1
|
Skalny M, Rokowska A, Szuwarzynski M, Gajewska M, Dziewit L, Bajda T. Nanoscale surface defects of goethite governing DNA adsorption process and formation of the Goethite-DNA conjugates. CHEMOSPHERE 2024; 362:142602. [PMID: 38871190 DOI: 10.1016/j.chemosphere.2024.142602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]
Abstract
In urbanized areas, extracellular DNA (exDNA) is suspected of carrying genes with undesirable traits like virulence genes (VGs) or antibiotic resistance genes (ARGs), which can spread through horizontal gene transfer (HGT). Hence, it is crucial to develop novel approaches for the mitigation of exDNA in the environment. Our research explores the role of goethite, a common iron mineral with high adsorption capabilities, in exDNA adsorption processes. We compare well-crystalline, semi-crystalline, and nano goethites with varying particle sizes to achieve various specific surface areas (SSAs) (18.7-161.6 m2/g) and porosities. We conducted batch adsorption experiments using DNA molecules of varying chain lengths (DNA sizes: <11 Kb, <6 Kb, and <3 Kb) and assessed the impact of Ca2+ and biomacromolecules on the adsorption efficacy and mechanisms. Results show that porosity and pore structure significantly influence DNA adsorption capacity. Goethite with well-developed meso- and macroporosity demonstrated enhanced DNA adsorption. The accumulation of DNA on the goethite interface led to substantial aggregation in the system, thus the formation of DNA-goethite conjugates, indicating the bridging between mineral particles. DNA chain length, the presence of Ca2+, and the biomacromolecule matrix also affected the adsorption capacity and mechanism. Interactions between DNA and positively charged biomacromolecules or Ca2+ led to DNA compaction, allowing greater DNA accumulation in pores. However, a high concentration of biomacromolecules led to the saturation of the goethite surface, inhibiting DNA adsorption. AFM imaging of goethite particles after adsorption suggested the formation of the DNA multilayer. The study advances understanding of the environmental behavior of exDNA and its interaction with iron oxyhydroxides, offering insights into developing more effective methods for ARGs removal in wastewater treatment plants. By manipulating the textural properties of goethite, it's possible to enhance exDNA removal, potentially reducing the spread of biocontamination in urban and industrial environments.
Collapse
Affiliation(s)
- Mateusz Skalny
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland.
| | - Anna Rokowska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Michal Szuwarzynski
- Academic Centre for Materials and Nanotechnology, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland
| | - Marta Gajewska
- Academic Centre for Materials and Nanotechnology, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Bajda
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Thomas R, Ghosh D, Pulimi M, Nirmala J, Anand S, Rai PK, Mukherjee A. Investigating the transport and colloidal behavior of Fe 3O 4 nanoparticles in aqueous and porous media under varying solution chemistry parameters. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:118693-118705. [PMID: 37917261 DOI: 10.1007/s11356-023-30628-z] [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: 07/21/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023]
Abstract
The possible adverse effects of engineered iron oxide nanoparticles, especially magnetite (Fe3O4 NP), on human health and the environment, have raised concerns about their transport and behavior in soil and water systems. Accumulating these NPs in the environment can substantially affect soil and water quality and the well-being of aquatic and terrestrial organisms. Therefore, it is essential to examine the factors that affect Fe3O4 NP transportation and behavior in soil and water systems to determine their possible environmental fate. In this work, experiments were conducted in aqueous and porous media using an environmentally relevant range of pH (5, 7, 9), ionic strength (IS) (10, 50, 100 mM), and humic acid (HA) (0.1, 1, 10 mg L-1) concentrations. Fe3O4 NPs exhibited severe colloidal instability at pH 7 (⁓ = pHPZC) and showed an improvement in apparent colloidal stability at pH 5 and 9 in aquatic and terrestrial environments. HA in the background solutions promoted the overall transport of Fe3O4 NPs by enhancing the colloidal stability. The increased ionic strength in aqueous media hindered the transport by electron double-layer compression and electrostatic repulsion; however, in porous media, the transport was hindered by ionic compression. Furthermore, the transport behavior of Fe3O4 NPs was investigated in different natural waters such as rivers, lakes, taps, and groundwater. The interaction energy pattern in aquatic systems was estimated using the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. This study showed the effects of various physical-chemical conditions on Fe3O4 NP transport in aqueous and porous (sand) media.
Collapse
Affiliation(s)
- Reetha Thomas
- Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Debayan Ghosh
- Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Mrudula Pulimi
- Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Joyce Nirmala
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, India
| | - Shalini Anand
- Centre for Fire, Explosive and Environment Safety, Timarpur, Delhi, India
| | - Pramod Kumar Rai
- Centre for Fire, Explosive and Environment Safety, Timarpur, Delhi, India
| | - Amitava Mukherjee
- Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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: 20] [Impact Index Per Article: 10.0] [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.
Collapse
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
| |
Collapse
|