitioning for all viruses toward the solid fraction except for PMMoV, which remained mostly in the liquid fraction. The surrogates more closely reflected the partitioning of SARS-CoV-2 under high centrifugation speed and duration while PMMoV did not. Interestingly, ultrafiltration devices were inconsistent in estimating RNA copies in wastewater, which can influence the interpretation of partitioning. Developing a better understanding of the fate of SARS-CoV-2 in wastewater and creating a foundation of best practices is the key to supporting the current pandemic response and preparing for future potential infectious diseases.
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Affiliation(s)
- Patrick R Breadner
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Hadi A Dhiyebi
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Azar Fattahi
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Nivetha Srikanthan
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Samina Hayat
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Marc G Aucoin
- Department of Chemical Engineering, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Scott J Boegel
- Department of Chemical Engineering, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Leslie M Bragg
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Paul M Craig
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Yuwei Xie
- Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; Toxicology Centre, University of Saskatchewan, 44 Campus Dr, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, 44 Campus Dr, Saskatoon, Saskatchewan S7N 5B3, Canada; Department of Environmental Science, Baylor University, One Bear Place, Waco, TX 76798, USA
| | - Mark R Servos
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada.
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13
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Brandão-Dias PFP, Tank JL, Snyder ED, Mahl UH, Peters B, Bolster D, Shogren AJ, Lamberti GA, Bibby K, Egan SP. Suspended Materials Affect Particle Size Distribution and Removal of Environmental DNA in Flowing Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13161-13171. [PMID: 37610829 DOI: 10.1021/acs.est.3c02638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Environmental DNA (eDNA) in aquatic systems is a complex mixture that includes dissolved DNA, intracellular DNA, and particle-adsorbed DNA. Information about the various components of eDNA and their relative proportions could be used to discern target organism abundance and location. However, a limited knowledge of eDNA adsorption dynamics and interactions with other materials hinders these applications. To address this gap, we used recirculating stream mesocosms to investigate the impact of suspended materials (fine particulate organic matter, plankton, clay, and titanium dioxide) on the eDNA concentration and particle size distribution (PSD) from two fish species in flowing water. Our findings revealed that eDNA rapidly adsorbs to other materials in the water column, affecting its concentration and PSD. Nonetheless, only particulate organic matter affected eDNA removal rate after 30 h. Moreover, we observed that the removal of larger eDNA components (≥10 μm) was more strongly influenced by physical processes, whereas the removal of smaller eDNA components was driven by biological degradation. This disparity in removal mechanisms between larger and smaller eDNA components could explain changes in eDNA composition over time and space, which have implications for modeling the spatial distribution and abundance of target species and optimizing eDNA detection in high turbidity systems.
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Affiliation(s)
| | - Jennifer L Tank
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Notre Dame Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Elise D Snyder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ursula H Mahl
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Brett Peters
- Notre Dame Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Diogo Bolster
- Notre Dame Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Arial J Shogren
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35401, United States
| | - Gary A Lamberti
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Notre Dame Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kyle Bibby
- Notre Dame Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Scott P Egan
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
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14
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Zhang M, Zou Y, Xiao S, Hou J. Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects. MARINE POLLUTION BULLETIN 2023; 194:115430. [PMID: 37647798 DOI: 10.1016/j.marpolbul.2023.115430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
Marine and freshwater biodiversity is under threat from both natural and manmade causes. Biological monitoring is currently a top priority for biodiversity protection. Given present limitations, traditional biological monitoring methods may not achieve the proposed monitoring aims. Environmental DNA metabarcoding technology reflects species information by capturing and extracting DNA from environmental samples, using molecular biology techniques to sequence and analyze the DNA, and comparing the obtained information with existing reference libraries to obtain species identification. However, its practical application has highlighted several limitations. This paper summarizes the main steps in the environmental application of eDNA metabarcoding technology in aquatic ecosystems, including the discovery of unknown species, the detection of invasive species, and evaluations of biodiversity. At present, with the rapid development of big data and artificial intelligence, certain advanced technologies and devices can be combined with environmental DNA metabarcoding technology to promote further development of aquatic species monitoring and management.
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Affiliation(s)
- Miaolian Zhang
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yingtong Zou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Xiao
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Jing Hou
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
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15
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Kraevsky SV, Barinov NA, Morozova OV, Palyulin VV, Kremleva AV, Klinov DV. Features of DNA-Montmorillonite Binding Visualized by Atomic Force Microscopy. Int J Mol Sci 2023; 24:9827. [PMID: 37372975 DOI: 10.3390/ijms24129827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
In the present work, complexes of DNA with nano-clay montmorillonite (Mt) were investigated by means of atomic force microscopy (AFM) under various conditions. In contrast to the integral methods of analysis of the sorption of DNA on clay, AFM allowed us to study this process at the molecular level in detail. DNA molecules in the deionized water were shown to form a 2D fiber network weakly bound to both Mt and mica. The binding sites are mostly along Mt edges. The addition of Mg2+ cations led to the separation of DNA fibers into separate molecules, which bound mainly to the edge joints of the Mt particles according to our reactivity estimations. After the incubation of DNA with Mg2+, the DNA fibers were capable of wrapping around the Mt particles and were weakly bound to the Mt edge surfaces. The reversible sorption of nucleic acids onto the Mt surface allows it to be used for both RNA and DNA isolation for further reverse transcription and polymerase chain reaction (PCR). Our results show that the strongest binding sites for DNA are the edge joints of Mt particles.
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Affiliation(s)
- Sergey V Kraevsky
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Street, 119435 Moscow, Russia
- Alikhanov Institute for Theoretical and Experimental Physics, National Research Center "Kurchatov Institute", ac. Kurchatov, sq, 1, 123182 Moscow, Russia
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, 119121 Moscow, Russia
| | - Nikolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Street, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 9 Institutsky Per., 141700 Dolgoprudny, Russia
| | - Olga V Morozova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Street, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 9 Institutsky Per., 141700 Dolgoprudny, Russia
- National Research Center of Epidemiology and Microbiology Named after N.F. Gamaleya, Ivanovsky Institute of Virology of the Russian Ministry of Health, 16 Gamaleya Street, 123098 Moscow, Russia
| | - Vladimir V Palyulin
- Applied AI Center, Skolkovo Institute of Science and Technology, Bol'shoy Bul'var, 30, bld 1, 121205 Moscow, Russia
| | - Alena V Kremleva
- Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Street, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 9 Institutsky Per., 141700 Dolgoprudny, Russia
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16
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Zhang K, Ho KP, Chatterjee A, Park G, Li Z, Catalano JG, Parker KM. RNA Hydrolysis at Mineral-Water Interfaces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37216349 DOI: 10.1021/acs.est.3c01407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
As an essential biomolecule for life, RNA is ubiquitous across environmental systems where it plays a central role in biogeochemical processes and emerging technologies. The persistence of RNA in soils and sediments is thought to be limited by enzymatic or microbial degradation, which occurs on timescales that are orders of magnitude faster than known abiotic pathways. Herein, we unveil a previously unreported abiotic pathway by which RNA rapidly hydrolyzes on the timescale of hours upon adsorption to iron (oxyhydr)oxide minerals such as goethite (α-FeOOH). The hydrolysis products were consistent with iron present in the minerals acting as a Lewis acid to accelerate sequence-independent hydrolysis of phosphodiester bonds comprising the RNA backbone. In contrast to acid- or base-catalyzed RNA hydrolysis in solution, mineral-catalyzed hydrolysis was fastest at circumneutral pH, which allowed for both sufficient RNA adsorption and hydroxide concentration. In addition to goethite, we observed that RNA hydrolysis was also catalyzed by hematite (α-Fe2O3) but not by aluminum-containing minerals (e.g., montmorillonite). Given the extensive adsorption of nucleic acids to environmental surfaces, we anticipate previously overlooked mineral-catalyzed hydrolysis of RNA may be prevalent particularly in iron-rich soils and sediments, which must be considered across biogeochemical applications of nucleic acid analysis in environmental systems.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kun-Pu Ho
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Grace Park
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Zhiyao Li
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jeffrey G Catalano
- Department of Earth & Planetary Sciences, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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17
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Yuan L, Wu Y, Fan Q, Li P, Liang J, Liu YH, Ma R, Li R, Shi L. Influence mechanism of organic matter and low-molecular-weight organic acids on the interaction between minerals and PAHs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160872. [PMID: 36521591 DOI: 10.1016/j.scitotenv.2022.160872] [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: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Investigate the effect of soil organic matter (SOM) and low molecular weight organic acids (LMWOAs) on minerals adsorption of PAHs. Batch adsorption experiments have been carried out to study the adsorption of PAHs (Naphthalene (NaP), Phenanthrene (Phe) and Pyrene (Pyr)) by minerals (Montmorillonite (Mnt), kaolinite (Kln) and calcite (Cal)). This research found that compared with Kln and Cal, Mnt showed the maximum adsorption capability for PAHs. And the order of PAHs adsorption by Mnt was: Pyr > Phe > Nap, which corresponds to the octanol-water partition coefficient (Kow) of different PAHs. The adsorption kinetic and isotherm were well fitted by Pseudo-second-order kinetic model, Freundlich and Linear isotherm model. Furthermore, inorganic ions (Ca2+) impacted PAHs adsorption by competitive adsorption and cation-π interactive. Cal has the maximum desorption of PAHs among three minerals, and there was desorption hysteresis phenomenon. Field emission-scanning electron microscope (Fe-SEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) analysis indicated that SOM enhanced the sorption of PAHs by van der Waals, hydrogen bonding, π-π interactions, and chemical bonding. LMWOAs significantly inhibited PAHs adsorption and promote PAHs desorption from the minerals. As a result, LMWOAs increased of PAHs bioavailability, which provide a new strategy to improve PAHs cleanup efficiency.
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Affiliation(s)
- Longmiao Yuan
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingqin Wu
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Petroleum Resources, Gansu Province, Lanzhou 730000, China.
| | - Qiaohui Fan
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou 730046, China; Key Laboratory of Petroleum Resources, Gansu Province, Lanzhou 730000, China.
| | - Ping Li
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou 730046, China; Key Laboratory of Petroleum Resources, Gansu Province, Lanzhou 730000, China
| | - Jianjun Liang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou 730046, China; Key Laboratory of Petroleum Resources, Gansu Province, Lanzhou 730000, China
| | - Yan Hong Liu
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Petroleum Resources, Gansu Province, Lanzhou 730000, China
| | - Rong Ma
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruijie Li
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - LeiPing Shi
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
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18
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Kjær KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, Sand KK, Jelavić S, Ruter AH, Schmidt AMA, Kjeldsen KK, Tesakov AS, Snowball I, Gosse JC, Alsos IG, Wang Y, Dockter C, Rasmussen M, Jørgensen ME, Skadhauge B, Prohaska A, Kristensen JÅ, Bjerager M, Allentoft ME, Coissac E, Rouillard A, Simakova A, Fernandez-Guerra A, Bowler C, Macias-Fauria M, Vinner L, Welch JJ, Hidy AJ, Sikora M, Collins MJ, Durbin R, Larsen NK, Willerslev E. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 2022; 612:283-291. [PMID: 36477129 PMCID: PMC9729109 DOI: 10.1038/s41586-022-05453-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/18/2022] [Indexed: 12/12/2022]
Abstract
Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1 had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11-19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.
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Affiliation(s)
- Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Binia De Cahsan
- Section for Molecular Ecology and Evolution, The Globe Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Thorfinn S Korneliussen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian S Michelsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Karina K Sand
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stanislav Jelavić
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, IRD, Université Gustave Eiffel, ISTerre, Grenoble, France
| | - Anthony H Ruter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Astrid M A Schmidt
- Nordic Foundation for Development and Ecology (NORDECO), Copenhagen, Denmark
- DIS Study Abroad in Scandinavia, University of Copenhagen, Copenhagen, Denmark
| | - Kristian K Kjeldsen
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Alexey S Tesakov
- Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Ian Snowball
- Department of Earth Sciences, Uppsala University, Uppsala, Sweden
| | - John C Gosse
- Department of Earth and Environmental Sciences, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Inger G Alsos
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Yucheng Wang
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Ana Prohaska
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jeppe Å Kristensen
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
- Geological Survey of Denmark and Greenland, (GEUS), Copenhagen, Denmark
| | - Morten Bjerager
- Department of Geophysics and Sedimentary Basins, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Eric Coissac
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
- University of Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Alexandra Rouillard
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | | | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM Université PSL, Paris, France
| | - Marc Macias-Fauria
- School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alan J Hidy
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Matthew J Collins
- Department of Archaeology, University of Cambridge, Cambridge, UK
- Section for GeoBiology, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Nicolaj K Larsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM, University of Bremen, Bremen, Germany.
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19
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Chowdhury NN, Hicks E, Wiesner MR. Investigating and Modeling the Regulation of Extracellular Antibiotic Resistance Gene Bioavailability by Naturally Occurring Nanoparticles. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15044-15053. [PMID: 35853206 PMCID: PMC9979080 DOI: 10.1021/acs.est.2c02878] [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] [Indexed: 05/23/2023]
Abstract
Extracellular antibiotic resistance genes (eARGs) are widespread in the environment and can genetically transform bacteria. This work examined the role of environmentally relevant nanoparticles (NPs) in regulating eARG bioavailability. eARGs extracted from antibiotic-resistant B. subtilis were incubated with nonresistant recipient B. subtilis cells. In the mixture, particle type (either humic acid coated nanoparticles (HASNPs) or their micron-sized counterpart (HASPs)), DNase I concentration, and eARG type were systematically varied. Transformants were counted on selective media. Particles decreased bacterial growth and eARG bioavailability in systems without nuclease. When DNase I was present (≥5 μg/mL), particles increased transformation via chromosomal (but not plasmid-borne) eARGs. HASNPs increased transformation more than HASPs, indicating that the smaller nanoparticle with greater surface area per volume is more effective in increasing eARG bioavailability. These results were also modeled via particle aggregation theory, which represented eARG-bacteria interactions as transport leading to collision, followed by attachment. Using attachment efficiency as a fitting factor, the model predicted transformant concentrations within 35% of experimental data. These results confirm the ability of NPs to increase eARG bioavailability and suggest that particle aggregation theory may be a simplified and suitable framework to broadly predict eARG uptake.
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Affiliation(s)
- Nadratun N Chowdhury
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Ethan Hicks
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Mark R Wiesner
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina 27708, United States
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20
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Zumstein M, Battagliarin G, Kuenkel A, Sander M. Environmental Biodegradation of Water-Soluble Polymers: Key Considerations and Ways Forward. Acc Chem Res 2022; 55:2163-2167. [PMID: 35929823 PMCID: PMC9386898 DOI: 10.1021/acs.accounts.2c00232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Water-soluble polymers (WSPs) have unique properties that are valuable in diverse applications ranging from home and personal care products to agricultural formulations. For applications that result in the release of WSPs into natural environments or engineered systems, such as agricultural soils and wastewater streams, biodegradable as opposed to nonbiodegradable WSPs have the advantage of breaking down and, thereby, eliminating the risk of persistence and accumulation. In this Commentary, we emphasize central steps in WSP biodegradation, discuss how these steps depend on both WSP properties and characteristics of the receiving environment, and highlight critical requirements for testing WSP biodegradability.
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Affiliation(s)
- Michael Zumstein
- Division
of Environmental Geosciences, Centre for Microbiology and Environmental
Systems Science, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,
| | | | - Andreas Kuenkel
- BASF
SE, Carl-Bosch-Strasse
38, 67056 Ludwigshafen
am Rhein, Germany
| | - Michael Sander
- Institute
of Biogeochemistry and Pollutant Dynamics, Department of Environmental
Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
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21
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Tian Y, Lu X, Hou J, Xu J, Zhu L, Lin D. Application of α-Fe 2O 3 nanoparticles in controlling antibiotic resistance gene transport and interception in porous media. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155271. [PMID: 35447184 DOI: 10.1016/j.scitotenv.2022.155271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/27/2022] [Accepted: 04/10/2022] [Indexed: 06/14/2023]
Abstract
Metal oxide nanoparticles (MONPs) with a large specific surface area are expected to bind with antibiotic resistance genes (ARGs), thereby controlling ARGs' contamination by reducing their concentration and mobilization. Here, adsorption experiments were carried out and it was found that α-Fe2O3 NPs could chemically bind with ARGs (tetM-carrying plasmids) in water with an adsorption rate of 0.04 min-1 and an adsorption capacity of 7.88 g/kg. Mixing α-Fe2O3 NPs into quartz sand column markedly increased the interceptive removal of ARGs from inflow water. The interception rate of 1.0 μg/mL ARGs in ultrapure water (25 mL, 5 pore volumes) through the sand column (plexiglass, length 8 cm, internal diameter 1.4 cm) with 1 g/kg α-Fe2O3 NPs was 1.73 times of that through the pure sand column; the interception rate overall increased with increasing addition of α-Fe2O3 NPs, reaching 68.8% with 20 g/kg α-Fe2O3 NPs. Coexisting Na+ (20 mM), Ca2+ (20 mM), and acidic condition (pH 4.0) could further increase the interception rate of ARGs by 1 g/kg α-Fe2O3 NPs from 21.1% to 86.2%, 90.7%, and 96.2%, respectively. The presence of PO43- and humic acid at environmentally relevant concentrations would not significantly affect the interception of ARGs. In the treatment groups with PO43- and humic acid, the removal rate decreased by only 1.8% and 0.1%, respectively. In addition, the interceptive removal of ARGs by α-Fe2O3 NPs-incorporated sand column was even better in actual surface water samples (87.2%) than that in the ultrapure water (21.1%). The findings provide a promising approach to treat ARGs-polluted water.
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Affiliation(s)
- Yiyang Tian
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Xinye Lu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Jie Hou
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Jiang Xu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Lizhong Zhu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Ecological Civilization Academy, Anji 313300, China
| | - Daohui Lin
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Ecological Civilization Academy, Anji 313300, China.
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22
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Mauvisseau Q, Harper LR, Sander M, Hanner RH, Kleyer H, Deiner K. The Multiple States of Environmental DNA and What Is Known about Their Persistence in Aquatic Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:5322-5333. [PMID: 35435663 PMCID: PMC9069692 DOI: 10.1021/acs.est.1c07638] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Increased use of environmental DNA (eDNA) analysis for indirect species detection has spurred the need to understand eDNA persistence in the environment. Understanding the persistence of eDNA is complex because it exists in a mixture of different states (e.g., dissolved, particle adsorbed, intracellular, and intraorganellar), and each state is expected to have a specific decay rate that depends on environmental parameters. Thus, improving knowledge about eDNA conversion rates between states and the reactions that degrade eDNA in different states is needed. Here, we focus on eukaryotic extraorganismal eDNA, outline how water chemistry and suspended mineral particles likely affect conversion among each eDNA state, and indicate how environmental parameters affect persistence of states in the water column. On the basis of deducing these controlling parameters, we synthesized the eDNA literature to assess whether we could already derive a general understanding of eDNA states persisting in the environment. However, we found that these parameters are often not being measured or reported when measured, and in many cases very few experimental data exist from which to draw conclusions. Therefore, further study of how environmental parameters affect eDNA state conversion and eDNA decay in aquatic environments is needed. We recommend analytic controls that can be used during the processing of water to assess potential losses of different eDNA states if all were present in a water sample, and we outline future experimental work that would help determine the dominant eDNA states in water.
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Affiliation(s)
- Quentin Mauvisseau
- Natural
History Museum, University of Oslo, Sars’ gate 1, 0562 Oslo, Norway
| | - Lynsey R. Harper
- Nature
Metrics Ltd, CABI Site, Bakeham Lane, Egham, Surrey TW20 9TY, United Kingdom
| | - Michael Sander
- Department
of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland
| | - Robert H. Hanner
- Department
of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hannah Kleyer
- Department
of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland
| | - Kristy Deiner
- Department
of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland
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23
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Wang H, Liu C, Teng X, Liang Z, Zhu L, Xu G, Chen C, Ma K, Liu R, Zhou L, Yan B. A TbPO 4-based capturer for environmental extracellular antibiotic genes by interrogating lanthanide phosphates nanoneedles. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127139. [PMID: 34537653 DOI: 10.1016/j.jhazmat.2021.127139] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/25/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Accurate determination of antibiotic resistance genes (ARGs) in environmental DNA molecules (eDNA) is challenging owing to its low abundance in the aquatic environment. Here we report a facile and cost-efficient approach to extract trace amount of eDNAs in the aquatic environment using LnPO4 nanomaterials. Among the nanomaterials, less crystalline TbPO4 nanoneedles was identified as the most prominent candidate for long stranded DNA and short stranded DNA with adsorption efficiency above 97%. The adsorbed DNA was washed off from TbPO4 nanoneedles by optimized eluant (85% PBS, 15% EtOH, 4 g/L glycine, pH 10.0) with an optimal DNA recovery of 78.83%. Our approach showed a comparable or better eDNA extraction efficiency than a commercial extraction method for different environmental samples, but 89% less cost. The high purity of the extracted eDNA was demonstrated by a high A260/280 ratio. Using qPCR experiment, the occurrence of six common ARGs in the eDNA were detected with abundance ranging from 4.06 × 103 to 3.51 × 109 copies/L in river samples. This specific DNA capturer is valuable for the evaluation of spatial and temporal dynamic of ARGs pollution to provide insight into the potential risk with regard to the human health.
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Affiliation(s)
- Haiqing Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Chao Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xuepeng Teng
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, China
| | - Zhenda Liang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Lishan Zhu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Gang Xu
- Nanzhou Waterworks of Guangzhou Water Supply Co. Ltd., Guangzhou 510000, China
| | - Chaoxiang Chen
- Nanzhou Waterworks of Guangzhou Water Supply Co. Ltd., Guangzhou 510000, China
| | - Kunyu Ma
- Nanzhou Waterworks of Guangzhou Water Supply Co. Ltd., Guangzhou 510000, China
| | - Rongrong Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Li Zhou
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Bing Yan
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
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24
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Cai C, Hui X, Yang W, Hua Y, Liu H, Dai X. Implications for mitigation of antibiotic resistance: Differential response of intracellular and extracellular antibiotic resistance genes to sludge fermentation coupled with thermal hydrolysis. WATER RESEARCH 2022; 209:117876. [PMID: 34864623 DOI: 10.1016/j.watres.2021.117876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/08/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Thermal hydrolysis pretreatment (THP) can effectively remove the antibiotic resistance genes (ARGs) from sewage sludge, but the rebounding effects in the subsequent anaerobic fermentation are often observed. The purpose of this study was to elucidate the distribution and fate of intracellular and extracellular ARGs (iARGs and eARGs) in the sludge acidogenic fermentation process coupled with THP. Our results revealed that THP significantly reduced the absolute abundance of total ARGs in raw sludge but increased eARGs by 0.3-1.4 log units under practical conditions (140 °C for 30 min). There is no significant difference in the removal of total ARGs between the two acidogenic fermenters receiving raw and hydrolyzed sludge, with iARGs prevailing in the produced biosolids. The succession of bacterial community and the co-occurrence relationships among ARG type, mobile genetic elements and bacterial taxa were observed, suggesting a phylogenetic basis for the iARGs patterns in fermented sludge. However, eARGs were susceptible to biodegradation with a half-life of 2.34 h and they contributed limitedly to the ARGs propagation through transformation. These findings suggest an emphasis on the mitigation of iARGs during the acidogenic fermentation of sludge, which would be achieved by lowering the richness and physicochemical destruction of potential hosts.
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Affiliation(s)
- Chen Cai
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xuesong Hui
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Wan Yang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Yu Hua
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Huiling Liu
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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25
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Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D'Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC, Sano D, Wuertz S, Xagoraraki I, Zhang Q, Zimmer-Faust AG, Shanks OC. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:149877. [PMID: 34818780 PMCID: PMC8386095 DOI: 10.1016/j.scitotenv.2021.149877] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 05/18/2023]
Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
| | | | - Paul M Bertsch
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - João Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisboa, Portugal
| | - Phil M Choi
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia; The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Mark Ciesielski
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA 5095, Australia
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostic, 166/5/3, Technische Universität Wien, Vienna, Austria; Research Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr. Karl-Dorrek-Straβe 30, 3500 Krems an der Donau, Austria
| | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Raul Gonzalez
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23455, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Porirua 5240, New Zealand
| | | | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ 85287, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rehnuma Haque
- Environmental Interventions Unit, Icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Greg Jackson
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, NSW 2052, Australia
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Blythe A Layton
- Department of Research & Innovation, Clean Water Services, Hillsboro, OR, USA
| | - Erin Lipp
- Environmental Health Sciences Department, University of Georgia, Athens, GA 30602, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Jochen F Mueller
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Heather Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Coleen C Naughton
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Rachel T Noble
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Susan Petterson
- Water and Health Pty Ltd., 13 Lord St, North Sydney, NSW 2060, Australia; School of Medicine, Griffith University, Parklands Drive, Gold Coast, Australia
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O. Box 95, FI-70701 Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O. Box 66, FI-00014, Finland
| | - Veronica B Rajal
- Facultad de Ingeniería and Instituto de Investigaciones para la Industria Química (INIQUI) - CONICET and Universidad Nacional de Salta, Av. Bolivia 5150, Salta, Argentina
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Fernando A Roman
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Michael J Sadowsky
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yin Xiang Setoh
- Environmental Health Institute, National Environment Agency, Singapore
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, New Orleans, LA 70112, USA
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok 10210, Thailand
| | - Wendy Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Rosalie Sabburg
- CSIRO Agriculture and Food, Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Phong Thai
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Josh Tynan
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Simon Toze
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Janelle Thompson
- Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551
| | | | | | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-Ku, Sendai, Miyagi 980-8597, Japan
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Qian Zhang
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | | | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
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26
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Calderón-Franco D, Apoorva S, Medema G, van Loosdrecht MCM, Weissbrodt DG. Upgrading residues from wastewater and drinking water treatment plants as low-cost adsorbents to remove extracellular DNA and microorganisms carrying antibiotic resistance genes from treated effluents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146364. [PMID: 34030392 DOI: 10.1016/j.scitotenv.2021.146364] [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] [Received: 12/16/2020] [Revised: 01/20/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Wastewater treatment is challenged by the continuous emergence of chemical and biological contaminants. Disinfection, advanced oxidation, and activated carbon technologies are accessible in high-income countries to suppress them. Low-cost, easily implementable, and scalable solutions are needed for sanitation across regions. We studied the properties of low-cost absorbents recycled from drinking water and wastewater treatment plant residues to remove environmental DNA and xenogenetic elements from used water. Materials characteristics and DNA adsorption properties of used iron-oxide-coated sands and of sewage-sludge biochar obtained by pyrolysis of surplus activated sludge were examined in bench-scale batch and up-flow column systems. Adsorption profiles followed Freundlich isotherms, suggesting a multilayer adsorption of nucleic acids on these materials. Sewage-sludge biochar exhibited high DNA adsorption capacity (1 mg g-1) and long saturation breakthrough times compared to iron-oxide-coated sand (0.2 mg g-1). Selected antibiotic resistance genes and mobile genetic elements present on the free-floating extracellular DNA fraction and on the total environmental DNA (i.e., both extra/intracellular) were removed at 85% and 97% by sewage-sludge biochar and at 54% and 66% by iron-oxide-coated sand, respectively. Sewage-sludge biochar is attractive as low-cost adsorbent to minimize the spread of antimicrobial resistances to the aquatic environment while strengthening the role of sewage treatment plants as resource recovery factories.
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Affiliation(s)
- David Calderón-Franco
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands.
| | - Seeram Apoorva
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands.
| | - Gertjan Medema
- KWR Watercycle Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands; Sanitary Engineering, Delft University of Technology, P.O. Box 5048, 2600 GA Delft, the Netherlands.
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands.
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands.
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27
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Sodnikar K, Parker KM, Stump SR, ThomasArrigo LK, Sander M. Adsorption of double-stranded ribonucleic acids (dsRNA) to iron (oxyhydr-)oxide surfaces: comparative analysis of model dsRNA molecules and deoxyribonucleic acids (DNA). ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:605-620. [PMID: 33723564 DOI: 10.1039/d1em00010a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Double-stranded ribonucleic acid (dsRNA) molecules are novel plant-incorporated protectants expressed in genetically modified RNA interference (RNAi) crops. Ecological risk assessment (ERA) of RNAi crops requires a heretofore-missing detailed understanding of dsRNA adsorption in soils, a key fate process. Herein, we systematically study the adsorption of a model dsRNA molecule and of two double-stranded deoxyribonucleic acid (DNA) molecules of varying lengths to three soil iron (oxyhydr-)oxides - goethite, lepidocrocite, and hematite - over a range of solution pH (4.5-10), ionic strength (I = 10-100 mM NaCl) and composition (0.5, 1, and 3 mM MgCl2) and in the absence and presence of phosphate (0.05-5 mM) as co-adsorbate. We hypothesized comparable adsorption characteristics of dsRNA and DNA based on their structural similarities. Consistently, the three nucleic acids (NAs) showed high adsorption affinities to the iron (oxyhydr-)oxides with decreasing adsorption in the order goethite, lepidocrocite, and hematite, likely reflecting a decrease in the hydroxyl group density and positive charges of the oxide surfaces in the same order. NA adsorption also decreased with increasing solution pH, consistent with weakening of NA electrostatic attraction to and inner-sphere complex formation with the iron (oxyhydr-)oxides surfaces as pH increased. Adsorbed NA concentrations increased with increasing I and in the presence of Mg2+, consistent with adsorbed NA molecules adopting more compact conformations. Strong NA-phosphate adsorption competition demonstrates that co-adsorbates need consideration in assessing dsRNA fate in soils. Comparable adsorption characteristics of dsRNA and DNA molecules to iron (oxyhydr-)oxides imply that information on DNA adsorption to soil particle surfaces can inform dsRNA ERA.
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Affiliation(s)
- Katharina Sodnikar
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, DUSYS, IBP, Universitätsstrasse 16, CHN H50.3, 8092 Zurich, Switzerland.
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Simona R Stump
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, DUSYS, IBP, Universitätsstrasse 16, CHN H50.3, 8092 Zurich, Switzerland.
| | - Laurel K ThomasArrigo
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, DUSYS, IBP, Universitätsstrasse 16, CHN H50.3, 8092 Zurich, Switzerland.
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, DUSYS, IBP, Universitätsstrasse 16, CHN H50.3, 8092 Zurich, Switzerland.
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Sun L, Tong H, Gao C, Liu Y, Feng C. Removal of antibiotic resistance genes from secondary effluent by processes combining nano-iron, ultrasound-activated persulfate, and ultrafiltration. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2021; 83:1578-1590. [PMID: 33843744 DOI: 10.2166/wst.2021.088] [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
Antibiotic resistance genes (ARGs), as a new type of environmental pollutant that threaten human health, have been detected in the effluent of sewage treatment systems. In this study, the removal from water of ARGs, 16S rRNA, class 1 integron (intI1), and dissolved organic carbon (DOC) were investigated using processes combining nano-iron (nFe), ultrasound (US), activated persulfate (PS) and ultrafiltration (UF). The oxidation mechanism was also studied. The results showed that both nFe and US activation could improve the oxidative effect of PS, and the effect of nFe was better than that of US. Compared with PS-UF, nFe/PS-UF and US/PS-UF significantly enhanced the removal of various ARGs and DOC. nFe/PS-UF was the most effective treatment, reducing cell-associated and cell-free ARGs by 1.74-3.14-log and 1.00-2.61-log, respectively, while removing 30% of DOC. Pre-oxidation methods using PS, nFe/PS, and US/PS significantly enhanced the efficacy of UF for removing DOC with molecular weights above 50 kDa and below 10 kDa, but the removal of DOC between 10 and 50 kDa decreased. The free radicals SO4·- and ·OH were shown to participate in the process of ARGs oxidation.
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Affiliation(s)
- Lihua Sun
- Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 100044, China E-mail:
| | - Hao Tong
- School of Environmental and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
| | - Cheng Gao
- Beijing General Municipal Engineering Design & Research Institute Co., Ltd, Beijing 100082, China
| | - Yehui Liu
- School of Environmental and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
| | - Cuimin Feng
- Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 100044, China E-mail:
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Xue G, Diao R, Jiang M, Chen H, Yu X, Xie J, Gao P, Li X. Significant effect of pH on tetracycline resistance genes reduction during sludge thermal hydrolysis treatment. WASTE MANAGEMENT (NEW YORK, N.Y.) 2021; 124:36-45. [PMID: 33601176 DOI: 10.1016/j.wasman.2021.01.019] [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: 06/29/2020] [Revised: 12/09/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
Thermal hydrolysis (TH) treatment has been verified to effectively reduce antibiotic resistance genes (ARGs) in waste activated sludge. This study focused on the effect of TH parameters on ARGs reduction, and the optimal conditions basing on tetracycline (tet) resistance genes reduction rate in sludge phase were pH 3, temperature 160 °C and reaction time 2 h. The pH was found to play a critical role in tet genes reduction behavior. Additionally, the tet genes distributions in TH supernatant are considered as well because genes will release from solid to liquid phase as sludge cell breaking. The lowest genes content in TH supernatant was also observed at pH 3. Further investigation revealed that contents of DNA and organics released from sludge phase to liquid phase under pH 3 were less than that in neutral and alkaline condition; moreover, the organics in TH supernatant was found to protect DNA. Therefore, under the acidic condition, the genes had less releasing from the sludge phase and the DNA protection effect of organics was weaker, resulting in the lowest tet genes content in TH supernatant. Moreover, bacterial community structure after TH was closely related with the ARGs content. The bacterial on phylum and genus level showed various responses to TH pH values. Although the Firmicutes phylum and Escherichia-Shigella genus exhibited the stronger resistance and had higher accumulation in TH acidic condition, more possible total tet genes hosts were destroyed in acidic condition, causing less ARGs remaining in the sludge phase under pH 3.
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Affiliation(s)
- Gang Xue
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai 201620, China; Shanghai Institute of Pollution Control and Ecological Security, 200000, China
| | - Ruqi Diao
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai 201620, China
| | - Mingji Jiang
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai 201620, China
| | - Hong Chen
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai 201620, China.
| | - Xin Yu
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai 201620, China
| | - Jing Xie
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai 201620, China
| | - Pin Gao
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai 201620, China
| | - Xiang Li
- School of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Songjiang District, Shanghai 201620, China
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Chowdhury NN, Cox AR, Wiesner MR. Nanoparticles as vectors for antibiotic resistance: The association of silica nanoparticles with environmentally relevant extracellular antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:143261. [PMID: 33223180 DOI: 10.1016/j.scitotenv.2020.143261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/04/2020] [Accepted: 10/20/2020] [Indexed: 05/09/2023]
Abstract
A relevant but yet unconsidered subset of particles that may alter the fate of extracellular antibiotic resistance genes (eARGs) are nano-scale particles (NPs), which are ubiquitous in natural environments and have unique properties. In this study, sorption isotherms were developed describing the association of linear DNA fragments isolated from widespread eARGs (blaI and nptII) with either micon-sized kaolinite or silica nanoparticles (SNPs), to determine if sorption capacity was enhanced at the nanoscale. For each isotherm, eARG fragments were added at five starting concentrations (5-40 μg/mL) to mixed batch systems with 0.25 g of particles and nuclease-free water. Sorption was quantified by the removal of DNA from solution, as detected by a Qubit fluorimeter. Isotherms were developed for eARGs of various fragment lengths (508, 680 and 861 bp), guanine-cytosine (GC) contents (34%, 47% and 54%) and both double and single stranded eARGs, to assess the impact of DNA properties on particle association. Sorption isotherms were also developed in systems with added humic acid and/or CaCl2, to assess the impact of these environmental parameters on sorption. FTIR analysis was performed to analyze the conformation of sorbed eARGs. Desorption of eARGs was studied by quantifying the removal of eDNA from washed and vortexed post-sorption particles. Statistically significant irreversible sorption of eARGs to environmentally relevant NPs (humic acid functionalized silica nanoparticles) was demonstrated for the first time. Nano-emergent properties did not increase sorption capacity of eARGs, but led to a unique compressed conformation of sorbed eARGs. The addition of humic acid, increased CaCl2 concentration and small DNA fragment size favored sorption. NPs showed a slight preference for the sorption of single-stranded DNA over double-stranded DNA. These findings suggest that NP association with eARGs may be a significant and unique environmental phenomenon that could influence the spread of antibiotic resistance.
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Affiliation(s)
- Nadratun N Chowdhury
- Department of Civil and Environmental Engineering, Duke Hudson Hall, Box 90287, Durham, NC 27708-0287, USA.
| | - Akylah R Cox
- Department of Civil and Environmental Engineering, Duke Hudson Hall, Box 90287, Durham, NC 27708-0287, USA
| | - Mark R Wiesner
- Department of Civil and Environmental Engineering, Duke Hudson Hall, Box 90287, Durham, NC 27708-0287, USA
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Fang J, Jin L, Meng Q, Wang D, Lin D. Interactions of extracellular DNA with aromatized biochar and protection against degradation by DNase I. J Environ Sci (China) 2021; 101:205-216. [PMID: 33334516 DOI: 10.1016/j.jes.2020.08.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 06/12/2023]
Abstract
With increasing environmental application, biochar (BC) will inevitably interact with and impact environmental behaviors of widely distributed extracellular DNA (eDNA), which however still remains to be studied. Herein, the adsorption/desorption and the degradation by nucleases of eDNA on three aromatized BCs pyrolyzed at 700 °C were firstly investigated. The results show that the eDNA was irreversibly adsorbed by aromatized BCs and the pseudo-second-order and Freundlich models accurately described the adsorption process. Increasing solution ionic strength or decreasing pH below 5.0 significantly increased the eDNA adsorption on BCs. However, increasing pH from 5.0 to 10.0 faintly decreased eDNA adsorption. Electrostatic interaction, Ca ion bridge interaction, and π-π interaction between eDNA and BC could dominate the eDNA adsorption, while ligand exchange and hydrophobic interactions were minor contributors. The presence of BCs provided a certain protection to eDNA against degradation by DNase I. BC-bound eDNA could be partly degraded by nuclease, while BC-bound nuclease completely lost its degradability. These findings are of fundamental significance for the potential application of biochar in eDNA dissemination management and evaluating the environmental fate of eDNA.
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Affiliation(s)
- Jing Fang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou 310023, China; School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Liang Jin
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Qingkang Meng
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Dengjun Wang
- Oak Ridge Institute for Science and Education (ORISE) Resident Research Associate, United States Environmental Protection Agency, Ada, OK 74820, USA
| | - Daohui Lin
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China.
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Model prediction of the point of zero net charge of layered double hydroxides and clay minerals. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2020.125860] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Kimprasit T, Nunome M, Iida K, Murakami Y, Wong ML, Wu CH, Kobayashi R, Hengjan Y, Takemae H, Yonemitsu K, Kuwata R, Shimoda H, Si L, Sohn JH, Asakawa S, Ichiyanagi K, Maeda K, Oh HS, Mizutani T, Kimura J, Iida A, Hondo E. Dispersal history of Miniopterus fuliginosus bats and their associated viruses in east Asia. PLoS One 2021; 16:e0244006. [PMID: 33444317 PMCID: PMC7808576 DOI: 10.1371/journal.pone.0244006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/02/2020] [Indexed: 12/23/2022] Open
Abstract
In this study, we examined the role of the eastern bent-winged bat (Miniopterus fuliginosus) in the dispersion of bat adenovirus and bat alphacoronavirus in east Asia, considering their gene flows and divergence times (based on deep-sequencing data), using bat fecal guano samples. Bats in China moved to Jeju Island and/or Taiwan in the last 20,000 years via the Korean Peninsula and/or Japan. The phylogenies of host mitochondrial D-loop DNA was not significantly congruent with those of bat adenovirus (m2XY = 0.07, p = 0.08), and bat alphacoronavirus (m2XY = 0.48, p = 0.20). We estimate that the first divergence time of bats carrying bat adenovirus in five caves studied (designated as K1, K2, JJ, N2, and F3) occurred approximately 3.17 million years ago. In contrast, the first divergence time of bat adenovirus among bats in the 5 caves was estimated to be approximately 224.32 years ago. The first divergence time of bats in caves CH, JJ, WY, N2, F1, F2, and F3 harboring bat alphacoronavirus was estimated to be 1.59 million years ago. The first divergence time of bat alphacoronavirus among the 7 caves was estimated to be approximately 2,596.92 years ago. The origin of bat adenovirus remains unclear, whereas our findings suggest that bat alphacoronavirus originated in Japan. Surprisingly, bat adenovirus and bat alphacoronavirus appeared to diverge substantially over the last 100 years, even though our gene-flow data indicate that the eastern bent-winged bat serves as an important natural reservoir of both viruses.
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Affiliation(s)
- Thachawech Kimprasit
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Keisuke Iida
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | | | - Min-Liang Wong
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Hsin Wu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ryosuke Kobayashi
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yupadee Hengjan
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hitoshi Takemae
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenzo Yonemitsu
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Ryusei Kuwata
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hiroshi Shimoda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Lifan Si
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan, China
| | - Joon-Hyuk Sohn
- Laboratory of Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Susumu Asakawa
- Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Ken Maeda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hong-Shik Oh
- Institute of Science Education, Jeju National University, Jeju, Korea
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Junpei Kimura
- Laboratory of Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Atsuo Iida
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Eiichi Hondo
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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Kirtane A, Atkinson JD, Sassoubre L. Design and Validation of Passive Environmental DNA Samplers Using Granular Activated Carbon and Montmorillonite Clay. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11961-11970. [PMID: 32659082 DOI: 10.1021/acs.est.0c01863] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Environmental DNA (eDNA) analysis is gaining prominence as a tool for species and biodiversity monitoring in aquatic environments. eDNA shed by organisms is captured in grab samples, concentrated by filtration, extracted, and analyzed using molecular methods. Conventional capture and filtration methods are limited because (1) filtration does not capture all extracellular DNA, (2) eDNA can degrade during sample transport and storage, (3) filters often clog in turbid waters, reducing the eDNA captured, and (4) grab samples are time sensitive due to pulse eDNA inputs. To address these limitations, this work designs and validates Passive Environmental DNA Samplers (PEDS). PEDS consist of an adsorbent-filled sachet that is suspended in water to collect eDNA over time. Both extracellular and cellular DNA are captured, and the extracellular DNA is protected from degradation. The eDNA captured over time may be more representative than a grab sample. Two adsorbents, Montmorillonite Clay (MC) and Granular Activated Carbon (GAC), are tested. In laboratory experiments, MC-PEDS adsorbed five times more extracellular DNA and desorbed up to four times more than GAC-PEDS (despite high levels of eDNA loss during desorption). In microcosm and field experiments, GAC-PEDS captured over an order of magnitude more eDNA than MC-PEDS. Field results further validated PEDS as an effective eDNA capture method compared to conventional methods.
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Affiliation(s)
- Anish Kirtane
- Department of Civil, Structural, and Environmental Engineering, The State University of New York at Buffalo, Buffalo, New York 14228, United States
| | - John D Atkinson
- Department of Civil, Structural, and Environmental Engineering, The State University of New York at Buffalo, Buffalo, New York 14228, United States
| | - Lauren Sassoubre
- Department of Civil, Structural, and Environmental Engineering, The State University of New York at Buffalo, Buffalo, New York 14228, United States
- Department of Engineering, University of San Francisco, San Francisco, California 94117, United States
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Microbial Interaction with Clay Minerals and Its Environmental and Biotechnological Implications. MINERALS 2020. [DOI: 10.3390/min10100861] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Clay minerals are very common in nature and highly reactive minerals which are typical products of the weathering of the most abundant silicate minerals on the planet. Over recent decades there has been growing appreciation that the prime involvement of clay minerals in the geochemical cycling of elements and pedosphere genesis should take into account the biogeochemical activity of microorganisms. Microbial intimate interaction with clay minerals, that has taken place on Earth’s surface in a geological time-scale, represents a complex co-evolving system which is challenging to comprehend because of fragmented information and requires coordinated efforts from both clay scientists and microbiologists. This review covers some important aspects of the interactions of clay minerals with microorganisms at the different levels of complexity, starting from organic molecules, individual and aggregated microbial cells, fungal and bacterial symbioses with photosynthetic organisms, pedosphere, up to environmental and biotechnological implications. The review attempts to systematize our current general understanding of the processes of biogeochemical transformation of clay minerals by microorganisms. This paper also highlights some microbiological and biotechnological perspectives of the practical application of clay minerals–microbes interactions not only in microbial bioremediation and biodegradation of pollutants but also in areas related to agronomy and human and animal health.
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Facile Fabrication of Natural Polyelectrolyte-Nanoclay Composites: Halloysite Nanotubes, Nucleotides and DNA Study. Molecules 2020; 25:molecules25153557. [PMID: 32759785 PMCID: PMC7436255 DOI: 10.3390/molecules25153557] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/16/2020] [Accepted: 07/31/2020] [Indexed: 12/22/2022] Open
Abstract
Complexation of biopolymers with halloysite nanotubes (HNTs) can greatly affect their applicability as materials building blocks. Here we have performed a systematic investigation of fabrication of halloysite nanotubes complexes with nucleotides and genomic DNA. The binding of DNA and various nucleotide species (polyAU, UMP Na2, ADP Na3, dATP Na, AMP, uridine, ATP Mg) by halloysite nanotubes was tested using UV-spectroscopy. The study revealed that binding of different nucleotides to the nanoclay varied but was low both in the presence and absence of MgCl2, while MgCl2 facilitated significantly the binding of longer molecules such as DNA and polyAU. Modification of the nanotubes with DNA and nucleotide species was further confirmed by measurements of ζ-potentials. DNA-Mg-modified nanotubes were characterized using transmission electron (TEM), atomic force (AFM) and hyperspectral microscopies. Thermogravimetric analysis corroborated the sorption of DNA by the nanotubes, and the presence of DNA on the nanotube surface was indicated by changes in the surface adhesion force measured by AFM. DNA bound by halloysite in the presence of MgCl2 could be partially released after addition of phosphate buffered saline. DNA binding and release from halloysite nanotubes was tested in the range of MgCl2 concentrations (10–100 mM). Even low MgCl2 concentrations significantly increased DNA sorption to halloysite, and the binding was leveled off at about 60 mM. DNA-Mg-modified halloysite nanotubes were used for obtaining a regular pattern on a glass surface by evaporation induced self-assembly process. The obtained spiral-like pattern was highly stable and resisted dissolution after water addition. Our results encompassing modification of non-toxic clay nanotubes with a natural polyanion DNA will find applications for construction of gene delivery vehicles and for halloysite self-assembly on various surfaces (such as skin or hair).
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Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics. SOIL SYSTEMS 2020. [DOI: 10.3390/soilsystems4020023] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology.
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38
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Zhang K, Wei J, Huff Hartz KE, Lydy MJ, Moon TS, Sander M, Parker KM. Analysis of RNA Interference (RNAi) Biopesticides: Double-Stranded RNA (dsRNA) Extraction from Agricultural Soils and Quantification by RT-qPCR. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:4893-4902. [PMID: 32212649 DOI: 10.1021/acs.est.9b07781] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Double-stranded RNA (dsRNA) molecules are used as a novel class of biopesticides. To enable assessments of the ecological risk associated with their release to receiving environments, we developed an approach to quantify dsRNA in agricultural soils using quantitative reverse transcription-polymerase chain reaction (RT-qPCR). To allow quantification of dsRNA adsorbed to particles, we also developed a protocol to transfer dsRNA from particles to the extraction buffer by changing particle surface charge and adding constituents to compete with dsRNA for adsorption sites. Our approach could quantify dsRNA amounts as low as 0.003 ngdsRNA/gsoil. This approach is the first available field-applicable approach able to quantify dsRNA biopesticides down to environmentally relevant concentrations. We applied this approach to investigate dsRNA dissipation (including dilution, degradation, and adsorption) in two agricultural soils. When we applied a low amount of dsRNA (1 ngdsRNA/gsoil) to the soils, we observed that a greater fraction of dsRNA was adsorbed to and extractable from soil particles in a silty clay loam soil than in a fine sandy loam soil. In both soils, dsRNA dissipated on the timescale of hours. Overall, these results demonstrate that our approach can be applied to assess the environmental fate of dsRNA biopesticides at concentrations relevant to their release to soils.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jingmiao Wei
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kara E Huff Hartz
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Department of Zoology, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Michael J Lydy
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Department of Zoology, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Tae Seok Moon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Michael Sander
- Department of Environmental Systems Science (DUSYS), ETH Zurich, 8092 Zurich, Switzerland
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Zhang Q, Peng Q, Shu X, Mo D, Jiang D. Spectroscopic analysis of tylosin adsorption on extracellular DNA reveals its interaction mechanism. Colloids Surf B Biointerfaces 2019; 183:110431. [PMID: 31421405 DOI: 10.1016/j.colsurfb.2019.110431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 10/26/2022]
Abstract
Extracellular DNA (eDNA), which is commonly detected in aquatic and terrestrial environments, may be involved in gene transfer, increases in genetic diversity, and evolution. However, it has been reported that some small organic molecules or heavy metal ions can influence the transformation of DNA and even destroy its structure. We previously found that tylosin (TYL, a kind of antibiotic) is adsorbed onto salmon sperm DNA in a mixed solution. However, it is not clear whether this antibiotic affects the structure of DNA, and the mechanism of their interaction needs to be clarified. Therefore, we investigated the adsorption of TYL on different concentrations of salmon sperm DNA using agarose gel electrophoresis, ultraviolet-visible (UV-vis) spectroscopy, fluorescence spectroscopy, and surface enhanced Raman spectroscopy (SERS) to elucidate the interaction mechanism between TYL and DNA. The results showed that the adsorption of TYL decreased with increased concentrations of DNA. The electrophoresis band of pristine DNA was at 5000 bps. The brightness of the DNA band decreased with the TYL concentration and their incubation time. As the concentration of TYL increased, the fluorescence absorption intensity of DNA decreased significantly. Redshift and hyperchromicity were observed in the UV-vis adsorption spectrum with the presence of TYL in DNA solution, and they weakened as the DNA concentration increased. The Raman spectrum intensities of characteristic peaks in the mixed solution were weaker than that of pure TYL solution, and the peak intensity increased with increasing DNA concentration. Even a part of TYL characteristic peaks disappeared in the mixed solution. These results indicated that the pyran and macrolide of TYL might intercalate into the base pair plane of DNA. In addition, electrostatic attraction between TYL and DNA and interactions among TYL molecules may also play a role in the interaction mechanism. However, the double helix structure of DNA was not subject to the interaction of TYL.
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Affiliation(s)
- Qian Zhang
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, 541000, China
| | - Qiuyan Peng
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, 541000, China; College of Environmental Science and Engineering, Guilin University of Technology, Guilin, Guangxi, 541000, China
| | - Xiaohua Shu
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, Guangxi, 541000, China.
| | - Deqing Mo
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, 541000, China
| | - Dongyun Jiang
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, 541000, China
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Sheng X, Qin C, Yang B, Hu X, Liu C, Waigi MG, Li X, Ling W. Metal cation saturation on montmorillonites facilitates the adsorption of DNA via cation bridging. CHEMOSPHERE 2019; 235:670-678. [PMID: 31276880 DOI: 10.1016/j.chemosphere.2019.06.159] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/02/2019] [Accepted: 06/21/2019] [Indexed: 05/19/2023]
Abstract
Extracellular DNA (eDNA) is widely present in soil, with potential ecological impacts. Metal cations are naturally present on the surface of soil clay minerals, although the adsorption mechanism of eDNA on clay minerals saturated with metal cations is still not fully understood. The research investigated the adsorption of eDNA, using salmon sperm DNA as a representative, on metal cation (Na+, Ca2+, and Fe3+)-saturated montmorillonites (Mt). Metal cation-saturated Mt have higher adsorption capacities for DNA. Compared with Mt (3500 mg⋅kg-1), the amounts of DNA adsorption on metal cation-saturated Mt (pH = 7.0) were increased by 0.74-5.38 times, and followed the descending order of Fe-Mt > Na-Mt > Ca-Mt > Mt. A temperature of 25 °C was found to be more suitable than 15 and 35 °C for DNA adsorption, while an increasing pH value (3.0-9.0) reduced DNA adsorption on Mt and metal cation-saturated Mt. Microscopic and spectroscopic analyses, together with a model computation technique, confirmed that metal cations saturated on the surface of Mt work like a "cation bridge" linking oxygen atoms in the phosphate groups of DNA and the negatively charged moieties of Mt, which were predominantly bound through electrostatic forces, thus, facilitating DNA adsorption at pH > 5. The results of this investigation provide valuable insight into eDNA adsorption on soil clay minerals and the transport and fate of eDNA in the natural soil environment.
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Affiliation(s)
- Xue Sheng
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Cun Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210023, China
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xuelin Li
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China.
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Zhai H, Wang L, Putnis CV. Molecular-Scale Investigations Reveal Noncovalent Bonding Underlying the Adsorption of Environmental DNA on Mica. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:11251-11259. [PMID: 31478650 DOI: 10.1021/acs.est.9b04064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mineral-soil organic matter (SOM including DNA, proteins, and polysaccharides) associations formed through various interactions, play a key role in regulating long-term SOM preservation. The mechanisms underlying DNA-mineral and DNA-protein/polysaccharide interactions at nanometer and molecular scales in environmentally relevant solutions remain uncertain. Here, we present a model mineral-SOM system consisting of mineral (mica)-nucleic acid (environmental DNA, eDNA)/protein (bovine serum albumin)/polysaccharide (alginate), and combine atomic force microscopy (AFM)-based dynamic force spectroscopy and PeakForce quantitative nanomechanical mapping using DNA-decorated tips. Single-molecule binding and adhesion force of eDNA to mineral and to mineral adsorbed by protein/polysaccharide reveal the noncovalent bonds and that systematically changing ion compositions, ionic strength, and pH result in significant differences in organic-organic and organic-mineral binding energies. Consistent with the bond-strength measurements, protein, rather than polysaccharide, promotes mineral-bound DNA molecules by ex situ AFM deposition observations in relatively high concentrations of divalent cation-containing acidic solutions. These molecular-scale determinations and nanoscale observations should substantially improve our understanding of how environmental factors influence the organic-mineral interfacial interactions through the synergy of collective noncovalent and/or covalent bonds in mineral-organic associations.
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Affiliation(s)
- Hang Zhai
- College of Resources and Environment , Huazhong Agricultural University , Wuhan 430070 , China
| | - Lijun Wang
- College of Resources and Environment , Huazhong Agricultural University , Wuhan 430070 , China
| | - Christine V Putnis
- Institut für Mineralogie , University of Münster , 48149 Münster , Germany
- Department of Chemistry , Curtin University , Perth 6845 , Australia
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Dong P, Wang H, Fang T, Wang Y, Ye Q. Assessment of extracellular antibiotic resistance genes (eARGs) in typical environmental samples and the transforming ability of eARG. ENVIRONMENT INTERNATIONAL 2019; 125:90-96. [PMID: 30711653 DOI: 10.1016/j.envint.2019.01.050] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/27/2018] [Accepted: 01/20/2019] [Indexed: 05/25/2023]
Abstract
The emergence and spread of antibiotic resistance has pose a huge threat to both human health and environmental ecosystem. However, little is known regarding the pool of ARGs in extracellular DNA (eDNA). In this study ten ARGs (sul1, sul2, tetW, tetX, ermA, ermB, blaTEM, ampC, cat and cmr) and class I integron (intI1) in the sludge from hospital, pharmaceutical industry, wastewater treatment plant (WWTP), and swine manure, and sediment in urban lake in the form of both eDNA and intracellular DNA (iDNA) were evaluated by quantitative polymerase chain reaction (qPCR). The results showed that every gram of sludge dry weight contained from 7.31 × 103 to 1.16 × 1010 copies of extracellular ARGs (eARGs) and from 1.04 × 105 to 2.74 × 1012 copies of intracellular ARGs (iARGs). The sludge from hospital with the highest ratio of eARGs to total ARGs (11.02-89.63%), followed by the sediment from urban lake, implying that most of the ARGs in these regions were contributed by eARGs. The relative abundance of eARGs were higher than iARGs in sludge from WWTP and pharmaceutical industry, moreover, 1/3 and 5/9 detected eARGs were higher than the ARGs in the iDNA extracted from sludge of hospital and sediment from urban lake, respectively. Furthermore, the transforming ability of eARGs suggesting that adsorbed eARG is more preferentially coupled to the competent cells than free eARG. These findings highlight the need to focus attention on the contribution of eARGs to the dissemination of antibiotic resistance into environment, and also future needs in mitigating the spread of eARGs in the environment.
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Affiliation(s)
- Peiyan Dong
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Tingting Fang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yun Wang
- College of Life Science, Shihezi University, Shihezi 832003, China; School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, China
| | - Quanhui Ye
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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Lamori JG, Xue J, Rachmadi AT, Lopez GU, Kitajima M, Gerba CP, Pepper IL, Brooks JP, Sherchan S. Removal of fecal indicator bacteria and antibiotic resistant genes in constructed wetlands. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:10188-10197. [PMID: 30758793 DOI: 10.1007/s11356-019-04468-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/03/2019] [Indexed: 06/09/2023]
Abstract
Wastewater discharge evidently increased bacterial diversity in the receiving waterbodies. The objective of this study was to evaluate the effectiveness of a constructed wetland in reducing fecal indicator bacteria (FIB) and antibiotic resistant genes (ARGs). We determined the prevalence and attenuation of fecal indicator bacteria including Escherichia coli and enterococci, along with ARGs, and human-associated Bacteroidales (HF183) markers by quantitative polymerase chain reaction (qPCR) method. Three types of water samples (inlet, intermediate, and outlet) from a constructed wetland were collected once a month from May to December in 2013. The overall reduction of E. coli was 50.0% based on culture method. According to the qPCR result, the overall removal rate of E. coli was only 6.7%. Enterococci were found in 62.5% of the wetland samples. HF183 genetic marker was detected in all final effluent samples with concentration ranging from 1.8 to 4.22 log10 gene copies (GC)/100 ml. Of the ARGs tested, erythromycin resistance genes (ermF) were detected in 79.2% of the wetland samples. The class 1 integrase (intI1) was detected in all water samples with concentration ranging from 0.83 to 5.54 log10 GC/100 ml. The overall removal rates of enterococci, HF183, intI1, and ermF were 84.0%, 66.6%, 67.2%, and 13.1%, respectively.
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Affiliation(s)
- Jennifer G Lamori
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Jia Xue
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Andri T Rachmadi
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North13 West8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Gerardo U Lopez
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North13 West8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Charles P Gerba
- Department of Soil, Water and Environmental Science, The University of Arizona, 1117 E. Lowell St., Tucson, AZ, 85721, USA
| | - Ian L Pepper
- Department of Soil, Water and Environmental Science, The University of Arizona, 1117 E. Lowell St., Tucson, AZ, 85721, USA
- Water and Energy Sustainable Technology (WEST) Center, The University of Arizona, 2959 West Calle Agua Nueva, Tucson, AZ, 85745, USA
| | - John P Brooks
- Genetics and Sustainable Agriculture Unit, USDA-ARS, Mississippi State, MS, 39762, USA
| | - Samendra Sherchan
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA.
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He H, Zhou P, Shimabuku KK, Fang X, Li S, Lee Y, Dodd MC. Degradation and Deactivation of Bacterial Antibiotic Resistance Genes during Exposure to Free Chlorine, Monochloramine, Chlorine Dioxide, Ozone, Ultraviolet Light, and Hydroxyl Radical. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:2013-2026. [PMID: 30712343 DOI: 10.1021/acs.est.8b04393] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
This work investigated degradation (measured by qPCR) and biological deactivation (measured by culture-based natural transformation) of extra- and intracellular antibiotic resistance genes (eARGs and iARGs) by free available chlorine (FAC), NH2Cl, O3, ClO2, and UV light (254 nm), and of eARGs by •OH, using a chromosomal ARG ( blt) of multidrug-resistant Bacillus subtilis 1A189. Rate constants for degradation of four 266-1017 bp amplicons adjacent to or encompassing the acfA mutation enabling blt overexpression increased in proportion to #AT+GC bps/amplicon, or in proportion to #5'-GG-3' or 5'-TT-3' doublets/amplicon, with respective values ranging from 0.59 to 2.3 (×1011 M-1 s-1) for •OH, 1.8-6.9 (×104 M-1 s-1) for O3, 3.9-9.2 (×103 M-1 s-1) for FAC, 0.35-1.2(×101 M-1 s-1) for ClO2, and 2.0-8.8 (×10-2 cm2/mJ) for UV at pH 7, and from 1.7-4.4 M-1 s-1 for NH2Cl at pH 8. For FAC, NH2Cl, O3, ClO2, and UV, ARG deactivation paralleled degradation of amplicons approximating a ∼800-1000 bp acfA-flanking sequence required for natural transformation in B. subtilis, whereas deactivation outpaced degradation for •OH. At practical disinfectant exposures, eARGs and iARGs were ≥90% degraded/deactivated by FAC, O3, and UV, but recalcitrant to NH2Cl and ClO2. iARG degradation/ deactivation always lagged cell inactivation. These findings provide a quantitative framework for evaluating ARG fate during disinfection/oxidation, and support using qPCR as a proxy for tracking ARG deactivation under carefully selected circumstances.
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Affiliation(s)
- Huan He
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Peiran Zhou
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Kyle K Shimabuku
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Xuzhi Fang
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Shu Li
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Yunho Lee
- School of Earth Sciences and Environmental Engineering , Gwangju Institute of Science and Technology (GIST) , Gwangju 61005 , Republic of Korea
| | - Michael C Dodd
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
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Mineral Surface-Templated Self-Assembling Systems: Case Studies from Nanoscience and Surface Science towards Origins of Life Research. Life (Basel) 2018; 8:life8020010. [PMID: 29738443 PMCID: PMC6027067 DOI: 10.3390/life8020010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/26/2018] [Accepted: 05/03/2018] [Indexed: 01/20/2023] Open
Abstract
An increasing body of evidence relates the wide range of benefits mineral surfaces offer for the development of early living systems, including adsorption of small molecules from the aqueous phase, formation of monomeric subunits and their subsequent polymerization, and supramolecular assembly of biopolymers and other biomolecules. Each of these processes was likely a necessary stage in the emergence of life on Earth. Here, we compile evidence that templating and enhancement of prebiotically-relevant self-assembling systems by mineral surfaces offers a route to increased structural, functional, and/or chemical complexity. This increase in complexity could have been achieved by early living systems before the advent of evolvable systems and would not have required the generally energetically unfavorable formation of covalent bonds such as phosphodiester or peptide bonds. In this review we will focus on various case studies of prebiotically-relevant mineral-templated self-assembling systems, including supramolecular assemblies of peptides and nucleic acids, from nanoscience and surface science. These fields contain valuable information that is not yet fully being utilized by the origins of life and astrobiology research communities. Some of the self-assemblies that we present can promote the formation of new mineral surfaces, similar to biomineralization, which can then catalyze more essential prebiotic reactions; this could have resulted in a symbiotic feedback loop by which geology and primitive pre-living systems were closely linked to one another even before life’s origin. We hope that the ideas presented herein will seed some interesting discussions and new collaborations between nanoscience/surface science researchers and origins of life/astrobiology researchers.
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46
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Progressive biogeochemical transformation of placer gold particles drives compositional changes in associated biofilm communities. FEMS Microbiol Ecol 2018; 94:4992300. [DOI: 10.1093/femsec/fiy080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/01/2018] [Indexed: 11/14/2022] Open
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Prosser CM, Hedgpeth BM. Effects of bioturbation on environmental DNA migration through soil media. PLoS One 2018; 13:e0196430. [PMID: 29689092 PMCID: PMC5915775 DOI: 10.1371/journal.pone.0196430] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/12/2018] [Indexed: 01/03/2023] Open
Abstract
Extracting and identifying genetic material from environmental media (i.e. water and soil) presents a unique opportunity for researchers to assess biotic diversity and ecosystem health with increased speed and decreased cost as compared to traditional methods (e.g. trapping). The heterogeneity of soil mineralogy, spatial and temporal variations however present unique challenges to sampling and interpreting results. Specifically, fate/transport of genetic material in the terrestrial environment represents a substantial data gap. Here we investigate to what degree, benthic fauna transport genetic material through soil. Using the red worm (Eisenia fetida), we investigate how natural movement through artificial soil affect the transport of genetic material. All experiments were run in Frabill® Habitat® II worm systems with approximately 5 cm depth of artificial soil. We selected an “exotic” source of DNA not expected to be present in soil, zebrafish (Danio rerio) tissue. Experiment groups contained homogenized zebrafish tissue placed in a defined location combined with a varying number of worms (10, 30 or 50 worms per experimental group). Experimental groups comprised two controls and three treatment groups (representing different worm biomass) in triplicate. A total of 210 soil samples were randomly collected over the course of 15 days to investigate the degree of genetic transfer, and the rate of detection. Positive detections were identified in 14% - 38% of samples across treatment groups, with an overall detection rate of 25%. These findings highlight two important issues when utilizing environmental DNA for biologic assessments. First, benthic fauna are capable of redistributing genetic material through a soil matrix. Second, despite a defined sample container and abundance of worm biomass, as many as 86% of the samples were negative. This has substantial implications for researchers and managers who wish to interpret environmental DNA results from terrestrial systems. Studies such as these will aid in future study protocol design and sample collection methodology.
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Affiliation(s)
- Christopher M. Prosser
- ExxonMobil Biomedical Sciences Incorporated, Annandale, NJ, United States of America
- * E-mail:
| | - Bryan M. Hedgpeth
- ExxonMobil Biomedical Sciences Incorporated, Annandale, NJ, United States of America
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48
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Zhen H, Krumins V, Fennell DE, Mainelis G. Analysis of airborne microbial communities using 16S ribosomal RNA: Potential bias due to air sampling stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 621:939-947. [PMID: 29079080 PMCID: PMC5805565 DOI: 10.1016/j.scitotenv.2017.10.154] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/11/2017] [Accepted: 10/15/2017] [Indexed: 05/16/2023]
Abstract
A limited number of studies have been conducted to analyze ribosomal RNA (rRNA, present in the ribosome) in bioaerosol samples to identify currently or potentially active airborne microbes, although its genomic counterpart, the rRNA gene (on the chromosome) has been frequently targeted for airborne microbial community analysis. A knowledge gap still exists regarding whether the bioaerosol rRNA abundances are affected by the bioaerosol collection process. We investigated the effect of air sampling stress on the measurement and characterization of 16S rRNA for bioaerosols in the laboratory and field experiments using quantitative polymerase chain reaction (qPCR) and high-throughput sequencing techniques. In a laboratory study, known quantities of freshly grown Escherichia coli cells were spiked onto the filter of a Button Aerosol Sampler and into liquids of BioSampler and SpinCon air samplers and then exposed to sampling stress when the samplers were operated for 2h. We found that the recovered cellular 16S rRNA abundance as determined by qPCR was dependent on sampler type. Further, two devices (Button Aerosol Sampler and BioSampler) that exhibited markedly different efficiency in preserving 16S rRNA were employed in an outdoor environment to collect bioaerosols simultaneously on eight days in two different seasons. The abundance of 16S rRNA in the outdoor air sample (1.3×106-4.9×107copies/m3) was about two orders of magnitude higher than that of 16S rRNA gene (6.9×103-1.5×105copies/m3). The 16S rRNA sequences revealed a different bacterial community compared with 16S rRNA gene-based results across all samples, and this difference depended on the sampling device. In addition, a number of bacterial taxa exhibited higher abundance in the 16S rRNA gene sequences than in 16S rRNA sequences, which suggests the potential activities of certain microbes in airborne phase. Overall, this study highlights the importance of sampling device selection when analyzing RNA in bioaerosols.
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Affiliation(s)
- Huajun Zhen
- Rutgers University, Department of Environmental Sciences, 14 College Farm Rd., New Brunswick, NJ 08901, United States
| | - Valdis Krumins
- Rutgers University, Department of Environmental Sciences, 14 College Farm Rd., New Brunswick, NJ 08901, United States
| | - Donna E Fennell
- Rutgers University, Department of Environmental Sciences, 14 College Farm Rd., New Brunswick, NJ 08901, United States
| | - Gediminas Mainelis
- Rutgers University, Department of Environmental Sciences, 14 College Farm Rd., New Brunswick, NJ 08901, United States.
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49
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Xue J, Feng Y. Determination of adsorption and desorption of DNA molecules on freshwater and marine sediments. J Appl Microbiol 2018; 124:1480-1492. [DOI: 10.1111/jam.13739] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/30/2018] [Accepted: 02/15/2018] [Indexed: 01/30/2023]
Affiliation(s)
- J. Xue
- Department of Crop, Soil and Environmental Sciences; Auburn University; Auburn AL USA
| | - Y. Feng
- Department of Crop, Soil and Environmental Sciences; Auburn University; Auburn AL USA
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50
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Yamaguchi N, Anraku S, Paineau E, Safinya CR, Davidson P, Michot LJ, Miyamoto N. Swelling Inhibition of Liquid Crystalline Colloidal Montmorillonite and Beidellite Clays by DNA. Sci Rep 2018. [PMID: 29531235 PMCID: PMC5847546 DOI: 10.1038/s41598-018-22386-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Exploring the interaction of nucleic acids with clay minerals is important to understand such issues as the persistence in soils of biomolecules and the appearance of genetic polymers in prebiotic environments. Colloidal dispersions of double stranded DNA and clay nanosheets may also provide interesting model systems to study the statistical physics of mixtures of semi-flexible rods and plates. Here, we show that adding very small amounts of DNA to liquid-crystalline montmorillonite and beidellite smectite clay suspensions strongly widens the isotropic/nematic phase coexistence region. Moreover, a spectroscopic study shows that, upon DNA addition, the first DNA molecules adsorb onto the clay particles. Remarkably, synchrotron small-angle X-ray scattering experiments reveal that the average distance between the clay sheets, in the nematic phase at coexistence, decreases with increasing DNA concentration and that the inhibition of swelling by DNA becomes almost independent of clay concentration. We interpret this DNA-mediated attraction between clay nanosheets by bridging conformations of DNA strands (plates on a string structure). In addition to bridging, DNA chains can form “loops” between sections adsorbed on the same particle, giving rise to sheet repulsions due to protruding loops. This interpretation agrees with the observed inter-clay spacings being dependent only on the DNA concentration.
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Affiliation(s)
- Naoya Yamaguchi
- Fukuoka Institute of Technology, Department of Life, Environment and Materials Science, 3-30-1 Wajirohigashi, Higashiku, Fukuoka, 811-0295, Japan
| | - Shinya Anraku
- Fukuoka Institute of Technology, Department of Life, Environment and Materials Science, 3-30-1 Wajirohigashi, Higashiku, Fukuoka, 811-0295, Japan
| | - Erwan Paineau
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - Cyrus R Safinya
- Physics Department, Materials Department, and Molecular, Cellular and Developmental Biology Department, University of California, Santa Barbara, California, 93106, United States
| | - Patrick Davidson
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France.
| | - Laurent J Michot
- Laboratoire Phenix, CNRS-Sorbonne Université-UPMC, UMR 8234, 4, Place Jussieu, 75252, Paris Cedex 5, France
| | - Nobuyoshi Miyamoto
- Fukuoka Institute of Technology, Department of Life, Environment and Materials Science, 3-30-1 Wajirohigashi, Higashiku, Fukuoka, 811-0295, Japan.
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