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Kariyawasam NL, Wereszczynski J. The Influence of Ionic Environment on Nucleosome-Mica Interactions Revealed via Molecular Dynamics Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600666. [PMID: 38979319 PMCID: PMC11230366 DOI: 10.1101/2024.06.25.600666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Mica serves as a crucial substrate in Atomic Force Microscopy (AFM) studies for visualizing and characterizing nucleosomes. Nucleosomes interact with the negatively charged mica surface via adsorbed cations. However, the specific influences of monovalent and divalent cations on nucleosome adsorption to the mica surface remain unclear. In this study, we investigated the binding of nucleosomes to the mica surface in the presence of monovalent potassium ions and divalent magnesium ions using molecular dynamics simulations. We also explored the impact of pre-treated mica surfaces on nucleosome binding and structure. Our findings reveal that nucleosome-mica interactions vary depending on the cations present, resulting in distinct effects on nucleosome structure. Notably, nucleosomes bind effectively to a mica surface in the presence of potassium ions with minimal structural perturbations.
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Affiliation(s)
- Nilusha L Kariyawasam
- Department of Physics, Illinois Institute of Technology, Chicago, USA
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, USA
| | - Jeff Wereszczynski
- Departments of Physics and Biology, Illinois Institute of Technology, Chicago, USA
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, USA
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2
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Cochran JP, Zhang L, Parrott BB, Seaman JC. Plasmid size determines adsorption to clay and breakthrough in a saturated sand column. Heliyon 2024; 10:e29679. [PMID: 38707295 PMCID: PMC11066139 DOI: 10.1016/j.heliyon.2024.e29679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 05/07/2024] Open
Abstract
Horizontal gene transfer (HGT) is a major factor in the spread of antibiotic resistant genes (ARG). Transformation, one mode of HGT, involves the acquisition and expression of extracellular DNA (eDNA). eDNA in soils is degraded rapidly by extracellular nucleases. However, if bound to a clay particle, eDNA can persist for long periods of time without losing its transformation ability. To better understand the mechanism of eDNA persistence in soil, this experiment assessed the effects of 1) clay mineralogy, 2) mixed salt solution, 3) plasmid size on DNA adsorption to clay and 4) breakthrough behavior of three differently sized plasmids in an environmentally relevant solution. Batch test methods were used to determine adsorption trends of three differently sized DNA plasmids, pUC19, pBR322, and pTYB21, to several pure clay minerals, goethite (α-FeOOH), illite, and kaolinite, and one environmental soil sample. Results show not all sorbents have equal adsorption capacity based on surface area with adsorption capacities decreasing from goethite > illite = kaolinite > bulk soil, and low ionic strength solutions will likely not significantly alter sorption trends. Additionally, plasmid DNA size (i.e., length) was shown to be a significant predictor of adsorption efficiency and that size affects DNA breakthrough, with breakthroughs occurring later with larger plasmids. Given that DNA persistence is linked to its adsorption to soil constituents and breakthrough, eDNA size is likely an important contributor to the spread of ARG within natural microbial communities.
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Affiliation(s)
- Jarad P. Cochran
- Savannah River Ecology Laboratory, Aiken, SC, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
| | - Liyun Zhang
- Savannah River Ecology Laboratory, Aiken, SC, United States
- Crops and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Benjamin B. Parrott
- Savannah River Ecology Laboratory, Aiken, SC, United States
- Odum School of Ecology, University of Georgia, Athens, GA, United States
| | - John C. Seaman
- Savannah River Ecology Laboratory, Aiken, SC, United States
- Crops and Soil Sciences, University of Georgia, Athens, GA, United States
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3
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Zhang J, Huang L, Wang Y. Changes in the level of biofilm development significantly affect the persistence of environmental DNA in flowing water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170162. [PMID: 38244634 DOI: 10.1016/j.scitotenv.2024.170162] [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: 10/12/2023] [Revised: 12/27/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024]
Abstract
As one of the powerful tools of species biomonitoring, the utilization of environmental DNA (eDNA) technology is progressively expanding in both scope and frequency within the field of ecology. Nonetheless, the growing dissemination of this technology has brought to light a multitude of intricate issues. The complex effects of environmental factors on the persistence of eDNA in water have brought many challenges to the interpretation of eDNA information. In this study, the primary objective was to examine how variations in the presence and development of biofilms impact the persistence of grass carp eDNA under different sediment types and flow conditions. This investigation encompassed the processes of eDNA removal and resuspension in water, shedding light on the complex interactions involved. The findings reveal that with an elevated biofilm development level, the total removal rate of eDNA gradually rose, resulting in a corresponding decrease in its residence time within the mesocosms. The influence of biofilms on the persistence of grass carp eDNA is more pronounced under flowing water conditions. However, changes in bottom sediment types did not significantly interact with biofilms. Lastly, in treatments involving alternating flow conditions between flowing and still water, significant resuspension of grass carp eDNA was not observed due to interference from multiple factors, including the effect of biofilms. Our study offers preliminary insights into the biofilm-mediated mechanisms of aquatic eDNA removal, emphasizing the need for careful consideration of environmental factors in the practical application of eDNA technology for biomonitoring in natural aquatic environments.
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Affiliation(s)
- Jianmin Zhang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, First Ring Road 24#, Chengdu 610065, People's Republic of China.
| | - Lei Huang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, First Ring Road 24#, Chengdu 610065, People's Republic of China.
| | - Yurong Wang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, First Ring Road 24#, Chengdu 610065, People's Republic of 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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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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Wegner CE, Stahl R, Velsko I, Hübner A, Fagernäs Z, Warinner C, Lehmann R, Ritschel T, Totsche KU, Küsel K. A glimpse of the paleome in endolithic microbial communities. MICROBIOME 2023; 11:210. [PMID: 37749660 PMCID: PMC10518947 DOI: 10.1186/s40168-023-01647-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/09/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards. RESULTS By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 105 cells × g-1 rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past. CONCLUSIONS Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.
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Affiliation(s)
- Carl-Eric Wegner
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Irina Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Alex Hübner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Zandra Fagernäs
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Robert Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Thomas Ritschel
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Kai U Totsche
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.
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7
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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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8
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Zhu Y, Liu Z, Hu B, Zhu L. Partitioning and migration of antibiotic resistance genes at soil-water-air interface mediated by plasmids. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121557. [PMID: 37019265 DOI: 10.1016/j.envpol.2023.121557] [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: 01/13/2023] [Revised: 03/13/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
The partitioning and migration of antibiotic resistance genes (ARGs) at the interfaces of soil, water, and air play a critical role in the environmental transmission of antibiotic resistance. This study investigated the partitioning and migration of resistant plasmids as representatives of extracellular-ARGs (eARGs) in artificially constructed soil-water-air systems. Additionally, it quantitatively studied the influence of soil pH, clay mineral content, organic matter content, and simulated rainfall on the migration of eARGs via orthogonal experiments. The findings revealed that the sorption equilibrium between eARGs and soil can be attained within 3 h, following the two-compartment first-order kinetic model. The average partition ratio of eARGs in soil, water, and air is 7:2:1, and soil pH and clay mineral content are identified as the main influencing factors. The proportion of eARGs migrating from soil to water and air is 8.05% and 0.52%, respectively. Correlation and significance analyses showed that soil pH has a significant impact on the soil-water and soil-air mobility of eARGs, while clay content affects the percentage of peaks during migration. Moreover, rainfall exerts a noticeable impact on the timing of peaks during migration. This study provided quantitative insights into the proportion of eARGs in soil, water, and air and elucidated the key factors influencing the partitioning and migration of eARGs from the perspectives of the sorption mechanism.
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Affiliation(s)
- Yang Zhu
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou, 310058, China.
| | - Zishu Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Baolan Hu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Lizhong Zhu
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou, 310058, China.
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9
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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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Jiang H, Zhang L, Wang X, Gu J, Song Z, Wei S, Guo H, Xu L, Qian X. Reductions in abundances of intracellular and extracellular antibiotic resistance genes by SiO 2 nanoparticles during composting driven by mobile genetic elements. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 341:118071. [PMID: 37148762 DOI: 10.1016/j.jenvman.2023.118071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/08/2023]
Abstract
Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO2 nanoparticles (SiO2NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO2NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_stricto_1, Terrisporobacter, and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i-intI1 and e-Tn916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO2NPs to reduce the propagation of ARGs.
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Affiliation(s)
- Haihong Jiang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China; School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, Guangdong, 510000, China
| | - Li Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Engineering Research Center of Utilization of Agricultural Waste Resources, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Engineering Research Center of Utilization of Agricultural Waste Resources, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zilin Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Engineering Research Center of Utilization of Agricultural Waste Resources, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shumei Wei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Honghong Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Liang Xu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
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11
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D'Agostino A, Di Marco G, Marvelli S, Marchesini M, Rizzoli E, Rolfo MF, Canini A, Gismondi A. Neolithic dental calculi provide evidence for environmental proxies and consumption of wild edible fruits and herbs in central Apennines. Commun Biol 2022; 5:1384. [PMID: 36536113 PMCID: PMC9763411 DOI: 10.1038/s42003-022-04354-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Looking for a biological fingerprint relative to new aspects of the relationship between humans and natural environment during prehistoric times is challenging. Although many issues still need to be addressed in terms of authentication and identification, microparticles hidden in ancient dental calculus can provide interesting information for bridging this gap of knowledge. Here, we show evidence about the role of edible plants for the early Neolithic individuals in the central Apennines of the Italian peninsula and relative cultural landscape. Dental calculi from human and animal specimens exhumed at Grotta Mora Cavorso (Lazio), one of the largest prehistoric burial deposits, have returned an archaeobotanical record made up of several types of palaeoecological proxies. The organic fraction of this matrix was investigated by a multidisciplinary approach, whose novelty consisted in the application of next generation sequencing to ancient plant DNA fragments, specifically codifying for maturase K barcode gene. Panicoideae and Triticeae starches, together with genetic indicators of Rosaceae fruits, figs, and Lamiaceae herbs, suggested subsistence practices most likely still based on wild plant resources. On the other hand, pollen, and non-pollen palynomorphs allowed us to outline a general vegetational framework dominated by woodland patches alternated with meadows, where semi-permanent settlements could have been established.
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Affiliation(s)
- Alessia D'Agostino
- PhD Program in Evolutionary Biology and Ecology, Department of Biology, University of Rome Tor Vergata, Rome, Italy
- Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Gabriele Di Marco
- Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Silvia Marvelli
- Laboratorio di Palinologia e Archeobotanica-C.A.A. Giorgio Nicoli, San Giovanni in Persiceto, Bologna, Italy
| | - Marco Marchesini
- Laboratorio di Palinologia e Archeobotanica-C.A.A. Giorgio Nicoli, San Giovanni in Persiceto, Bologna, Italy
| | - Elisabetta Rizzoli
- Laboratorio di Palinologia e Archeobotanica-C.A.A. Giorgio Nicoli, San Giovanni in Persiceto, Bologna, Italy
| | - Mario Federico Rolfo
- Department of History, Culture and Society, University of Rome "Tor Vergata", Rome, Italy
| | - Antonella Canini
- Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Angelo Gismondi
- Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
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Andreeva TV, Malyarchuk AB, Soshkina AD, Dudko NA, Plotnikova MY, Rogaev EI. Methodologies for Ancient DNA Extraction from Bones for Genomic Analysis: Approaches and Guidelines. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422090034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Nischwitz V, Stelmaszyk L, Piel S, Tiehm A. Cascade Filtration With PCR Detection and Field-Flow-Fractionation Online With ICP-MS for the Characterization of DNA Interaction With Suspended Particulate Matter. Front Chem 2022; 10:919442. [PMID: 35836676 PMCID: PMC9274009 DOI: 10.3389/fchem.2022.919442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/18/2022] [Indexed: 12/02/2022] Open
Abstract
The variety of applied antibiotics in animal and human medicine results in the release, development, and spread of relevant numbers of antibiotic resistance genes (ARGs) in the environment. The majority of ARGs are present in intracellular forms (in bacteria). Neglected aspects are extracellular variants of ARGs (eARGs) and their fragments, which have been detected in surface-water samples and sediments. The stability of eARGs is expected to be low; however, binding to particulate matter is likely to improve their stability and also affect their transport and dissemination behavior. Few studies have investigated DNA particle interactions, mostly via indirect characterization of adduct formation in model systems but not in real environmental matrices. Therefore, our study aims at a novel approach for direct characterization of desoxyribonucleic acid (DNA) particle interactions using both cascade filtration and field-flow fractionation. Cascade filtration with quantitative polymerase chain reaction (qPCR) detection indicated retention of ARGs on filters with much larger pore sizes supporting the hypothesis of ARG-particle interactions. However, artifacts from membrane clogging or DNA–membrane interaction cannot be excluded. Consequently, asymmetric flow field-flow fractionation was investigated as an alternative separation technique with the advantage of particle separation in a thin channel, reducing the risk of artifacts. The key method parameters, membrane composition, molecular weight cut off, and carrier composition, were systematically investigated using a calf-thymus DNA-spiked surface-water sample as a model. The results clearly showed a shift in the elution time of clay particles suggesting the presence of DNA–clay adducts. Multi-element detection by inductively coupled plasma mass spectrometry (ICP-MS) enabled monitoring of clay via the Al, Fe, and Si signals and DNA via the P signal. Matching peak profiles for the new fraction in the fractograms of the ARG and DNA-spiked water sample support adduct formation. Further evidence was provided by a novel post-channel filtration approach for the separation of free DNA from DNA–clay adducts.
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Affiliation(s)
- Volker Nischwitz
- Central Institute for Engineering, Electronics and Analytics, Analytics (ZEA-3), Forschungszentrum Juelich, Juelich, Germany
- *Correspondence: Volker Nischwitz,
| | - Lara Stelmaszyk
- Department Water Microbiology, TZW: DVGW Technologiezentrum Wasser, Karlsruhe, Germany
| | - Sandra Piel
- Central Institute for Engineering, Electronics and Analytics, Analytics (ZEA-3), Forschungszentrum Juelich, Juelich, Germany
| | - Andreas Tiehm
- Department Water Microbiology, TZW: DVGW Technologiezentrum Wasser, Karlsruhe, Germany
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14
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Han X, Tolu J, Deng L, Fiskal A, Schubert CJ, Winkel LHE, Lever MA. Long-term preservation of biomolecules in lake sediments: potential importance of physical shielding by recalcitrant cell walls. PNAS NEXUS 2022; 1:pgac076. [PMID: 36741427 PMCID: PMC9896894 DOI: 10.1093/pnasnexus/pgac076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/27/2022] [Indexed: 02/07/2023]
Abstract
Even though lake sediments are globally important organic carbon (OC) sinks, the controls on long-term OC storage in these sediments are unclear. Using a multiproxy approach, we investigate changes in diatom, green algae, and vascular plant biomolecules in sedimentary records from the past centuries across five temperate lakes with different trophic histories. Despite past increases in the input and burial of OC in sediments of eutrophic lakes, biomolecule quantities in sediments of all lakes are primarily controlled by postburial microbial degradation over the time scales studied. We, moreover, observe major differences in biomolecule degradation patterns across diatoms, green algae, and vascular plants. Degradation rates of labile diatom DNA exceed those of chemically more resistant diatom lipids, suggesting that chemical reactivity mainly controls diatom biomolecule degradation rates in the lakes studied. By contrast, degradation rates of green algal and vascular plant DNA are significantly lower than those of diatom DNA, and in a similar range as corresponding, much less reactive lipid biomarkers and structural macromolecules, including lignin. We propose that physical shielding by degradation-resistant cell wall components, such as algaenan in green algae and lignin in vascular plants, contributes to the long-term preservation of labile biomolecules in both groups and significantly influences the long-term burial of OC in lake sediments.
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Affiliation(s)
| | - Julie Tolu
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland,Department of Water Resources and Drinking Water, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Longhui Deng
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | | | - Carsten Johnny Schubert
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland,Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Lenny H E Winkel
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland,Department of Water Resources and Drinking Water, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
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15
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Environmental Factors Affecting Feather Taphonomy. BIOLOGY 2022; 11:biology11050703. [PMID: 35625431 PMCID: PMC9138376 DOI: 10.3390/biology11050703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022]
Abstract
The exceptional preservation of feathers in the fossil record has led to a better understanding of both phylogeny and evolution. Here we address factors that may have contributed to the preservation of feathers in ancient organisms using experimental taphonomy. We show that the atmospheres of the Mesozoic, known to be elevated in both CO2 and with temperatures above present levels, may have contributed to the preservation of these soft tissues by facilitating rapid precipitation of hydroxy- or carbonate hydroxyapatite, thus outpacing natural degradative processes. Data also support that that microbial degradation was enhanced in elevated CO2, but mineral deposition was also enhanced, contributing to preservation by stabilizing the organic components of feathers.
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16
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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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17
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Brasell KA, Pochon X, Howarth J, Pearman JK, Zaiko A, Thompson L, Vandergoes MJ, Simon KS, Wood SA. Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.78128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Lake sediments hold a wealth of information from past environments that is highly valuable for paleolimnological reconstructions. These studies increasingly apply modern molecular tools targeting sedimentary DNA (sedDNA). However, sediment core sampling can be logistically difficult, making immediate subsampling for sedDNA challenging. Sediment cores are often refrigerated (4 °C) for weeks or months before subsampling. We investigated the impact of storage time on changes in DNA (purified or as cell lysate) concentrations and shifts in biological communities following storage of lake surface sediment at 4 °C for up to 24 weeks. Sediment samples (~ 0.22 g, in triplicate per time point) were spiked with purified DNA (100 or 200 ng) or lysate from a brackish water cyanobacterium that produces the cyanotoxin nodularin or non-spiked. Samples were analysed every 1–4 weeks over a 24-week period. Droplet digital PCR showed no significant decrease in the target gene (nodularin synthetase – subunit F; ndaF) over the 24-week period for samples spiked with purified DNA, while copy number decreased by more than half in cell lysate-spiked samples. There was significant change over time in bacteria and eukaryotic community composition assessed using metabarcoding. Amongst bacteria, the cyanobacterial signal became negligible after 5 weeks while Proteobacteria increased. In the eukaryotic community, Cercozoa became dominant after 6 weeks. These data demonstrate that DNA yields and community composition data shift significantly when sediments are stored chilled for more than 5 weeks. This highlights the need for rapid subsampling and appropriate storage of sediment core samples for paleogenomic studies.
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18
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Morales-García AL, Walton R, Blakeman JT, Banwart SA, Harding JH, Geoghegan M, Freeman CL, Rolfe SA. The Role of Extracellular DNA in Microbial Attachment to Oxidized Silicon Surfaces in the Presence of Ca 2+ and Na . LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9838-9850. [PMID: 34347486 PMCID: PMC8397393 DOI: 10.1021/acs.langmuir.1c01410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Attachment assays of a Pseudomonas isolate to fused silica slides showed that treatment with DNaseI significantly inhibited cellular adsorption, which was restored upon DNA treatment. These assays confirmed the important role of extracellular DNA (eDNA) adsorption to a surface. To investigate the eDNA adsorption mechanism, single-molecule force spectroscopy (SMFS) was used to measure the adsorption of eDNA to silicon surfaces in the presence of different concentrations of sodium and calcium ions. SMFS reveals that the work of adhesion required to remove calcium-bound eDNA from the silicon oxide surface is substantially greater than that for sodium. Molecular dynamics simulations were also performed, and here, it was shown that the energy gain in eDNA adsorption to a silicon oxide surface in the presence of calcium ions is small and much less than that in the presence of sodium. The simulations show that the length scales involved in eDNA adsorption are less in the presence of sodium ions than those in the presence of calcium. In the presence of calcium, eDNA is pushed above the surface cations, whereas in the presence of sodium ions, short-range interactions with the surface dominate. Moreover, SMFS data show that increasing [Ca2+] from 1 to 10 mM increases the adsorption of the cations to the silicon oxide surface and consequently enhances the Stern layer, which in turn increases the length scale associated with eDNA adsorption.
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Affiliation(s)
- Ana L. Morales-García
- Department
of Physics and Astronomy, The University
of Sheffield, Hounsfield Road, Sheffield S3 7RH, U.K.
| | - Rachel Walton
- Department
of Physics and Astronomy, The University
of Sheffield, Hounsfield Road, Sheffield S3 7RH, U.K.
- Department
of Animal and Plant Sciences, The University
of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - Jamie T. Blakeman
- Department
of Physics and Astronomy, The University
of Sheffield, Hounsfield Road, Sheffield S3 7RH, U.K.
| | - Steven A. Banwart
- Department
of Civil and Structural Engineering, The
University of Sheffield, Sheffield S3 7HQ, U.K.
| | - John H. Harding
- Department
of Materials Science and Engineering, The
University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
| | - Mark Geoghegan
- Department
of Physics and Astronomy, The University
of Sheffield, Hounsfield Road, Sheffield S3 7RH, U.K.
| | - Colin L. Freeman
- Department
of Materials Science and Engineering, The
University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
| | - Stephen A. Rolfe
- Department
of Animal and Plant Sciences, The University
of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
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19
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Bag S, Rauwolf S, Schwaminger SP, Wenzel W, Berensmeier S. DNA Binding to the Silica: Cooperative Adsorption in Action. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5902-5908. [PMID: 33951395 DOI: 10.1021/acs.langmuir.1c00381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The adsorption and desorption of nucleic acid to a solid surface is ubiquitous in various research areas like pharmaceutics, nanotechnology, molecular biology, and molecular electronics. In spite of this widespread importance, it is still not well understood how the negatively charged deoxyribonucleic acid (DNA) binds to the negatively charged silica surface in an aqueous solution. In this article, we study the adsorption of DNA to the silica surface using both modeling and experiments and shed light on the complicated binding (DNA to silica) process. The binding agent mediated DNA adsorption was elegantly captured by cooperative Langmuir model. Bulk-depletion experiments were performed to conclude the necessity of a positively charged binding agent for efficient DNA binding, which complements the findings from the model. A profound understanding of DNA binding will help to tune various processes for efficient nucleic acid extraction and purification. However, this work goes beyond the DNA binding and can shed light on other binding agent mediated surface-surface, surface-molecule, molecule-molecule interaction.
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Affiliation(s)
- Saientan Bag
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz-1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Rauwolf
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich (TUM), Munich 85748, Germany
| | - Sebastian P Schwaminger
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich (TUM), Munich 85748, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz-1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Sonja Berensmeier
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich (TUM), Munich 85748, Germany
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20
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Vilela PB, Martins AS, Starling MCVM, de Souza FAR, Pires GFF, Aguilar AP, Pinto MEA, Mendes TAO, de Amorim CC. Solar photon-Fenton process eliminates free plasmid DNA harboring antimicrobial resistance genes from wastewater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 285:112204. [PMID: 33618138 PMCID: PMC7988504 DOI: 10.1016/j.jenvman.2021.112204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/02/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
This work aimed to assess the elimination and inactivation of resistance-conferring plasmids (RCPs) present in suspension in secondary wastewater by solar photo-Fenton as these are important vectors for the dissemination of antimicrobial resistance. Experiments were performed in synthetic secondary wastewater (SWW) and municipal wastewater treatment plant effluent (MWWTPE). Solar photo-Fenton (50 mg L-1 of H2O2 and 30 mg L-1 of Fe2+) was carried out for 60 min at neutral pH by applying the intermittent iron addition strategy. The removal of RCPs was assessed by Real-Time Polymerase Chain Reaction (qPCR). The transformation of competent non-resistant E. coli was used to evaluate the inactivation of target RCPs harboring antibiotic resistance genes (ARGs) to ampicillin (pSB1A2) or kanamycin (pSB1K3) after treatment and controls. Solar photo-Fenton completely removed RCPs initially present in both matrixes (SWW and MWWTPE), showing enhanced performance compared to the dark Fenton process. Both RCPs were inactivated after 30 min of solar photo-Fenton treatment, while 60 min were necessary to achieve the same effect for the dark Fenton reaction under similar conditions. These results indicate the potential of solar photo-Fenton to improve wastewater quality and reduce the spread of antimicrobial resistance in the environment by hampering the discharge of cell-free RCPs present in suspension in MWWTP onto environmental waters.
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Affiliation(s)
- Pâmela B Vilela
- Research Group on the Environmental Application of Advanced Oxidation Processes (GruPOA), Universidade Federal de Minas Gerais, Engineering School - Sanitary and Environmental Engineering Department, Av. Antônio Carlos 6627, 31270-901, Pampulha, Belo Horizonte, Brazil
| | - Alessandra S Martins
- Research Group on the Environmental Application of Advanced Oxidation Processes (GruPOA), Universidade Federal de Minas Gerais, Engineering School - Sanitary and Environmental Engineering Department, Av. Antônio Carlos 6627, 31270-901, Pampulha, Belo Horizonte, Brazil
| | - Maria Clara V M Starling
- Research Group on the Environmental Application of Advanced Oxidation Processes (GruPOA), Universidade Federal de Minas Gerais, Engineering School - Sanitary and Environmental Engineering Department, Av. Antônio Carlos 6627, 31270-901, Pampulha, Belo Horizonte, Brazil
| | - Felipe A R de Souza
- Research Group on the Environmental Application of Advanced Oxidation Processes (GruPOA), Universidade Federal de Minas Gerais, Engineering School - Sanitary and Environmental Engineering Department, Av. Antônio Carlos 6627, 31270-901, Pampulha, Belo Horizonte, Brazil
| | - Giovana F F Pires
- Research Group on the Environmental Application of Advanced Oxidation Processes (GruPOA), Universidade Federal de Minas Gerais, Engineering School - Sanitary and Environmental Engineering Department, Av. Antônio Carlos 6627, 31270-901, Pampulha, Belo Horizonte, Brazil
| | - Ananda P Aguilar
- Universidade Federal de Viçosa, Department of Biochemistry and Molecular Biology, Av. Peter Henry Rolfs, Viçosa, Brazil
| | - Maria Eduarda A Pinto
- Universidade Federal de Viçosa, Department of Biochemistry and Molecular Biology, Av. Peter Henry Rolfs, Viçosa, Brazil
| | - Tiago A O Mendes
- Universidade Federal de Viçosa, Department of Biochemistry and Molecular Biology, Av. Peter Henry Rolfs, Viçosa, Brazil
| | - Camila C de Amorim
- Research Group on the Environmental Application of Advanced Oxidation Processes (GruPOA), Universidade Federal de Minas Gerais, Engineering School - Sanitary and Environmental Engineering Department, Av. Antônio Carlos 6627, 31270-901, Pampulha, Belo Horizonte, Brazil.
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21
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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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22
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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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23
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Cai J, Ye ZL, Ye C, Ye X, Chen S. Struvite crystallization induced the discrepant transports of antibiotics and antibiotic resistance genes in phosphorus recovery from swine wastewater. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115361. [PMID: 32810833 DOI: 10.1016/j.envpol.2020.115361] [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: 05/03/2020] [Revised: 07/28/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
Struvite (MgNH4PO3·6H2O) crystallization is one of important methods of phosphorus recovery from wastewater. As to livestock wastewater, the high-strength occurrence of antibiotics and antibiotic resistance genes might induce struvite recovery to spread antibiotic resistance to the environment. However, limited information has been reported on the simultaneous transport of antibiotics and ARGs in struvite recovery. In the present study, tetracyclines (TCs) and tetracyclines antibiotic resistance genes (ARGs) were selected as the targeted pollutants, and their discrepant residues in struvite recovery from swine wastewater were investigated. TCs and ARGs were obviously detected, with their contents of 4.88-79.5 mg/kg and 6.99 × 107-2.14 × 1011 copies/g, notably higher than those of TCs 0.550-1.94 mg/kg and ARGs 3.98 × 104-5.66 × 107 copies/g obtained from synthetic wastewater. The correlational relationship revealed that predominant factors affecting TCs and ARGs transports were different. Results from network analyses indicated that among the total edges, the negative correlations between TCs and ARGs predominately occupied 18.0%. The redundancy analysis revealed that mineral components in the recovered products, including struvite, K-struvite and amorphous calcium phosphate, coupling with organic contents, displayed insignificant roles on TCs residues, where heavy metals exerted positive and remarkable functions to boost TCs migration. Unexpectedly, mineral components and heavy metals did not displayed significant promotion on ARGs transport as a whole.
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Affiliation(s)
- Jiasheng Cai
- Key Laboratory of Urban Pollution Conversion, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen City, Fujian, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Long Ye
- Key Laboratory of Urban Pollution Conversion, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen City, Fujian, 361021, China.
| | - Chengsong Ye
- College of the Environment and Ecology, Xiamen University, Xiamen City, Fujian, 361005, China
| | - Xin Ye
- Key Laboratory of Urban Pollution Conversion, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen City, Fujian, 361021, China
| | - Shaohua Chen
- Key Laboratory of Urban Pollution Conversion, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen City, Fujian, 361021, China
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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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25
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Porter TM, Hajibabaei M. Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00248] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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26
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Shillito LM, Whelton HL, Blong JC, Jenkins DL, Connolly TJ, Bull ID. Pre-Clovis occupation of the Americas identified by human fecal biomarkers in coprolites from Paisley Caves, Oregon. SCIENCE ADVANCES 2020; 6:eaba6404. [PMID: 32743069 PMCID: PMC7363456 DOI: 10.1126/sciadv.aba6404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
When and how people first settled in the Americas is an ongoing area of research and debate. The earliest sites typically only contain lithic artifacts that cannot be directly dated. The lack of human skeletal remains in these early contexts means that alternative sources of evidence are needed. Coprolites, and the DNA contained within them, are one such source, but unresolved issues concerning ancient DNA taphonomy and potential for contamination make this approach problematic. Here, we use fecal lipid biomarkers to demonstrate unequivocally that three coprolites dated to pre-Clovis are human, raise questions over the reliance on DNA methods, and present a new radiocarbon date on basketry further supporting pre-Clovis human occupation.
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Affiliation(s)
- Lisa-Marie Shillito
- School of History, Classics and Archaeology, Armstrong Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Helen L. Whelton
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - John C. Blong
- School of History, Classics and Archaeology, Armstrong Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Dennis L. Jenkins
- Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA
| | - Thomas J. Connolly
- Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA
| | - Ian D. Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
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27
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Schostag MD, Albers CN, Jacobsen CS, Priemé A. Low Turnover of Soil Bacterial rRNA at Low Temperatures. Front Microbiol 2020; 11:962. [PMID: 32523564 PMCID: PMC7261852 DOI: 10.3389/fmicb.2020.00962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/22/2020] [Indexed: 12/02/2022] Open
Abstract
Ribosomal RNA (rRNA) is used widely to investigate potentially active microorganisms in environmental samples, including soil microorganisms and other microbial communities that are subjected to pronounced seasonal variation in temperature. This raises a question about the turnover of intracellular microbial rRNA at environmentally relevant temperatures. We analyzed the turnover at four temperatures of RNA isolated from soil bacteria amended with 14C-labeled uridine. We found that the half-life of recently produced RNA increased from 4.0 days at 20°C to 15.8 days at 4°C, and 215 days at −4°C, while no degradation was detected at −18°C during a 1-year period. We discuss the implications of the strong temperature dependency of rRNA turnover for interpretation of microbiome data based on rRNA isolated from environmental samples.
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Affiliation(s)
- Morten Dencker Schostag
- Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Christian Nyrop Albers
- Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, Denmark.,Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Carsten Suhr Jacobsen
- Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, Denmark.,Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Anders Priemé
- Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
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28
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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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Goetsch HE, Love NG, Wigginton KR. Fate of Extracellular DNA in the Production of Fertilizers from Source-Separated Urine. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:1808-1815. [PMID: 31965791 DOI: 10.1021/acs.est.9b04263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The practice of urine source-separation for fertilizer production necessitates an understanding of the presence and impact of extracellular DNA in the urine. This study examines the fate of plasmid DNA carrying ampicillin and tetracycline resistance genes in aged urine, including its ability to be taken up and expressed by competent bacteria. Plasmid DNA incubated in aged urine resulted in a >2 log loss of bacterial transformation efficiency in Acinetobacter baylyi within 24 h. The concentration of ampicillin and tetracycline resistance genes, as measured with quantitative polymerase chain reaction, did not correspond with the observed transformation loss. When the plasmid DNA was incubated in aged urine that had been filtered (0.22 μm) or heated (75 °C), the transformation efficiencies were more stable than when the plasmids were incubated in unfiltered and unheated aged urine. Gel electrophoresis results indicated that plasmid linearization by materials larger than 100 kDa in the aged urine caused the observed transformation efficiency decreases. The results of this study suggest that extracellular DNA released into aged urine poses a low potential for the spread of antibiotic resistance genes to bacteria once it is released to the environment.
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Affiliation(s)
- Heather E Goetsch
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Nancy G Love
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
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30
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He P, Zhou Y, Shao L, Huang J, Yang Z, Lü F. The discrepant mobility of antibiotic resistant genes: Evidence from their spatial distribution in sewage sludge flocs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134176. [PMID: 31491625 DOI: 10.1016/j.scitotenv.2019.134176] [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: 06/13/2019] [Revised: 08/09/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
The present study stratified excess activated sludge from six municipal wastewater treatment plants into four extracellular fractions including supernatant, slime, slightly-bond extracellular polymeric substances (LB-EPS) and tightly-bond EPS (TB-EPS) and one intracellular fraction (pellet) according to their different degrees of tight binding to sludge microbial aggregates and determined the abundance of seven antibiotic resistance genes (ARGs) (sul-I, sul-II, tet-C, tet-X, blaTEM, mefA and cat) and one mobile genetic elements (MGEs) (IntI-1) in each fraction. Extracellular ARGs were found to make up 0.1% - 74.2% of total ARGs, while the ratio of extracellular DNA to total DNA was only 1.2% - 4.2%, implying that EPS was a major ARG reservoir in sewage sludge. The genes of sul-I, tet-C and mefA have the highest mobility owing to a large proportion ranging from 0.5% to 32.7% in the fractions of LB-EPS, slime and supernatant, which indicates an increased risk of mediating the transfer of ARGs to environment. Comparatively, the proportion of blaTEM in the TB-EPS of sludge accounted for 0.3%-34.9% and caused limited-mobility. Sul-II, tet-X and cat and IntI-1, made up approximately 82.6% - 99.6% proportion in the cells, and were thus less mobile. This study proposes that ARGs and MGEs can have different mobilities. Those located in the outermost layers of sludge have a higher mobility potential of propagation into the natural environment during wastewater treatment and sludge utilization, leading to an increased risk of transferability.
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Affiliation(s)
- Pinjing He
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, People's Republic of China; Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, People's Republic of China; Centre for the Technology Research and Training on Household Waste in Small Towns & Rural Area, Ministry of Housing and Urban-Rural Development of P. R. China (MOHURD), Shanghai 200092, People's Republic of China
| | - Yizhou Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, People's Republic of China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, People's Republic of China
| | - Liming Shao
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, People's Republic of China; Centre for the Technology Research and Training on Household Waste in Small Towns & Rural Area, Ministry of Housing and Urban-Rural Development of P. R. China (MOHURD), Shanghai 200092, People's Republic of China
| | - Jinghua Huang
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, People's Republic of China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, People's Republic of China
| | - Zhan Yang
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, People's Republic of China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, People's Republic of China
| | - Fan Lü
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, People's Republic of China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, People's Republic of China.
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31
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Harrison JB, Sunday JM, Rogers SM. Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proc Biol Sci 2019; 286:20191409. [PMID: 31744434 DOI: 10.1098/rspb.2019.1409] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Environmental DNA (eDNA) applications are transforming the standard of characterizing aquatic biodiversity via the presence, location and abundance of DNA collected from environmental samples. As eDNA studies use DNA fragments as a proxy for the presence of organisms, the ecological properties of the complex and dynamic environments from which eDNA is sampled need to be considered for accurate biological interpretation. In this review, we discuss the role that differing environments play on the major processes that eDNA undergoes between organism and collection, including shedding, decay and transport. We focus on a mechanistic understanding of these processes and highlight how decay and transport models are being developed towards more accurate and robust predictions of the fate of eDNA. We conclude with five recommendations for eDNA researchers and practitioners, to advance current best practices, as well as to support a future model of eDNA spatio-temporal persistence.
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Affiliation(s)
- Jori B Harrison
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | | | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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32
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Nnadozie CF, Odume ON. Freshwater environments as reservoirs of antibiotic resistant bacteria and their role in the dissemination of antibiotic resistance genes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:113067. [PMID: 31465907 DOI: 10.1016/j.envpol.2019.113067] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 05/12/2023]
Abstract
Freshwater environments are susceptible to possible contamination by residual antibiotics that are released through different sources, such as agricultural runoffs, sewage discharges and leaching from nearby farms. Freshwater environment can thus become reservoirs where an antibiotic impact microorganisms, and is an important public health concern. Degradation and dilution processes are fundamental for predicting the actual risk of antibiotic resistance dissemination from freshwater reservoirs. This study reviews major approaches for detecting and quantifying antibiotic resistance bacteria (ARBs) and genes (ARGs) in freshwater and their prevalence in these environments. Finally, the role of dilution, degradation, transmission and the persistence and fate of ARB/ARG in these environments are also reviewed. Culture-based single strain approaches and molecular techniques that include polymerase chain reaction (PCR), quantitative polymerase chain reaction (qPCR) and metagenomics are techniques for quantifying ARB and ARGs in freshwater environments. The level of ARBs is extremely high in most of the river systems (up to 98% of the total detected bacteria), followed by lakes (up to 77% of the total detected bacteria), compared to dam, pond, and spring (<1%). Of most concern is the occurrence of extended-spectrum β-lactamase producing Enterobacteriaceae, methicillin resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus (VRE), which cause highly epidemic infections. Dilution and natural degradation do not completely eradicate ARBs and ARGs in the freshwater environment. Even if the ARBs in freshwater are effectively inactivated by sunlight, their ARG-containing DNA can still be intact and capable of transferring resistance to non-resistant strains. Antibiotic resistance persists and is preserved in freshwater bodies polluted with high concentrations of antibiotics. Direct transmission of indigenous freshwater ARBs to humans as well as their transitory insertion in the microbiota can occur. These findings are disturbing especially for people that rely on freshwater resources for drinking, crop irrigation, and food in form of fish.
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Affiliation(s)
- Chika F Nnadozie
- Unilever Centre for Environmental Water Quality, Institute for Water Research, Rhodes University, PO Box 94, Grahamstown 6140, South Africa.
| | - Oghenekaro Nelson Odume
- Unilever Centre for Environmental Water Quality, Institute for Water Research, Rhodes University, PO Box 94, Grahamstown 6140, South Africa
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33
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Parker KM, Barragán Borrero V, van Leeuwen DM, Lever MA, Mateescu B, Sander M. Environmental Fate of RNA Interference Pesticides: Adsorption and Degradation of Double-Stranded RNA Molecules in Agricultural Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:3027-3036. [PMID: 30681839 DOI: 10.1021/acs.est.8b05576] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Double-stranded RNA (dsRNA) pesticides are a new generation of crop protectants that interfere with protein expression in targeted pest insects by a cellular mechanism called RNA interference (RNAi). The ecological risk assessment of these emerging pesticides necessitates an understanding of the fate of dsRNA molecules in receiving environments, among which agricultural soils are most important. We herein present an experimental approach using phosphorus-32 (32P)-radiolabeled dsRNA that allows studying key fate processes of dsRNA in soils with unprecedented sensitivity. This approach resolves previous analytical challenges in quantifying unlabeled dsRNA and its degradation products in soils. We demonstrate that 32P-dsRNA and its degradation products are quantifiable at concentrations as low as a few nanograms of dsRNA per gram of soil by both Cerenkov counting (to quantify total 32P-activity) and by polyacrylamide gel electrophoresis followed by phosphorimaging (to detect intact 32P-dsRNA and its 32P-containing degradation products). We show that dsRNA molecules added to soil suspensions undergo adsorption to soil particle surfaces, degradation in solution, and potential uptake by soil microorganisms. The results of this work on dsRNA adsorption and degradation advance a process-based understanding of the fate of dsRNA in soils and will inform ecological risk assessments of emerging dsRNA pesticides.
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Affiliation(s)
- Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering , Washington University in St. Louis , St. Louis , Missouri 63130 , United States
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , 8092 Zürich , Switzerland
| | - Verónica Barragán Borrero
- Institute of Molecular Plant Biology, Department of Biology , ETH Zürich , 8092 Zürich , Switzerland
| | - Daniël M van Leeuwen
- Institute of Molecular Plant Biology, Department of Biology , ETH Zürich , 8092 Zürich , Switzerland
| | - Mark A Lever
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , 8092 Zürich , Switzerland
| | - Bogdan Mateescu
- Institute of Molecular Plant Biology, Department of Biology , ETH Zürich , 8092 Zürich , Switzerland
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , 8092 Zürich , Switzerland
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Wegner CE, Gaspar M, Geesink P, Herrmann M, Marz M, Küsel K. Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon. Appl Environ Microbiol 2019; 85:e02346-18. [PMID: 30578263 PMCID: PMC6384109 DOI: 10.1128/aem.02346-18] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/14/2018] [Indexed: 11/20/2022] Open
Abstract
Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbor autotrophic microbial communities linked to nitrogen and sulfur metabolism. Here, we use multi-omic profiling to gain holistic insights into the turnover of inorganic nitrogen compounds, carbon fixation processes, and organic matter processing in groundwater. We sampled microbial biomass from two superimposed aquifers via monitoring wells that follow groundwater flow from its recharge area through differences in hydrogeochemical settings and land use. Functional profiling revealed that groundwater microbiomes are mainly driven by nitrogen (nitrification, denitrification, and ammonium oxidation [anammox]) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), depending on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Being dominated by a few phyla (Bacteroidetes, Proteobacteria, Planctomycetes, and Thaumarchaeota), the taxonomic profiling of groundwater metagenomes and metatranscriptomes revealed pronounced differences between merely present microbiome members and those actively participating in community gene expression and biogeochemical cycling. Unexpectedly, we observed a constitutive expression of carbohydrate-active enzymes encoded by different microbiome members, along with the groundwater flow path. The turnover of organic carbon apparently complements for lithoautotrophic carbon assimilation pathways mainly used by the groundwater microbiome depending on the availability of oxygen and inorganic electron donors, like ammonium.IMPORTANCE Groundwater is a key resource for drinking water production and irrigation. The interplay between geological setting, hydrochemistry, carbon storage, and groundwater microbiome ecosystem functioning is crucial for our understanding of these important ecosystem services. We targeted the encoded and expressed metabolic potential of groundwater microbiomes along an aquifer transect that diversifies in terms of hydrochemistry and land use. Our results showed that the groundwater microbiome has a higher spatial differentiation potential than does hydrochemistry.
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Affiliation(s)
- Carl-Eric Wegner
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Michael Gaspar
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, Jena, Germany
| | - Patricia Geesink
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Martina Herrmann
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, Jena, Germany
- Leibniz Institute on Aging, Fritz Lipman Institute, Jena, Germany
| | - Kirsten Küsel
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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35
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Kisand V, Talas L, Kisand A, Stivrins N, Reitalu T, Alliksaar T, Vassiljev J, Liiv M, Heinsalu A, Seppä H, Veski S. From microbial eukaryotes to metazoan vertebrates: Wide spectrum paleo-diversity in sedimentary ancient DNA over the last ~14,500 years. GEOBIOLOGY 2018; 16:628-639. [PMID: 30035382 DOI: 10.1111/gbi.12307] [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: 02/09/2018] [Revised: 06/09/2018] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
Most studies that utilize ancient DNA have focused on specific groups of organisms or even single species. Instead, the whole biodiversity of eukaryotes can be described using universal phylogenetic marker genes found within well-preserved sediment cores that cover the post-glacial period. Sedimentary ancient DNA samples from Lake Lielais Svētiņu, eastern Latvia, at a core depth of 1,050 cm in ~150 year intervals were used to determine phylotaxonomy in domain Eukaryota. Phylotaxonomic affiliation of >1,200 eukaryotic phylotypes revealed high richness in all major eukaryotic groups-Alveolata, Stramenopiles, Cercozoa, Chlorophyta, Charophyta, Nucletmycea, and Holozoa. The share of organisms that originate from terrestrial ecosystems was about one third, of which the most abundant molecular operational taxonomic units were Fungi and tracheal/vascular plants, which demonstrates the usefulness of using lake sediments to reconstruct the terrestrial paleoecosystems that surround them. Phylotypes that originate from the lake ecosystem belonged to various planktonic organisms; phyto-, proto,- and macrozooplankton, and vascular aquatic plants. We observed greater richness of several planktonic organisms that can be associated with higher trophic status during the warm climate period between 4,000 and 8,000 years ago and an increase in eukaryotic richness possibly associated with moderate human impact over the last 2,000 years.
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Affiliation(s)
- Veljo Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Liisi Talas
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Anu Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Normunds Stivrins
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
- Department of Geography, Faculty of Geography and Earth Sciences, University of Latvia, Riga, Latvia
| | - Triin Reitalu
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Tiiu Alliksaar
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Jüri Vassiljev
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Merlin Liiv
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Atko Heinsalu
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Heikki Seppä
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Siim Veski
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
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36
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Altuntop Yayla ME, Ekinci Doğan C, Sarioğlan Ş. Purification and analysis of DNA from low DNA content food samples. J Verbrauch Lebensm 2018. [DOI: 10.1007/s00003-018-1192-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Sand KK, Jelavić S. Mineral Facilitated Horizontal Gene Transfer: A New Principle for Evolution of Life? Front Microbiol 2018; 9:2217. [PMID: 30319562 PMCID: PMC6167411 DOI: 10.3389/fmicb.2018.02217] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/30/2018] [Indexed: 11/22/2022] Open
Abstract
A number of studies have highlighted that adsorption to minerals increases DNA longevity in the environment. Such DNA-mineral associations can essentially serve as pools of genes that can be stored across time. Importantly, this DNA is available for incorporation into alien organisms through the process of horizontal gene transfer (HGT). Here we argue that minerals hold an unrecognized potential for successfully transferring genetic material across environments and timescales to distant organisms and hypothesize that this process has significantly influenced the evolution of life. Our hypothesis is illustrated in the context of the evolution of early microbial life and the oxygenation of the Earth's atmosphere and offers an explanation for observed outbursts of evolutionary events caused by HGT.
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Affiliation(s)
- Karina Krarup Sand
- Department of Geography and Earth Sciences, Aberystwyth University, Aberystwyth, United Kingdom
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Stanislav Jelavić
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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Effect of calcium ions on peptide adsorption at the aqueous rutile titania (110) interface. Biointerphases 2018; 13:06D403. [PMID: 30180596 DOI: 10.1116/1.5046531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
How the presence of Ca2+ ions at the aqueous TiO2 interface influences the binding modes of two experimentally identified titania-binding peptides, Ti-1 and Ti-2, is investigated using replica exchange with solute tempering molecular dynamics simulations. The findings are compared with available experimental data, and the results are contrasted with those obtained under NaCl solution conditions. For Ti-1, Ca2+ ions enhance the adsorption of the negatively charged Asp8 residue in this sequence to the negatively charged surface, via Asp–Ca2+–TiO2 bridging. This appears to generate a nonlocal impact on the adsorption of Lys12 in Ti-1, which then pins the peptide to the surface via direct surface contact. For Ti-2, fewer residues were predicted to adsorb directly to the surface in CaCl2, compared with predictions made for NaCl solution, possibly due to competition between the other peptide residues and Ca2+ ions to adsorb to the surface. This reduction in direct surface contact gives rise to a more extensive solvent-mediated contact for Ti-2. In general, the presence of Ca2+ ions resulted in a loss of conformational diversity of the surface-adsorbed conformational ensembles of these peptides, compared to counterpart data predicted for NaCl solution. The findings provide initial insights into how peptide–TiO2 interactions might be tuned at the molecular level via modification of the salt composition of the liquid medium.
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Abstract
Extracellular or “relic” DNA is one of the largest pools of nucleic acids in the biosphere. Relic DNA can influence a number of important ecological and evolutionary processes, but it may also affect estimates of microbial abundance and diversity, which has implications for understanding environmental, engineered, and host-associated ecosystems. We developed models capturing the fundamental processes that regulate the size and composition of the relic DNA pools to identify scenarios leading to biased estimates of biodiversity. Our models predict that bias increases with relic DNA pool size, but only when the species abundance distributions (SADs) of relic and intact DNA are distinct from one another. We evaluated our model predictions by quantifying relic DNA and assessing its contribution to bacterial diversity using 16S rRNA gene sequences collected from different ecosystem types, including soil, sediment, water, and the mammalian gut. On average, relic DNA made up 33% of the total bacterial DNA pool but exceeded 80% in some samples. Despite its abundance, relic DNA had a minimal effect on estimates of taxonomic and phylogenetic diversity, even in ecosystems where processes such as the physical protection of relic DNA are common and predicted by our models to generate bias. Our findings are consistent with the expectation that relic DNA from different taxa degrades at a constant and equal rate, suggesting that it may not fundamentally alter estimates of microbial diversity. The ability to rapidly obtain millions of gene sequences and transcripts from a range of environments has greatly advanced understanding of the processes that regulate microbial communities. However, nucleic acids extracted from complex samples do not come only from viable microorganisms. Dead microorganisms can generate large pools of relic DNA that distort insight into the ecology and evolution of microbial systems. Here, we develop a conceptual and quantitative framework for understanding how relic DNA influences the structure of microbiomes. Our theoretical models and empirical results demonstrate that a large relic DNA pool does not automatically lead to biased estimates of microbial diversity. Rather, relic DNA effects emerge in combination with microscale processes that alter the commonness and rarity of sequences found in heterogeneous DNA pools.
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40
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Abstract
Purifying DNA is the key to successful cloning. The cleaner the final preparation of DNA, the more efficient will be the enzymatic reactions that use the DNA as a template or a substrate. In the 1930s and 1940s, the scientific literature began to accumulate methods to release DNA from cells and to remove cellular constituents that inhibit or act as competitors on enzymatically catalyzed reactions. Since then, thousands of protocols for purification of DNA from a wide variety of organisms, tissues, and bodily fluids have been published. This introduction provides an overview of methods for isolation and quantification of DNA.
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41
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Cappellini E, Prohaska A, Racimo F, Welker F, Pedersen MW, Allentoft ME, de Barros Damgaard P, Gutenbrunner P, Dunne J, Hammann S, Roffet-Salque M, Ilardo M, Moreno-Mayar JV, Wang Y, Sikora M, Vinner L, Cox J, Evershed RP, Willerslev E. Ancient Biomolecules and Evolutionary Inference. Annu Rev Biochem 2018; 87:1029-1060. [PMID: 29709200 DOI: 10.1146/annurev-biochem-062917-012002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.
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Affiliation(s)
- Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Frido Welker
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | | | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Peter de Barros Damgaard
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Petra Gutenbrunner
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Julie Dunne
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Simon Hammann
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom; .,Department of Anthropology and Archaeology, University of Bristol, Bristol BS8 1UU, United Kingdom
| | - Mélanie Roffet-Salque
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Melissa Ilardo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Yucheng Wang
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; , .,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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42
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Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples. Sci Rep 2018; 8:5711. [PMID: 29632323 PMCID: PMC5890260 DOI: 10.1038/s41598-018-24082-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 03/27/2018] [Indexed: 11/17/2022] Open
Abstract
Here we show that a commercial blocking reagent (G2) based on modified eukaryotic DNA significantly improved DNA extraction efficiency. We subjected G2 to an inter-laboratory testing, where DNA was extracted from the same clay subsoil using the same batch of kits. The inter-laboratory extraction campaign revealed large variation among the participating laboratories, but the reagent increased the number of PCR-amplified16S rRNA genes recovered from biomass naturally present in the soils by one log unit. An extensive sequencing approach demonstrated that the blocking reagent was free of contaminating DNA, and may therefore also be used in metagenomics studies that require direct sequencing.
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43
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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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44
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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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45
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Buxton AS, Groombridge JJ, Griffiths RA. Seasonal variation in environmental DNA detection in sediment and water samples. PLoS One 2018; 13:e0191737. [PMID: 29352294 PMCID: PMC5774844 DOI: 10.1371/journal.pone.0191737] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/10/2018] [Indexed: 11/18/2022] Open
Abstract
The use of aquatic environmental DNA (eDNA) to detect the presence of species depends on the seasonal activity of the species in the sampled habitat. eDNA may persist in sediments for longer than it does in water, and analysing sediment could potentially extend the seasonal window for species assessment. Using the great crested newt as a model, we compare how detection probability changes across the seasons in eDNA samples collected from both pond water and pond sediments. Detection of both aquatic and sedimentary eDNA varied through the year, peaking in the summer (July), with its lowest point in the winter (January): in all seasons, detection probability of eDNA from water exceeded that from sediment. Detection probability of eDNA also varied between study areas, and according to great crested newt habitat suitability and sediment type. As aquatic and sedimentary eDNA show the same seasonal fluctuations, the patterns observed in both sample types likely reflect current or recent presence of the target species. However, given the low detection probabilities found in the autumn and winter we would not recommend using either aquatic or sedimentary eDNA for year-round sampling without further refinement and testing of the methods.
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Affiliation(s)
- Andrew S. Buxton
- Durrell Institute for Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent, United Kingdom
- * E-mail:
| | - Jim J. Groombridge
- Durrell Institute for Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent, United Kingdom
| | - Richard A. Griffiths
- Durrell Institute for Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent, United Kingdom
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46
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Abstract
Surface-attached colonies of bacteria known as biofilms play a major role in the pathogenesis of medical device infections. Biofilm colonies are notorious for their resistance to antibiotics and host defenses, which makes most device infections difficult or impossible to eradicate. Bacterial cells in a biofilm are held together by an extracellular polymeric matrix that is synthesized by the bacteria themselves. Enzymes that degrade biofilm matrix polymers have been shown to inhibit bio film formation, detach established bio film colonies, and render biofilm cells sensitive to killing by antimicrobial agents. This review discusses the potential use of biofilm matrix-degrading enzymes as anti-biofilm agents for the treatment and prevention of device infections. Two enzymes, deoxyribonuclease I and the glycoside hydrolase dispersin B, will be reviewed in detail. In vitro and in vivo studies demonstrating the anti-biofilm activities of these two enzymes will be summarized, and the therapeutic potential and possible drawbacks of using these enzymes as clinical agents will be discussed.
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Affiliation(s)
- Jeffrey B. Kaplan
- Department of Oral Biology, New Jersey Dental School, Newark, NJ - USA
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47
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Zhang Y, Li A, Dai T, Li F, Xie H, Chen L, Wen D. Cell-free DNA: A Neglected Source for Antibiotic Resistance Genes Spreading from WWTPs. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:248-257. [PMID: 29182858 DOI: 10.1021/acs.est.7b04283] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cell-associated ARGs in wastewater treatment plants (WWTPs) has been concerned, however, cell-free ARGs in WWTPs was rarely studied. In this study, the abundances of four representative ARGs, sulII, tetC, blaPSE-1, and ermB, in a large municipal WWTP were investigated in both cell-associated and cell-free fractions. Cell-associated ARGs was the dominant ARGs fraction in the raw wastewater. After biological treatment, sludge settling, membrane filtration, and disinfection, cell-associated ARGs were substantially reduced, though the ratios of ARG/16S rRNA gene were increased with disinfection. Cell-free ARGs persisted in the WWTP with a removal of 0.36 log to 2.68 logs, which was much lower than the removal of cell-associated ARGs (3.21 logs to 4.14 logs). Therefore, the abundance ratio of cell-free ARGs to cell-associated ARGs increased from 0.04-1.59% to 2.00-1895.08% along the treatment processes. After 25-day-storage, cell-free ARGs in both biological effluent and disinfection effluent increased by 0.14 log to 1.99 logs and 0.12 log to 1.77 logs respectively, reflecting the persistence and low decay rate of cell-free ARGs in the discharge water. Therefore, cell-free ARGs might be a kind of important but previously neglected pollutant from WWTPs, which added potential risks to the effluent receiving environments.
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Affiliation(s)
- Yan Zhang
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University , Wuxi 214122, China
| | - Aolin Li
- School of Environment, Tsinghua University , Beijing 100084, China
| | - Tianjiao Dai
- College of Environmental Sciences and Engineering, Peking University , Beijing 100871, China
| | - Feifei Li
- School of Water Resource and Environment, China University of Geosciences , Beijing, 100083, China
| | - Hui Xie
- School of Environment, Tsinghua University , Beijing 100084, China
| | - Lujun Chen
- School of Environment, Tsinghua University , Beijing 100084, China
- Zhejiang Provincial Key Laboratory of Water Science and Technology, Department of Environmental Technology and Ecology, Yangtze Delta Region Institute of Tsinghua University , Zhejiang Jiaxing 314050, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University , Beijing 100871, China
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48
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Parker KM, Sander M. Environmental Fate of Insecticidal Plant-Incorporated Protectants from Genetically Modified Crops: Knowledge Gaps and Research Opportunities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:12049-12057. [PMID: 28968072 DOI: 10.1021/acs.est.7b03456] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Plant-incorporated protectants (PIPs) are biopesticides expressed in genetically modified (GM) crops and are typically macromolecular in nature. First-generation insecticidal PIPs were Cry proteins expressed in GM crops containing transgenes from the soil bacterium Bacillus thuringiensis; next-generation double-stranded ribonucleic acid (dsRNA) PIPs have been recently approved. Like conventional synthetic pesticides, the use of either Cry protein or dsRNA PIPs results in their release to receiving environments. However, as opposed to conventional low molecular weight pesticides, the environmental fate of macromolecular PIPs remains less studied and is poorly understood. This Feature highlights the knowledge gaps and challenges that have emerged while investigating the environmental fate of Cry protein PIPs and suggests new avenues to advance the state of the research necessary for the ongoing environmental fate assessment of dsRNA PIPs.
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Affiliation(s)
- Kimberly M Parker
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich , 8092 Zurich, Switzerland
- Department of Energy, Environmental and Chemical Engineering, Washington University , St. Louis, Missouri 63130, United States
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich , 8092 Zurich, Switzerland
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49
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Polinski MP, Meyer GR, Lowe GJ, Abbott CL. Seawater detection and biological assessments regarding transmission of the oyster parasite Mikrocytos mackini using qPCR. DISEASES OF AQUATIC ORGANISMS 2017; 126:143-153. [PMID: 29044044 DOI: 10.3354/dao03167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mikrocytos mackini is an intracellular parasite of oysters and causative agent of Denman Island disease in Pacific oysters Crassostrea gigas. Although M. mackini has been investigated for decades, its natural mode of transmission, mechanism for host entry, and environmental stability are largely unknown. We explored these biological characteristics of M. mackini using a recently described quantitative PCR (qPCR) assay. We detected M. mackini in the flow-through tank water of experimentally infected oysters and during disease remission in host tissues following 6 wk of elevated water temperature. Waterborne exposure of oysters to M. mackini further confirmed the potential for extracellular seawater transmission of this parasite and also identified host gill to have the highest early and continued prevalence for M. mackini DNA compared to stomach, mantle, labial palps, or adductor muscle samples. However, infections following waterborne challenge were slow to develop despite a substantial exposure (>106 M. mackini l-1 for 24 h), and further investigation demonstrated that M. mackini occurrence and infectivity severely declined following extracellular seawater incubation of more than 24 h. This study demonstrates a potential for using qPCR to monitor M. mackini in wild or farmed oyster populations during periods of disease remission or from environmental seawater samples. This work also suggests that gill tissues may provide a primary site for waterborne entry and possibly shedding of M. mackini in oysters. Further, although extracellular seawater transmission of M. mackini was possible, poor environmental stability and infection efficiency likely restricts the geographic transmission of M. mackini between oysters in natural environs and may help to explain localized areas of infection.
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Affiliation(s)
- Mark P Polinski
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
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50
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Gardner CM, Gunsch CK. Adsorption capacity of multiple DNA sources to clay minerals and environmental soil matrices less than previously estimated. CHEMOSPHERE 2017; 175:45-51. [PMID: 28211334 DOI: 10.1016/j.chemosphere.2017.02.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/15/2016] [Accepted: 02/04/2017] [Indexed: 05/25/2023]
Abstract
The cultivation and consumption of transgenic crops continues to be a widely debated topic, as the potential ecological impacts are not fully understood. In particular, because antibiotic resistance genes (ARGs) have historically been used as selectable markers in the genetic engineering of transgenic crops, it is important to determine if the genetic constructs found in decomposing transgenic crops persist long enough in the environment and if they can be transferred horizontally to indigenous microorganisms. In the present study, we address the question of persistence. Others have also estimated the DNA adsorption capacity of various clays, but have done so by manipulating the surface charge and size of particles tested which may overestimate sorption and underestimate the DNA available for horizontal transfer. In the present study, isotherms were generated using model Calf Thymus DNA and transgenic maize DNA without surface modification. Montmorillonite, kaolinite, and 3 soil mixtures with varying clay content were used in this study. The adsorption capacity of pure montmorillonite and kaolinite minerals was found to be one to two orders of magnitude less than previously estimated likely due to the distribution of clay particle sizes and heteroionic particle surface charge. However, it appears that a substantial amount of DNA is still able to adsorb onto these matrices (up to 200 mg DNA per gram of clay) suggesting the potential availability of free transgenic DNA in the environment may still be significant. Future studies should be conducted to determine the fate of these genes in agricultural soils.
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Affiliation(s)
- Courtney M Gardner
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27708, USA
| | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27708, USA.
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