1
|
Lin H, Li R, Chen Y, Cheng Y, Yuan Q, Luo Y. Enhanced sensitivity of extracellular antibiotic resistance genes (ARGs) to environmental concentrations of antibiotic. CHEMOSPHERE 2024; 360:142434. [PMID: 38797215 DOI: 10.1016/j.chemosphere.2024.142434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
As emerging contaminants, antibiotics are frequently present in various environments, particularly rivers, albeit often at sublethal concentrations (ng/L∼μg/L). Assessing the risk associated with these low levels, which are far below the lethal threshold for most organisms, remains challenging. In this study, using microcosms containing planktonic bacteria and biofilm, we examined how antibiotic resistance genes (ARGs) in different physical states, including intracellular ARGs (iARGs) and extracellular ARGs (eARGs) responded to these low-level antibiotics. Our findings reveal a positive correlation between sub-lethal antibiotic exposure (ranging from 0.1 to 10 μg/L) and increased prevalence (measured as ARG copies/16s rDNA) of both iARGs and eARGs in planktonic bacteria. Notably, eARGs demonstrated greater sensitivity to antibiotic exposure compared to iARGs, with a lower threshold (0.1 μg/L for eARGs versus 1 μg/L for iARGs) for abundance increase. Moreover, ARGs in biofilms demonstrates higher sensitivity to antibiotic exposure compared to planktonic bacteria. To elucidate the underlying mechanisms, we established an integrated population dynamics-pharmacokinetics-pharmacodynamics (PD-PP) model. This model indicates that the enhanced sensitivity of eARGs is primarily driven by an increased potential for plasmid release from cells under low antibiotic concentrations. Furthermore, the accumulation of antibiotic in biofilms induces a greater sensitivity of ARG compared to the planktonic bacteria. This study provides a fresh perspective on the development of antibiotic resistance and offers an innovative approach for assessing the risk of sublethal antibiotic in the environment.
Collapse
Affiliation(s)
- Huai Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China; Shenzhen Research Institute of Nanjing University, Shen Zhen, 518000, China
| | - Ruiqing Li
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Yuying Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Yuan Cheng
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Qingbin Yuan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China; School of Environmental Science and Engineering, Nanjing Tech University, Nanjing, 211816, China.
| | - Yi Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China.
| |
Collapse
|
2
|
Ekram MAE, Campbell M, Kose SH, Plet C, Hamilton R, Bijaksana S, Grice K, Russell J, Stevenson J, Vogel H, Coolen MJL. A 1 Ma sedimentary ancient DNA (sedaDNA) record of catchment vegetation changes and the developmental history of tropical Lake Towuti (Sulawesi, Indonesia). GEOBIOLOGY 2024; 22:e12599. [PMID: 38745401 DOI: 10.1111/gbi.12599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/24/2023] [Accepted: 04/18/2024] [Indexed: 05/16/2024]
Abstract
Studying past ecosystems from ancient environmental DNA preserved in lake sediments (sedaDNA) is a rapidly expanding field. This research has mainly involved Holocene sediments from lakes in cool climates, with little known about the suitability of sedaDNA to reconstruct substantially older ecosystems in the warm tropics. Here, we report the successful recovery of chloroplast trnL (UAA) sequences (trnL-P6 loop) from the sedimentary record of Lake Towuti (Sulawesi, Indonesia) to elucidate changes in regional tropical vegetation assemblages during the lake's Late Quaternary paleodepositional history. After the stringent removal of contaminants and sequence artifacts, taxonomic assignment of the remaining genuine trnL-P6 reads showed that native nitrogen-fixing legumes, C3 grasses, and shallow wetland vegetation (Alocasia) were most strongly associated with >1-million-year-old (>1 Ma) peats and silts (114-98.8 m composite depth; mcd), which were deposited in a landscape of active river channels, shallow lakes, and peat-swamps. A statistically significant shift toward partly submerged shoreline vegetation that was likely rooted in anoxic muddy soils (i.e., peatland forest trees and wetland C3 grasses (Oryzaceae) and nutrient-demanding aquatic herbs (presumably Oenanthe javanica)) occurred at 76 mcd (~0.8 Ma), ~0.2 Ma after the transition into a permanent lake. This wetland vegetation was most strongly associated with diatom ooze (46-37 mcd), thought to be deposited during maximum nutrient availability and primary productivity. Herbs (Brassicaceae), trees/shrubs (Fabaceae and Theaceae), and C3 grasses correlated with inorganic parameters, indicating increased drainage of ultramafic sediments and laterite soils from the lakes' catchment, particularly at times of inferred drying. Downcore variability in trnL-P6 from tropical forest trees (Toona), shady ground cover herbs (Zingiberaceae), and tree orchids (Luisia) most strongly correlated with sediments of a predominantly felsic signature considered to be originating from the catchment of the Loeha River draining into Lake Towuti during wetter climate conditions. However, the co-correlation with dry climate-adapted trees (i.e., Castanopsis or Lithocarpus) plus C4 grasses suggests that increased precipitation seasonality also contributed to the increased drainage of felsic Loeha River sediments. This multiproxy approach shows that despite elevated in situ temperatures, tropical lake sediments potentially comprise long-term archives of ancient environmental DNA for reconstructing ecosystems, which warrants further exploration.
Collapse
Affiliation(s)
- Md Akhtar-E Ekram
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Matthew Campbell
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Sureyya H Kose
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Chloe Plet
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Rebecca Hamilton
- ARC Centre of Excellence for Australian Biodiversity and Heritage and Archaeology and Natural History, School of Culture, History, and Language, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Satria Bijaksana
- Faculty of Mining and Petroleum Engineering, Institut Teknologi Bandung, Bandung, Indonesia
| | - Kliti Grice
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - James Russell
- Department of Earth, Environmental, and Planetary Sciences (DEEPS), Brown University, Providence, Rhode Island, USA
| | - Janelle Stevenson
- ARC Centre of Excellence for Australian Biodiversity and Heritage and Archaeology and Natural History, School of Culture, History, and Language, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Hendrik Vogel
- Institute of Geological Sciences & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Marco J L Coolen
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| |
Collapse
|
3
|
Chatterjee A, Zhang K, Parker KM. Binding of Dissolved Organic Matter to RNA and Protection from Nuclease-Mediated Degradation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16086-16096. [PMID: 37811805 DOI: 10.1021/acs.est.3c05019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The persistence of RNA in environmental systems is an important parameter for emerging applications, including ecological surveys, wastewater-based epidemiology, and RNA interference biopesticides. RNA persistence is controlled by its rate of biodegradation, particularly by extracellular enzymes, although the specific factors determining this rate have not been characterized. Due to prior work suggesting that nucleic acids-specifically DNA-interact with dissolved organic matter (DOM), we hypothesized that DOM may bind RNA and impede its biodegradation in natural systems. We first adapted a technique previously used to assess RNA-protein binding to differentiate RNA that is bound at all sites by DOM from RNA that is unbound or partially bound by DOM. Results from this technique suggested that humic acids bound RNA more extensively than fulvic acids. At concentrations of 8-10 mgC/L, humic acids were also found to be more effective than fulvic acids at suppressing enzymatic degradation of RNA. In surface water and soil extract containing DOM, RNA degradation was suppressed by 39-46% relative to pH-adjusted controls. Due to the ability of DOM to both bind and suppress the enzymatic degradation of RNA, RNA biodegradation may be slowed in environmental systems with high DOM concentrations, which may increase its persistence.
Collapse
Affiliation(s)
- Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| |
Collapse
|
4
|
Liu W, Xiang P, Ji Y, Chen Z, Lei Z, Huang W, Huang W, Liu D. Response of viable bacteria to antibiotics in aerobic granular sludge: Resistance mechanisms and behaviors, bacterial communities, and driving factors. WATER RESEARCH 2023; 245:120656. [PMID: 37748345 DOI: 10.1016/j.watres.2023.120656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/31/2023] [Accepted: 09/20/2023] [Indexed: 09/27/2023]
Abstract
The assessment of antimicrobial resistance (AMR) risk by DNA-based techniques mainly relies on total bacterial DNA. In this case, AMR risk recognition is restricted to the genotype level, lacking crucial phenotypic information, such as the distribution of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in dead and viable bacteria. This limitation hinders the recognition of AMR behavior. Herein, based on propidium monoazide (PMA) shielding method, this work firstly quantified the intracellular ARGs/MGEs in viable and dead bacteria, and the impact of viable bacteria composition on the formation of intracellular/extracellular polymeric substance-related /cell-free ARGs (i/e/cARGs) and MGEs (i/e/cMGEs) in aerobic granular sludge (AGS). The shielding efficiency of PMA against dead bacteria was optimized to be as high as 97.5% when the MLSS of AGS was 2.0 g/L. Under antibiotic stimulation, 29.0% ∼ 49.0% of iARGs/iMGEs were carried by viable bacteria, and the remaining proportion were carried by dead bacteria. 18 out of the top 20 dominant genera showed a change in abundance by more than 1% after PMA treatment. 29 viable hosts were identified to associate with 52 iARGs, of which 28 and 15 hosts were also linked to 40 eARGs and 26 cARGs. Also, partial least-squares path model and variance partitioning analysis disclosed that viable bacteria and i/e/cMGEs had a positive effect on i/e/cARGs, with both contributing as much as 64.5% to the total ARGs enrichment. These results better visualized the AMR risk carried by viable bacteria and the categories of viable hosts. This work provides a novel insight into analyzing the actual AMR risk and viable hosts, helping to the reduction and control of AMR in wastewater treatment plants.
Collapse
Affiliation(s)
- Wenhao Liu
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Peng Xiang
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yuan Ji
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Zeyou Chen
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Zhongfang Lei
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Weiwei Huang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Renmin Road, Haikou 570228, China
| | - Wenli Huang
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Dongfang Liu
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| |
Collapse
|
5
|
Xue Y, Abdullah Al M, Chen H, Xiao P, Zhang H, Jeppesen E, Yang J. Relic DNA obscures DNA-based profiling of multiple microbial taxonomic groups in a river-reservoir ecosystem. Mol Ecol 2023; 32:4940-4952. [PMID: 37452629 DOI: 10.1111/mec.17071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/08/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Numerous studies have investigated the spatiotemporal variability in water microbial communities, yet the effects of relic DNA on microbial community profiles, especially microeukaryotes, remain far from fully understood. Here, total and active bacterial and microeukaryotic community compositions were characterized using propidium monoazide (PMA) treatment coupled with high-throughput sequencing in a river-reservoir ecosystem. Beta diversity analysis showed a significant difference in community composition between both the PMA untreated and treated bacteria and microeukaryotes; however, the differentiating effect was much stronger for microeukaryotes. Relic DNA only resulted in underestimation of the relative abundances of Bacteroidota and Nitrospirota, while other bacterial taxa exhibited no significant changes. As for microeukaryotes, the relative abundances of some phytoplankton (e.g. Chlorophyta, Dinoflagellata and Ochrophyta) and fungi were greater after relic DNA removal, whereas Cercozoa and Ciliophora showed the opposite trend. Moreover, relic DNA removal weakened the size and complexity of cross-trophic microbial networks and significantly changed the relationships between environmental factors and microeukaryotic community composition. However, there was no significant difference in the rates of temporal community turnover between the PMA untreated and treated samples for either bacteria or microeukaryotes. Overall, our results imply that the presence of relic DNA in waters can give misleading information of the active microbial community composition, co-occurrence networks and their relationships with environmental conditions. More studies of the abundance, decay rate and functioning of nonviable DNA in freshwater ecosystems are highly recommended in the future.
Collapse
Affiliation(s)
- Yuanyuan Xue
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Mamun Abdullah Al
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Huihuang Chen
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Xiao
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Hongteng Zhang
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Erik Jeppesen
- Department of Ecoscience, Aarhus University, Aarhus, Denmark
- Sino-Danish Centre for Education and Research, Beijing, China
- Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara, Turkey
- Institute of Marine Sciences, Middle East Technical University, Mersin, Turkey
| | - Jun Yang
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Deng P, Hu X, Cai W, Zhang Z, Zhang Y, Huang Y, Yang Y, Li C, Ai S. Profiling of intracellular and extracellular antibiotic resistance genes in municipal wastewater treatment plant and their effluent-receiving river. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:33516-33523. [PMID: 36480142 DOI: 10.1007/s11356-022-24545-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
The presence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) in extracellular and intracellular DNA (eDNA and iDNA) has received considerable attention in recent years owing to the potential threat to human health and the ecosystem. As a result, we investigated six ARGs, three MRGs, and two mobile genetic elements (MGEs) in the municipal wastewater treatment plant (MWWTP) and its adjacent environments. Results revealed that the absolute abundances of eARGs and eMRGs were lower than iARGs and iMRGs in MWWTP. By contrast, eARGs and eMRGs were higher in river sediments. Among ARGs, aminoglycoside resistance genes (aadA) was the most abundant gene (3.13 × 102 to 2.31 × 106 copies/mL in iDNA; 1.27 × 103 to 7.23 × 105 copies/mL in eDNA) in MWWTP, while zntA gene (9.4 × 102 to 3.97 × 106 copies/mL in iDNA; 3.2 × 103 to 6 × 105 copies/mL in eDNA) was amongst the MRGs. Notably, intI1 was enriched and positively correlated with iDNA (tetA, sul1, blaCTX-M, ermB, and merA) and eDNA (blaCTX-M, ermB, and merA), demonstrating its function in the proliferation of resistance genes. This widespread distribution of ARGs, MRGs, and MGEs in MWWTP and its adjacent river sediments will help clarify the transmission routes within these environments and provide a theoretical basis for better monitoring and mitigation of such dissemination.
Collapse
Affiliation(s)
- Peiyuan Deng
- Henan Engineering Research Center of Bird-Related Outage, Zhengzhou Normal University, Zhengzhou, 450044, Henan, China
| | - Xiaojia Hu
- School of Environmental and Municipal Engineering, North China University of Water Resources and Electric Power, Zhengzhou, 450046, Henan, China
| | - Wentao Cai
- Ural Institute, North China University of Water Resources and Electric Power, Zhengzhou, 450045, Henan, China
| | - Zuoxu Zhang
- School of Environment, Beijing Jiaotong University, Beijing, 100044, China
| | - Yuli Zhang
- Zhengzhou Veterinary Drug Feed Quality and Safety Inspection Center, Zhengzhou, 450052, Henan, China
| | - Yihe Huang
- Henan Engineering Research Center of Bird-Related Outage, Zhengzhou Normal University, Zhengzhou, 450044, Henan, China
| | - Yingying Yang
- Henan Engineering Research Center of Bird-Related Outage, Zhengzhou Normal University, Zhengzhou, 450044, Henan, China
| | - Changkan Li
- Henan Engineering Research Center of Bird-Related Outage, Zhengzhou Normal University, Zhengzhou, 450044, Henan, China
| | - Shu Ai
- School of Environmental and Municipal Engineering, North China University of Water Resources and Electric Power, Zhengzhou, 450046, Henan, China.
| |
Collapse
|
8
|
Soil Component: A Potential Factor Affecting the Occurrence and Spread of Antibiotic Resistance Genes. Antibiotics (Basel) 2023; 12:antibiotics12020333. [PMID: 36830244 PMCID: PMC9952537 DOI: 10.3390/antibiotics12020333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
In recent years, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil have become research hotspots in the fields of public health and environmental ecosystems, but the effects of soil types and soil components on the occurrence and spread of ARGs still lack systematic sorting and in-depth research. Firstly, investigational information about ARB and ARGs contamination of soil was described. Then, existing laboratory studies about the influence of the soil component on ARGs were summarized in the following aspects: the influence of soil types on the occurrence of ARGs during natural or human activities and the control of exogenously added soil components on ARGs from the macro perspectives, the effects of soil components on the HGT of ARGs in a pure bacterial system from the micro perspectives. Following that, the similarities in pathways by which soil components affect HGT were identified, and the potential mechanisms were discussed from the perspectives of intracellular responses, plasmid activity, quorum sensing, etc. In the future, related research on multi-component systems, multi-omics methods, and microbial communities should be carried out in order to further our understanding of the occurrence and spread of ARGs in soil.
Collapse
|
9
|
Guo ZF, Boeing WJ, Xu YY, Borgomeo E, Liu D, Zhu YG. Data-driven discoveries on widespread contamination of freshwater reservoirs by dominant antibiotic resistance genes. WATER RESEARCH 2023; 229:119466. [PMID: 36502654 DOI: 10.1016/j.watres.2022.119466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/16/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
The propagation of antibiotic resistance genes (ARGs) in freshwater reservoirs threatens ecosystem security and human health, and has attracted increasing attention. A series of recent research articles on ARGs provides a unique opportunity for data-driven discoveries in this emerging field. Here, we mined data from a total of 290 samples from 60 reservoirs worldwide with a data-driven framework (DD) developed to discover geographical distribution, influencing factors and pollution hotspots of ARGs in freshwater reservoirs. Most data came from Asia and Europe where nine classes of ARGs were most frequently detected in reservoirs with multi-drug resistance and sulfonamide resistance genes prevailing. Factors driving distribution of reservoir ARGs differed between reservoir waters and sediments, and interactions among these factors had linear or nonlinear enhancement effects on the explanatory power of ARG distribution. During the cold season, small-sized reservoir waters rich in organic carbon, mobile genetic elements (MGEs) and antibiotics had a higher pollution potential of ARGs; during the spring drought, sediments in large reservoirs located in densely populated areas were more conducive to dissemination of ARGs due to their richness in antibiotics and MGEs. Thus, distribution pattern of ARG pollution hotspots in reservoir waters and sediments varies greatly depending on the differences of internal and external factors. From the "One Health" perspective, this widespread contamination of freshwater reservoirs by ARGs we discovered through the DD framework should be a push to promote integrated research across regions and disciplines. Especially the human - food-chain - ecosystem interface needs an improved understanding of ARG contamination mechanisms and targeted monitoring and evaluation systems should be developed to maintain all ecosystem services in freshwater reservoirs as well as to safeguard human health.
Collapse
Affiliation(s)
- Zhao-Feng Guo
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Wiebke J Boeing
- Department of Fish, Wildlife & Conservation Ecology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Yao-Yang Xu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China.
| | - Edoardo Borgomeo
- Environmental Change Institute, University of Oxford, Oxford OX1 3QY, UK
| | - Dong Liu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| |
Collapse
|
10
|
Zhang X, Yao MC, Chen L, Sheng GP. Lewis Acid-Base Interaction Triggering Electron Delocalization to Enhance the Photodegradation of Extracellular Antibiotic Resistance Genes Adsorbed on Clay Minerals. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17684-17693. [PMID: 36455257 DOI: 10.1021/acs.est.2c05785] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The transformation of extracellular antibiotic resistance genes (eARGs) is largely influenced by their inevitable photodegradation in environments where they tend to be adsorbed by ubiquitous clay minerals instead of being in a free form. However, the photodegradation behaviors and mechanisms of the adsorbed eARGs may be quite different from those of the free form and still remain unclear. Herein, we found that kaolinite, a common 1:1-type clay, markedly enhanced eARG photodegradation and made eARGs undergo direct photodegradation under UVA. The decrease in the transformation efficiency of eARGs caused by photodegradation was also promoted. Spectroscopy methods combined with density functional theory calculations revealed that the Lewis acid-base interaction between P-O in eARGs and Al-OH on kaolinite delocalized electrons of eARGs, thus resulting in increased photon absorption ability of eARGs. This ultimately led to enhanced photodegradation of kaolinite-adsorbed eARGs. Additionally, divalent Ca2+ could reduce the Lewis acid-base interaction-mediated adsorption of eARGs by kaolinite, thereby weakening the enhanced photodegradation of eARGs caused by electron delocalization. In contrast, the 2:1-type clay montmorillonite without strong Lewis acid sites was unable to delocalize the electrons to enhance the photodegradation of eARGs. This work allowed us to better evaluate eARGs' fate and risk in real aqueous environments.
Collapse
Affiliation(s)
- Xin Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei230026, China
| | - Mu-Cen Yao
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei230026, China
| | - Lin Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei230026, China
| | - Guo-Ping Sheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei230026, China
| |
Collapse
|
11
|
Chowdhury NN, Hicks E, Wiesner MR. Investigating and Modeling the Regulation of Extracellular Antibiotic Resistance Gene Bioavailability by Naturally Occurring Nanoparticles. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15044-15053. [PMID: 35853206 PMCID: PMC9979080 DOI: 10.1021/acs.est.2c02878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Extracellular antibiotic resistance genes (eARGs) are widespread in the environment and can genetically transform bacteria. This work examined the role of environmentally relevant nanoparticles (NPs) in regulating eARG bioavailability. eARGs extracted from antibiotic-resistant B. subtilis were incubated with nonresistant recipient B. subtilis cells. In the mixture, particle type (either humic acid coated nanoparticles (HASNPs) or their micron-sized counterpart (HASPs)), DNase I concentration, and eARG type were systematically varied. Transformants were counted on selective media. Particles decreased bacterial growth and eARG bioavailability in systems without nuclease. When DNase I was present (≥5 μg/mL), particles increased transformation via chromosomal (but not plasmid-borne) eARGs. HASNPs increased transformation more than HASPs, indicating that the smaller nanoparticle with greater surface area per volume is more effective in increasing eARG bioavailability. These results were also modeled via particle aggregation theory, which represented eARG-bacteria interactions as transport leading to collision, followed by attachment. Using attachment efficiency as a fitting factor, the model predicted transformant concentrations within 35% of experimental data. These results confirm the ability of NPs to increase eARG bioavailability and suggest that particle aggregation theory may be a simplified and suitable framework to broadly predict eARG uptake.
Collapse
Affiliation(s)
- Nadratun N Chowdhury
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Ethan Hicks
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Mark R Wiesner
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina 27708, United States
| |
Collapse
|
12
|
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]
|
13
|
Zuo X, Chen S, Wang T, Zhang S, Li T. Leaching risks of antibiotic resistance genes in urban underlying surface sediments during the simulated stormwater runoff and its controls. WATER RESEARCH 2022; 221:118735. [PMID: 35714468 DOI: 10.1016/j.watres.2022.118735] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/16/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Recently, increasing attention has been paid to antibiotic resistance genes (ARGs) in urban stormwater runoff. However, no available literature could be found on ARGs leaching from urban underlying surface sediments during stormwater runoff. In this study, surface sediments from commercial public squares around Nanjing (China) was selected for the investigation of target ARGs leaching kinetics, showing that absolute abundances of target ARGs desorption reached at the equilibrium during leaching time of 120-240min with all of the desorption efficiencies about 30%, indicating that there would be low proportion of leaching ARGs in the total ARGs migrating with runoff during rainfall events. Five target ARGs leaching including intI1 (clinic), strA, strB, tetM and tetX can be better described by the pseudo-second-order equation, while qacEdelta1 leaching can be better described by the pseudo-first-order equation, and the leaching for both sul1 and sul2 can be well described by the pseudo-first-order and pseudo-second-order equations. The effects of environmental factors including S/L ratios, pH values and water temperatures indicated that leaching efficiencies of target ARGs enhanced significantly with the increase of S/L ratios and water temperatures, but decreased with the increase of pH values. The transmission experiments after the simulated solar irradiation and heat implied that both large solar UV irradiation (30W/m2) and high temperature (40℃) were conducive to conjugation and transformation frequencies of ARGs. Furthermore, both high Cao and medium PAM levels could be effective for blocking ARGs transmission in the leachate from underlying surface sediments.
Collapse
Affiliation(s)
- XiaoJun Zuo
- Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China; Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Jiangsu Joint Laboratory of Atmospheric Pollution Control, Nanjing, 210044, China.
| | - ShaoJie Chen
- Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China; Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Jiangsu Joint Laboratory of Atmospheric Pollution Control, Nanjing, 210044, China
| | - Tao Wang
- School of Environment Engineering, Wuxi University, Wuxi 214105, China
| | - SongHu Zhang
- Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China; Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Jiangsu Joint Laboratory of Atmospheric Pollution Control, Nanjing, 210044, China
| | - Ting Li
- Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China; Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Jiangsu Joint Laboratory of Atmospheric Pollution Control, Nanjing, 210044, China
| |
Collapse
|
14
|
Palomba E, Chiaiese P, Termolino P, Paparo R, Filippone E, Mazzoleni S, Chiusano ML. Effects of Extracellular Self- and Nonself-DNA on the Freshwater Microalga Chlamydomonas reinhardtii and on the Marine Microalga Nannochloropsis gaditana. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111436. [PMID: 35684209 PMCID: PMC9183124 DOI: 10.3390/plants11111436] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 05/11/2023]
Abstract
The role of extracellular DNA (exDNA) in soil and aquatic environments was mainly discussed in terms of source of mineral nutrients and of genetic material for horizontal gene transfer. Recently, the self-exDNA (conspecific) has been shown to have an inhibitory effect on the growth of that organism, while the same was not evident for nonself-exDNA (non conspecific). The inhibitory effect of self-exDNA was proposed as a universal phenomenon, although evidence is mainly reported for terrestrial species. The current study showed the inhibitory effect of self-exDNA also on photosynthetic aquatic microorganisms. We showed that self-exDNA inhibits the growth of the microalgae Chlamydomonas reinhardtii and Nannochloropsis gaditana, a freshwater and a marine species, respectively. In addition, the study also revealed the phenotypic effects post self-exDNA treatments. Indeed, Chlamydomonas showed the formation of peculiar heteromorphic aggregates of palmelloid cells embedded in an extracellular matrix, favored by the presence of DNA in the environment, that is not revealed after exposure to nonself-exDNA. The differential effect of self and nonself-exDNA on both microalgae, accompanied by the inhibitory growth effect of self-exDNA are the first pieces of evidence provided for species from aquatic environments.
Collapse
Affiliation(s)
- Emanuela Palomba
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn”, 80121 Naples, Italy;
| | - Pasquale Chiaiese
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources, National Research Council, 80055 Portici, Italy; (P.T.); (R.P.)
| | - Rosa Paparo
- Institute of Biosciences and Bioresources, National Research Council, 80055 Portici, Italy; (P.T.); (R.P.)
| | - Edgardo Filippone
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
| | - Maria Luisa Chiusano
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn”, 80121 Naples, Italy;
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
- Correspondence: ; Tel.: +39-81-2539492
| |
Collapse
|
15
|
Extracellular DNA in environmental samples: Occurrence, extraction, quantification, and impact on microbial biodiversity assessment. Appl Environ Microbiol 2021; 88:e0184521. [PMID: 34818108 DOI: 10.1128/aem.01845-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Environmental DNA, i.e., DNA directly extracted from environmental samples, has been applied to understand microbial communities in the environments and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggest several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by: (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods including qPCR and fluorescent DNA binding dyes; (iii) carefully interpretating effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.
Collapse
|
16
|
Yanlong C, Kejian Y, Yin Y, Yuhan Z, Huizi M, Cui L, Zhonghui L, Ziru P, Fan C, Jiangtao Y, Xianwei W, Yuheng W. Reductive soil disinfestation attenuates antibiotic resistance genes in greenhouse vegetable soils. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126632. [PMID: 34293692 DOI: 10.1016/j.jhazmat.2021.126632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
Reductive soil disinfestation (RSD) is an emerging technique that ameliorates soil degradation, but its effects against antibiotic resistance genes (ARGs) were unclear. Here, we examined soil properties, ARG types and numbers, and ARG profiles, and bacterial community compositions following 4 soil treatments: control; straw addition (SA); water flooding (WF); and RSD, both straw addition and water flooding. The results showed that the numbers of ARG types and subtypes decreased by 10.8% and 21.1%, respectively, after RSD, and the numbers of ARGs decreased by 18.6%. The attenuated multidrug, beta-lactam, macrolide, and phenicol resistance genes in the RSD soil corresponded to a decreased relative abundance of ARG subtypes (i.e., adeF, mdtM, TypeB_NfxB, mecA, nalC, OXA-60, and cmlA4). Taxa in phyla Proteobacteria, Actinobacteria, and Deinococcus-Thermus were the main hosts for dominant ARG subtypes and were inhibited by RSD. The selected bacterial genera and soil properties explained 83.4% of the variance in ARG composition, suggesting that the improved soil properties and the reduced potential ARG hosts produced by the interactions of straw addition and water flooding are likely responsible for ARG attenuation by RSD. Therefore, RSD has the potential to mitigate ARG pollution in soils.
Collapse
Affiliation(s)
- Chen Yanlong
- School of Ecology and Environment, Northwestern Polytechnical University, 710000 Xi'an, Shaanxi, China.
| | - Yang Kejian
- Shaanxi Hydrogeology Engineering Geology and Environment Geology Survey Center, 710068 Xi'an, Shaanxi, China
| | - Ye Yin
- School of Ecology and Environment, Northwestern Polytechnical University, 710000 Xi'an, Shaanxi, China
| | - Zhang Yuhan
- School of Ecology and Environment, Northwestern Polytechnical University, 710000 Xi'an, Shaanxi, China
| | - Mi Huizi
- School of Ecology and Environment, Northwestern Polytechnical University, 710000 Xi'an, Shaanxi, China
| | - Li Cui
- School of Ecology and Environment, Northwestern Polytechnical University, 710000 Xi'an, Shaanxi, China
| | - Li Zhonghui
- Shaanxi Hydrogeology Engineering Geology and Environment Geology Survey Center, 710068 Xi'an, Shaanxi, China
| | - Pei Ziru
- School of Ecology and Environment, Northwestern Polytechnical University, 710000 Xi'an, Shaanxi, China
| | - Chen Fan
- School of Ecology and Environment, Northwestern Polytechnical University, 710000 Xi'an, Shaanxi, China
| | - Yan Jiangtao
- Shaanxi Hydrogeology Engineering Geology and Environment Geology Survey Center, 710068 Xi'an, Shaanxi, China
| | - Wang Xianwei
- Shaanxi Hydrogeology Engineering Geology and Environment Geology Survey Center, 710068 Xi'an, Shaanxi, China
| | - Wang Yuheng
- School of Ecology and Environment, Northwestern Polytechnical University, 710000 Xi'an, Shaanxi, China
| |
Collapse
|
17
|
Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11199182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.
Collapse
|
18
|
Yang J, Li T, Feng T, Yu Q, Su W, Zhou R, Li X, Li H. Water volume influences antibiotic resistomes and microbiomes during fish corpse decomposition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:147977. [PMID: 34052485 DOI: 10.1016/j.scitotenv.2021.147977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
Corpse decomposition may cause serious pollution (e.g., releasing antibiotic resistance genes) to the water environment, thereby threatening public health. However, whether antibiotic resistance genes (ARGs) and microbiomes are affected by different water volumes during carcass decomposition remains unknown. Here, we investigated the effects of large/small water volumes on microbial communities and ARGs during fish cadaver decomposition by 16S rRNA high-throughput sequencing and high-throughput quantitative PCR. The results showed that the large water volume almost eliminated the effects of corpse decomposition on pH, total organic carbon (TOC), and total nitrogen (TN). When the water volume enlarged by 62.5 fold, the relative abundances of some ARGs resisting tetracycline and sulfonamide during carcass decomposition decreased by 217 fold on average, while there was also a mean 5267 fold increase of vancomycin resistance genes. Compared with the control group, the enriched types of ARGs varied between the large and small volume. Water volume, mobile genetic elements, and carcass decomposition were the most important factors affecting ARG profiles. Many opportunistic pathogens (like Bacteroides and Comamonas) were enriched in the corpse group. Bacteroides and Comamonas may be potential hosts of ARGs, indicating the potential for the spread of ARGs to humans by water pathogenic bacteria. This research highlights that the "dilution effect" can contribute to eliminating this adverse effect during corpse decomposition to a certain extent. It may provide references for environmental governance and public health.
Collapse
Affiliation(s)
- Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Tongtong Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Tianshu Feng
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Rui Zhou
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China.
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China.
| |
Collapse
|
19
|
Xue X, Wang L, Xing H, Zhao Y, Li X, Wang G, Wang Z. Characteristics of phytoplankton-zooplankton communities and the roles in the transmission of antibiotic resistance genes under the pressure of river contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146452. [PMID: 33770605 DOI: 10.1016/j.scitotenv.2021.146452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Insight into the distribution of antibiotic resistance genes (ARGs) in phytoplankton-zooplankton communities (PZCs) is essential for the management and control of antibiotic resistance in aquatic ecosystems. This study characterized the profiles of PZCs and their carried ARGs in a typical urban river and ranked the factors (water physicochemical parameters, PZCs, bacterial abundance, and mobile genetic elements) influencing the dynamic of ARG profiles by the partial least squares path modeling. Results showed Cyanobacteria, Bacillariophyta and Chlorophyta were dominant phyla of phytoplankton, and Rotifera was with the highest abundance in zooplankton. River contamination markedly altered the structure of PZCs, increasing the abundance of phytoplankton and zooplankton, decreasing the diversity of phytoplankton while elevating in zooplankton. PZCs harbored large amounts of ARGs with average relative abundance of 2.35 × 10-2/copies nearly an order magnitude higher than the living water and most ARGs exhibited significant accumulation in PZCs with the aggravated environmental pollution. The partial least squares path modeling predicted the water parameters as the most important factor mainly playing indirect effects on ARGs via PZCs and bacterial communities, followed by mobile genetic elements as the most essential direct factor for ARGs profiles. Besides, PZCs were also important drivers for the carried ARGs via direct effects on the ARGs' composition and indirect effects on host bacterial communities of ARGs and their mobile genetic elements. The present study fills the gaps in knowledge about the distribution of ARGs in PZCs and provided a new perspective to decipher the key roles of PZCs in the maintenance and dissemination of ARGs in urban river ecosystems.
Collapse
Affiliation(s)
- Xue Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lihong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haoran Xing
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangju Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gaoxue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
20
|
Lin Z, Yuan T, Zhou L, Cheng S, Qu X, Lu P, Feng Q. Impact factors of the accumulation, migration and spread of antibiotic resistance in the environment. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2021; 43:1741-1758. [PMID: 33123928 DOI: 10.1007/s10653-020-00759-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance is a great concern, which leads to global public health risks and ecological and environmental risks. The presence of antibiotic-resistant genes and antibiotic-resistant bacteria in the environment exacerbates the risk of spreading antibiotic resistance. Among them, horizontal gene transfer is an important mode in the spread of antibiotic resistance genes, and it is one of the reasons that the antibiotic resistance pollution has become increasingly serious. At the same time, free antibiotic resistance genes and resistance gene host bacterial also exist in the natural environment. They can not only affect horizontal gene transfer, but can also migrate and aggregate among environmental media in many ways and then continue to affect the proliferate and transfer of antibiotic resistance genes. All this shows the seriousness of antibiotic resistance pollution. Therefore, in this review, we reveal the sensitive factors affecting the distribution and spread of antibiotic resistance through three aspects: the influencing factors of horizontal gene transfer, the host bacteria of resistance genes and the migration of antibiotic resistance between environmental media. This review reveals the huge role of environmental migration in the spread of antibiotic resistance, and the environmental behavior of antibiotic resistance deserves wider attention. Meanwhile, extracellular antibiotic resistance genes and intracellular antibiotic resistance genes play different roles, so they should be studied separately.
Collapse
Affiliation(s)
- Zibo Lin
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
| | - Tao Yuan
- Department of Construction Equipment and Municipal Engineering, Jiangsu Vocational Institute of Architectural Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
- Jiangsu Collaborative Innovation Center for Building Energy Saving and Construct Technology, Xuzhou, 221116, China
| | - Lai Zhou
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
| | - Sen Cheng
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
| | - Xu Qu
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
| | - Ping Lu
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China.
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China.
| | - Qiyan Feng
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Fang J, Jin L, Meng Q, Wang D, Lin D. Interactions of extracellular DNA with aromatized biochar and protection against degradation by DNase I. J Environ Sci (China) 2021; 101:205-216. [PMID: 33334516 DOI: 10.1016/j.jes.2020.08.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 06/12/2023]
Abstract
With increasing environmental application, biochar (BC) will inevitably interact with and impact environmental behaviors of widely distributed extracellular DNA (eDNA), which however still remains to be studied. Herein, the adsorption/desorption and the degradation by nucleases of eDNA on three aromatized BCs pyrolyzed at 700 °C were firstly investigated. The results show that the eDNA was irreversibly adsorbed by aromatized BCs and the pseudo-second-order and Freundlich models accurately described the adsorption process. Increasing solution ionic strength or decreasing pH below 5.0 significantly increased the eDNA adsorption on BCs. However, increasing pH from 5.0 to 10.0 faintly decreased eDNA adsorption. Electrostatic interaction, Ca ion bridge interaction, and π-π interaction between eDNA and BC could dominate the eDNA adsorption, while ligand exchange and hydrophobic interactions were minor contributors. The presence of BCs provided a certain protection to eDNA against degradation by DNase I. BC-bound eDNA could be partly degraded by nuclease, while BC-bound nuclease completely lost its degradability. These findings are of fundamental significance for the potential application of biochar in eDNA dissemination management and evaluating the environmental fate of eDNA.
Collapse
Affiliation(s)
- Jing Fang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou 310023, China; School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Liang Jin
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Qingkang Meng
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Dengjun Wang
- Oak Ridge Institute for Science and Education (ORISE) Resident Research Associate, United States Environmental Protection Agency, Ada, OK 74820, USA
| | - Daohui Lin
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
23
|
Xu M, Wang F, Sheng H, Stedtfeld RD, Li Z, Hashsham SA, Jiang X, Tiedje JM. Does anaerobic condition play a more positive role in dissipation of antibiotic resistance genes in soil? THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143737. [PMID: 33243511 DOI: 10.1016/j.scitotenv.2020.143737] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
The persistence of antibiotic resistance genes (ARGs) under the aerobic vs. anaerobic conditions is unknown, especially under different fertilization. Towards this goal, a microcosm experiment was carried out with chemical fertilized and manured soil under aerobic and anaerobic conditions. High throughput qPCR was used to analyze ARGs with 144 primer sets and sequencing for microorganisms. Completely different dynamics of ARGs were observed in soil under aerobic and anaerobic conditions, regardless of the fertilization type. ARGs had different half-lives, even though they confer resistance to the same type of antibiotics. Aminoglycoside, chloramphenicol, macrolide - lincosamide - streptogramin B (MLSB) and tetracycline resistance genes were significantly accumulated in the aerobic soils. Anaerobic soil possessed a higher harboring capacity for exogenous microorganisms and ARGs than aerobic soil. The interaction between ARGs and mobile genetic elements (MGEs) in manured soil under aerobic condition was more pronounced than the anaerobic condition. These findings unveil that anaerobic soil could play a more positive role in reducing potential risk of ARGs in the farmland environment.
Collapse
Affiliation(s)
- Min Xu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA.
| | - Hongjie Sheng
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA
| | - Zhongpei Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
| |
Collapse
|
24
|
Guo XP, Zhao S, Chen YR, Yang J, Hou LJ, Liu M, Yang Y. Antibiotic resistance genes in sediments of the Yangtze Estuary: From 2007 to 2019. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140713. [PMID: 32693274 DOI: 10.1016/j.scitotenv.2020.140713] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/01/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
To better understand the occurrence and succession of antibiotic resistance genes (ARGs) in the environment, the investigation of ARGs in sediment for a long time scale is urgently needed. In this study, sediment samples were taken in the Yangtze Estuarine area from 2007 to 2019, and the interannual variations in ARGs and their possible physicochemical and socioeconomic influencing factors were analyzed. The results showed that the abundance of ARGs, including sul1, sul2, tetM, tetW, aac(6')-Ib and qnrS, was higher in recent years (from 2015 to 2019) than that in earlier years (from 2007 to 2011), and heavier ARG pollution was found in Wusongkou (WSK) samples than in Liuhekou (LHK) samples. According to the redundancy discriminant analysis (RDA) and correlation analysis, the antibiotics (especially individual antibiotic categories, including oxytetracycline, doxycycline hyclate and norfloxacin), metals and a metal resistance gene (zntA) and total organic carbon (TOC) showed significant correlations to ARGs. In addition, antibiotics, metals, TOC and ARGs were also significantly correlated with several socioeconomic indices. Furthermore, the extended STIRPAT model analysis revealed that the second industry product and the first industry product were the major socioeconomic driver factors for the ARG distribution at WSK and LHK, respectively. Overall, with socioeconomic development, antibiotics, metals, TOC and ARGs increased in sediment. In addition, antibiotics, metals and TOC may participate in the regulation of the occurrence and distribution of ARGs in the Yangtze Estuary for the long time scale.
Collapse
Affiliation(s)
- Xing-Pan Guo
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Sai Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yu-Ru Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jing Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China; Institute of Eco-Chongming, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China; Institute of Eco-Chongming, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| |
Collapse
|
25
|
Wang Z, Chen Q, Zhang J, Guan T, Chen Y, Shi W. Critical roles of cyanobacteria as reservoir and source for antibiotic resistance genes. ENVIRONMENT INTERNATIONAL 2020; 144:106034. [PMID: 32777621 DOI: 10.1016/j.envint.2020.106034] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 06/11/2023]
Abstract
The widespread occurrence of antibiotic resistance genes (ARGs) throughout aquatic environments has raised global concerns for public health, but understanding of the emergence and propagation of ARGs in diverse environmental media remains limited. This study investigated the occurrence and spatio-temporal patterns of six classes of ARGs in cyanobacteria isolated from Taihu Lake. Tetracycline and sulfonamide resistance genes were identified as dominant ARGs. The abundance of ARGs in cyanobacteria was significantly higher in the bloom period than in the non-bloom period. The contribution and persistence of ARGs were higher in extracellular DNA (eDNA) than in intracellular DNA (iDNA) from cyanobacteria. Cyanobacteria-associated eDNA carrying ARGs was more stable at lower temperature. The relative abundances of ARGs in Microcystis and Synechococcus, the dominant genera of cyanobacterial blooms in Taihu Lake, were significantly higher than those in other cyanobacterial strains. The conjugative transfer efficiency for bacterial assimilation of ARGs in cyanobacteria was facilitated by increasing temperature and cyanobacterial cell concentration. Our results demonstrated that cyanobacteria could act as a significant reservoir and source for the acquisition and dissemination of ARGs in aquatic environments, hence the definition of negative ecological effects of cyanobacterial blooms was expanded.
Collapse
Affiliation(s)
- Zhiyuan Wang
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Qiuwen Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China.
| | - Jianyun Zhang
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Tiesheng Guan
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Yuchen Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Wenqing Shi
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Microbial Interaction with Clay Minerals and Its Environmental and Biotechnological Implications. MINERALS 2020. [DOI: 10.3390/min10100861] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Clay minerals are very common in nature and highly reactive minerals which are typical products of the weathering of the most abundant silicate minerals on the planet. Over recent decades there has been growing appreciation that the prime involvement of clay minerals in the geochemical cycling of elements and pedosphere genesis should take into account the biogeochemical activity of microorganisms. Microbial intimate interaction with clay minerals, that has taken place on Earth’s surface in a geological time-scale, represents a complex co-evolving system which is challenging to comprehend because of fragmented information and requires coordinated efforts from both clay scientists and microbiologists. This review covers some important aspects of the interactions of clay minerals with microorganisms at the different levels of complexity, starting from organic molecules, individual and aggregated microbial cells, fungal and bacterial symbioses with photosynthetic organisms, pedosphere, up to environmental and biotechnological implications. The review attempts to systematize our current general understanding of the processes of biogeochemical transformation of clay minerals by microorganisms. This paper also highlights some microbiological and biotechnological perspectives of the practical application of clay minerals–microbes interactions not only in microbial bioremediation and biodegradation of pollutants but also in areas related to agronomy and human and animal health.
Collapse
|
28
|
Chen YR, Guo XP, Niu ZS, Lu DP, Sun XL, Zhao S, Hou LJ, Liu M, Yang Y. Antibiotic resistance genes (ARGs) and their associated environmental factors in the Yangtze Estuary, China: From inlet to outlet. MARINE POLLUTION BULLETIN 2020; 158:111360. [PMID: 32573452 DOI: 10.1016/j.marpolbul.2020.111360] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
The occurrence of antibiotic resistance genes (ARGs) and their associated environmental factors in estuaries are poorly understood. In this study, we comprehensively analyzed ARGs in both water and sediments from inlet to outlet of the Yangtze Estuary, China. The relative abundances of ARGs were higher in the turbidity maximum zone (TMZ) than other sites, implying that suspended particulate matter (SPM) was the major reservoir for ARGs in water. ARGs showed an increasing trend from inlet to outlet in sediments. Positively correlation between intI1 and sul1 in both water and sediments indicated that sul1 may be regulated by intI1. Correlation analysis and redundancy analysis showed that the spatial variations of estuarine ARGs were positively correlated with sample properties (e.g., temperature, SPM, pH) and chemical pollutants (e.g., heavy metals and antibiotic residues), among which chemical pollutants were the major drivers for the ARG distribution in both water and sediments.
Collapse
Affiliation(s)
- Yu-Ru Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xing-Pan Guo
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zuo-Shun Niu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Da-Pei Lu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiao-Li Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Sai Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
| |
Collapse
|
29
|
Wang C, Song L, Zhang Z, Wang Y, Xie X. Microwave-induced release and degradation of airborne antibiotic resistance genes (ARGs) from Escherichia coli bioaerosol based on microwave absorbing material. JOURNAL OF HAZARDOUS MATERIALS 2020; 394:122535. [PMID: 32213383 DOI: 10.1016/j.jhazmat.2020.122535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/18/2020] [Accepted: 03/12/2020] [Indexed: 06/10/2023]
Abstract
Antibiotic resistance genes (ARGs) have been detected in the atmosphere. Airborne ARGs transmission threatens human health. In the present study, we investigated the release and degradation of airborne ARGs from Escherichia coli bioaerosol through microwave (MW) irradiation. In this study, a new MW absorbing material (Fe3O4@SiC ceramic foam) that contributed to its stronger MW absorption is presented. When the MW input energy density was 7.4 × 103 kJ/m3, the concentration of airborne Escherichia coli decreased by 4.4 log. Different DNA forms were found in the air because MW irradiation ruptured cell membranes. The bound particles provide more protection for bound DNA in the degradation process than free DNA. After the self-degradation of the released airborne free ARGs, some of them would remain and continue to spread in the atmosphere. The released airborne free ARGs cannot be ignored. Total ARGs concentrations decrease rapidly with increased temperature. The inactivation rate constant of ARGs through MW irradiation is higher than that through the Fenton and UV, however, the energy efficiency per order of MW irradiation is lower. Therefore, MW irradiation with Fe3O4@SiC ceramic foam could efficiently degrade the distribution of ARGs in the atmosphere.
Collapse
Affiliation(s)
- Can Wang
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, PR China; School of Environmental Science and Engineering, Tianjin University, Tianjin, PR China; School of Civil and Environmental Engineering, Georgia Institute of Technology, GA, USA.
| | - Lu Song
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, PR China; School of Environmental Science and Engineering, Tianjin University, Tianjin, PR China
| | - ZhiWei Zhang
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, PR China; School of Environmental Science and Engineering, Tianjin University, Tianjin, PR China
| | - YiZhu Wang
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, PR China; School of Environmental Science and Engineering, Tianjin University, Tianjin, PR China
| | - Xing Xie
- School of Civil and Environmental Engineering, Georgia Institute of Technology, GA, USA
| |
Collapse
|
30
|
Pathan SI, Arfaioli P, Ceccherini MT, Ascher-Jenull J, Pietramellara G. Preliminary evidences of the presence of extracellular DNA single stranded forms in soil. PLoS One 2020; 15:e0227296. [PMID: 31910237 PMCID: PMC6946138 DOI: 10.1371/journal.pone.0227296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/16/2019] [Indexed: 11/18/2022] Open
Abstract
The relevance of extracellular DNA (eDNA) in the soil ecosystem is becoming more and more evident to the scientific community by the progressive discovery of functions accompanying to natural gene transformation. However, despite the increased number of published articles dedicated to eDNA in soil, so far only few are focused on its single stranded form (eDNAss). The present paper is the first to investigate the quantitative relevance of eDNAss in the total soil eDNA pool, discriminating between its linear (eDNAssl) and circular (eDNAssc) forms and the respective weakly (wa) and tightly (ta) adsorbed fractions. The results showed the prevalence of eDNAss and its linear form in both the total soil eDNA pool and its wa and ta fractions. Both of the eDNAss fractions (linear and circular) were characterized by small fragments.
Collapse
Affiliation(s)
- Shamina Imran Pathan
- Department of Agri-food, Environmental, Forestry Science and Technology (DAGRI), University of Florence, Piazzale delle Cascine, Florence, Italy
| | - Paola Arfaioli
- Department of Agri-food, Environmental, Forestry Science and Technology (DAGRI), University of Florence, Piazzale delle Cascine, Florence, Italy
| | - Maria Teresa Ceccherini
- Department of Agri-food, Environmental, Forestry Science and Technology (DAGRI), University of Florence, Piazzale delle Cascine, Florence, Italy
| | | | - Giacomo Pietramellara
- Department of Agri-food, Environmental, Forestry Science and Technology (DAGRI), University of Florence, Piazzale delle Cascine, Florence, Italy
- * E-mail:
| |
Collapse
|
31
|
Development and validation of rapid environmental DNA (eDNA) detection methods for bog turtle (Glyptemys muhlenbergii). PLoS One 2019; 14:e0222883. [PMID: 31725720 PMCID: PMC6855662 DOI: 10.1371/journal.pone.0222883] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/09/2019] [Indexed: 11/24/2022] Open
Abstract
Bog turtles (Glyptemys muhlenbergii) are listed as Species of Greatest Conservation Need (SGCN) for wildlife action plans in every state it occurs and multi-state efforts are underway to better characterize extant populations and prioritize restoration efforts. However, traditional sampling methods can be ineffective due to the turtle’s wetland habitat, small size, and burrowing nature. Molecular methods, such as qPCR, provide the ability to overcome this challenge by effectively quantifying minute amounts of turtle DNA left behind in its environment (eDNA). Developing such methods for bog turtles has proved difficult partly because of the high sequence similarity between bog turtles and closely-related, cohabitating species, most often wood turtles (Glyptemys insculpta). Additionally, substrates containing bog turtle eDNA are often rich in organics or other substances that frequently inhibit both DNA extraction and qPCR amplification. Here, we describe the development and validation of a qPCR assay, BT3, targeting the mitochondrial cytochrome oxidase I gene that correctly identifies bog turtles with 100% specificity and sensitivity when tested on 201 blood samples collected from six species over a wide geographic range. We also developed a full-process internal control employing a genetically modified strain of Caenorhabditis elegans to improve DNA extraction methods, limit false negative results due to qPCR inhibition, and measure total DNA recovery from each sample. Using the internal control, we found that DNA recovery varied by over an order of magnitude between samples and likely explains the lack of bog turtle detection in some cases. Methods presented herein are highly-specific and may offer a more cost effective, non-invasive tool to supplement bog turtle population assessments in the Eastern United States. Poor or differential DNA recovery, which remains unmeasured in the vast majority of eDNA studies, significantly reduced the ability to detect bog turtle in their natural environment.
Collapse
|
32
|
Sheng X, Qin C, Yang B, Hu X, Liu C, Waigi MG, Li X, Ling W. Metal cation saturation on montmorillonites facilitates the adsorption of DNA via cation bridging. CHEMOSPHERE 2019; 235:670-678. [PMID: 31276880 DOI: 10.1016/j.chemosphere.2019.06.159] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/02/2019] [Accepted: 06/21/2019] [Indexed: 05/19/2023]
Abstract
Extracellular DNA (eDNA) is widely present in soil, with potential ecological impacts. Metal cations are naturally present on the surface of soil clay minerals, although the adsorption mechanism of eDNA on clay minerals saturated with metal cations is still not fully understood. The research investigated the adsorption of eDNA, using salmon sperm DNA as a representative, on metal cation (Na+, Ca2+, and Fe3+)-saturated montmorillonites (Mt). Metal cation-saturated Mt have higher adsorption capacities for DNA. Compared with Mt (3500 mg⋅kg-1), the amounts of DNA adsorption on metal cation-saturated Mt (pH = 7.0) were increased by 0.74-5.38 times, and followed the descending order of Fe-Mt > Na-Mt > Ca-Mt > Mt. A temperature of 25 °C was found to be more suitable than 15 and 35 °C for DNA adsorption, while an increasing pH value (3.0-9.0) reduced DNA adsorption on Mt and metal cation-saturated Mt. Microscopic and spectroscopic analyses, together with a model computation technique, confirmed that metal cations saturated on the surface of Mt work like a "cation bridge" linking oxygen atoms in the phosphate groups of DNA and the negatively charged moieties of Mt, which were predominantly bound through electrostatic forces, thus, facilitating DNA adsorption at pH > 5. The results of this investigation provide valuable insight into eDNA adsorption on soil clay minerals and the transport and fate of eDNA in the natural soil environment.
Collapse
Affiliation(s)
- Xue Sheng
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Cun Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210023, China
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xuelin Li
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China.
| |
Collapse
|
33
|
Roki N, Tsinas Z, Solomon M, Bowers J, Getts RC, Muro S. Unprecedently high targeting specificity toward lung ICAM-1 using 3DNA nanocarriers. J Control Release 2019; 305:41-49. [PMID: 31100312 DOI: 10.1016/j.jconrel.2019.05.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/05/2019] [Accepted: 05/13/2019] [Indexed: 12/17/2022]
Abstract
DNA nanostructures hold great potential for drug delivery. However, their specific targeting is often compromised by recognition by scavenger receptors involved in clearance. In our previous study in cell culture, we showed targeting specificity of a 180 nm, 4-layer DNA-built nanocarrier called 3DNA coupled with antibodies against intercellular adhesion molecule-1 (ICAM-1), a glycoprotein overexpressed in the lungs in many diseases. Here, we examined the biodistribution of various 3DNA formulations in mice. A formulation consisted of 3DNA whose outer-layer arms were hybridized to secondary antibody-oligonucleotide conjugates. Anchoring IgG on this formulation reduced circulation and kidney accumulation vs. non-anchored IgG, while increasing liver and spleen clearance, as expected for a nanocarrier. Anchoring anti-ICAM changed the biodistribution of this antibody similarly, yet this formulation specifically accumulated in the lungs, the main ICAM-1 target. Since lung targeting was modest (2-fold specificity index over IgG formulation), we pursued a second preparation involving direct hybridization of primary antibody-oligonucleotide conjugates to 3DNA. This formulation had prolonged stability in serum and showed a dramatic increase in lung distribution: the specificity index was 424-fold above a matching IgG formulation, 144-fold more specific than observed for PLGA nanoparticles of similar size, polydispersity, ζ-potential and antibody valency, and its lung accumulation increased with the number of anti-ICAM molecules per particle. Immunohistochemistry showed that anti-ICAM and 3DNA components colocalized in the lungs, specifically associating with endothelial markers, without apparent histological changes. The degree of in vivo targeting for anti-ICAM/3DNA-nanocarriers is unprecedented, for which this platform technology holds great potential to develop future therapeutic applications.
Collapse
Affiliation(s)
- Nikša Roki
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Zois Tsinas
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Melani Solomon
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | | | | | - Silvia Muro
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA; Institute for Bioengineering of Catalonia of the Barcelona Institute of Science and Technology, Institution of Catalonia for Research and Advanced Studies, Barcelona, Spain.
| |
Collapse
|
34
|
Organochlorinated pesticides expedite the enzymatic degradation of DNA. Commun Biol 2019; 2:81. [PMID: 30820476 PMCID: PMC6391446 DOI: 10.1038/s42003-019-0326-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 01/24/2019] [Indexed: 01/31/2023] Open
Abstract
Extracellular DNA in the environment may play important roles in genetic diversity and biological evolution. However, the influence of environmental persistent organic contaminants such as organochlorinated pesticides (e.g., hexachlorocyclohexanes [HCHs]) on the enzymatic degradation of extracellular DNA has not been elucidated. In this study, we observed expedited enzymatic degradation of extracellular DNA in the presence of α-HCH, β-HCH and γ-HCH. The HCH-expedited DNA degradation was not due to increased deoxyribonuclease I (DNase I) activity. Our spectroscopic and computational results indicate that HCHs bound to DNA bases (most likely guanine) via Van der Waals forces and halogen bonds. This binding increased the helicity and accumulation of DNA base pairs, leading to a more compact DNA structure that exposed more sites susceptible to DNase I and thus expedited DNA degradation. This study provided insight into the genotoxicity and ecotoxicity of pesticides and improved our understanding of DNA persistence in contaminated environments.
Collapse
|
35
|
High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.07.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
36
|
Guo XP, Liu X, Niu ZS, Lu DP, Zhao S, Sun XL, Wu JY, Chen YR, Tou FY, Hou L, Liu M, Yang Y. Seasonal and spatial distribution of antibiotic resistance genes in the sediments along the Yangtze Estuary, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:576-584. [PMID: 30014935 DOI: 10.1016/j.envpol.2018.06.099] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/28/2018] [Accepted: 06/28/2018] [Indexed: 05/26/2023]
Abstract
Antibiotics resistance genes (ARGs) are considered as an emerging pollutant among various environments. As a sink of ARGs, a comprehensive study on the spatial and temporal distribution of ARGs in the estuarine sediments is needed. In the present study, six ARGs were determined in sediments taken along the Yangtze Estuary temporally and spatially. The sulfonamides, tetracyclines and fluoroquinolones resistance genes including sul1, sul2, tetA, tetW, aac(6')-Ib, and qnrS, were ubiquitous, and the average abundances of most ARGs showed significant seasonal differences, with relative low abundances in winter and high abundances in summer. Moreover, the relative high abundances of ARGs were found at Shidongkou (SDK) and Wusongkou (WSK), which indicated that the effluents from the wastewater treatment plant upstream and inland river discharge could influence the abundance of ARGs in sediments. The positive correlation between intI1 and sul1 implied intI1 may be related to the occurrence and propagation of sulfonamides resistance genes. Correlation analysis and redundancy discriminant analysis showed that antibiotic concentrations had no significant correlation to their corresponding ARGs, while the total extractable metal, especially the bioavailable metals, as well as other environmental factors including temperature, clay, total organic carbon and total nitrogen, could regulate the occurrence and distribution of ARGs temporally and spatially. Our findings suggested the comprehensive effects of multiple pressures on the distribution of ARGs in the sediments, providing new insight into the distribution and dissemination of ARGs in estuarine sediments, spatially and temporally.
Collapse
Affiliation(s)
- Xing-Pan Guo
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xinran Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zuo-Shun Niu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Da-Pei Lu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Sai Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiao-Li Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jia-Yuan Wu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yu-Ru Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Fei-Yun Tou
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
| |
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
Jesus CRN, Molina EF, Pulcinelli SH, Santilli CV. Highly Controlled Diffusion Drug Release from Ureasil-Poly(ethylene oxide)-Na +-Montmorillonite Hybrid Hydrogel Nanocomposites. ACS APPLIED MATERIALS & INTERFACES 2018; 10:19059-19068. [PMID: 29749723 DOI: 10.1021/acsami.8b04559] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this work, we report the effects of incorporation of variable amounts (1-20 wt %) of sodium montmorillonite (MMT) into a siloxane-poly(ethylene oxide) hybrid hydrogel prepared by the sol-gel route. The aim was to control the nanostructural features of the nanocomposite, improve the release profile of the sodium diclofenac (SDCF) drug, and optimize the swelling behavior of the hydrophilic matrix. The nanoscopic characteristics of the siloxane-cross-linked poly(ethylene oxide) network, the semicrystallinity of the hybrid, and the intercalated or exfoliated structure of the clay were investigated by X-ray diffraction, small-angle X-ray scattering, and differential scanning calorimetry. The correlation between the nanoscopic features of nanocomposites containing different amounts of MMT and the swelling behavior revealed the key role of exfoliated silicate in controlling the water uptake by means of a flow barrier effect. The release of the drug from the nanocomposite displayed a stepped pattern kinetically controlled by the diffusion of SDCF molecules through the mass transport barrier created by the exfoliated silicate. The sustained SDCF release provided by the hybrid hydrogel nanocomposite could be useful for the prolonged treatment of painful conditions, such as arthritis, sprains and strains, gout, migraine, and pain after surgical procedures.
Collapse
Affiliation(s)
- Celso R N Jesus
- Instituto de Química, UNESP , Rua Professor Francisco Degni 55 , Araraquara , São Paulo 14800-900 , Brazil
| | - Eduardo F Molina
- Universidade de Franca , Av. Dr. Armando Salles Oliveira 201 , Franca , São Paulo 14404-600 , Brazil
| | - Sandra H Pulcinelli
- Instituto de Química, UNESP , Rua Professor Francisco Degni 55 , Araraquara , São Paulo 14800-900 , Brazil
| | - Celso V Santilli
- Instituto de Química, UNESP , Rua Professor Francisco Degni 55 , Araraquara , São Paulo 14800-900 , Brazil
| |
Collapse
|
39
|
Zhang Y, Niu Z, Zhang Y, Zhang K. Occurrence of intracellular and extracellular antibiotic resistance genes in coastal areas of Bohai Bay (China) and the factors affecting them. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 236:126-136. [PMID: 29414333 DOI: 10.1016/j.envpol.2018.01.033] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 06/08/2023]
Abstract
Coastal areas are the transition zones between ocean and land where intracellular antibiotic resistance genes (iARGs) and extracellular antibiotic resistance genes (eARGs) could spread among marine organisms, and between humans and marine organisms. However, little attention has been paid to the combined research on iARGs and eARGs in marine environment. In this context, we collected water and sediment samples from the coastal areas of the Bohai Bay in China and performed molecular and chemical analyses. The results of quantitative real-time PCR (qPCR) showed that the relative abundance of eARGs was up to 4.3 ± 1.3 × 10-1 gene copies/16S rRNA copies in the water samples and 2.6 ± 0.3 × 10-3 gene copies/16S rRNA copies in the sediment samples. Also, the abundance of eARGs was significantly higher than that of iARGs. Furthermore, the average abundances of antibiotic resistance genes (ARGs, include iARGs and eARGs) were the highest in both the water and sediment samples from the estuaries. The results of liquid chromatography-mass spectrometry showed that the concentrations of antibiotics in estuaries and areas near the mariculture site were higher than that in the other sites. The class 1 integron gene (int1) and sul1 in the intracellular DNA were significantly correlated in the water samples. Moreover, significant correlation between int1 and sul2 in the extracellular DNA was also found in the sediment samples. The combination of sulfamerazine and tetracycline as well as the combination of sulfamethazine and dissolved oxygen can both explain the abundance of ARGs, implying the combined effects of multiple stresses on ARGs.
Collapse
Affiliation(s)
- Yongpeng Zhang
- School of Marine Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhiguang Niu
- School of Marine Science and Technology, Tianjin University, Tianjin, 300072, China.
| | - Ying Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
| | - Kai Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| |
Collapse
|
40
|
Zhu YG, Gillings M, Simonet P, Stekel D, Banwart S, Penuelas J. Human dissemination of genes and microorganisms in Earth's Critical Zone. GLOBAL CHANGE BIOLOGY 2018; 24:1488-1499. [PMID: 29266645 DOI: 10.1111/gcb.14003] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
Earth's Critical Zone sustains terrestrial life and consists of the thin planetary surface layer between unaltered rock and the atmospheric boundary. Within this zone, flows of energy and materials are mediated by physical processes and by the actions of diverse organisms. Human activities significantly influence these physical and biological processes, affecting the atmosphere, shallow lithosphere, hydrosphere, and biosphere. The role of organisms includes an additional class of biogeochemical cycling, this being the flow and transformation of genetic information. This is particularly the case for the microorganisms that govern carbon and nitrogen cycling. These biological processes are mediated by the expression of functional genes and their translation into enzymes that catalyze geochemical reactions. Understanding human effects on microbial activity, fitness and distribution is an important component of Critical Zone science, but is highly challenging to investigate across the enormous physical scales of impact ranging from individual organisms to the planet. One arena where this might be tractable is by studying the dynamics and dissemination of genes for antibiotic resistance and the organisms that carry such genes. Here we explore the transport and transformation of microbial genes and cells through Earth's Critical Zone. We do so by examining the origins and rise of antibiotic resistance genes, their subsequent dissemination, and the ongoing colonization of diverse ecosystems by resistant organisms.
Collapse
Affiliation(s)
- Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Université de Lyon, Lyon, France
| | - Dov Stekel
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Steven Banwart
- Department of Geography, The University of Sheffield, Sheffield, UK
| | - Josep Penuelas
- CSIC, Global Ecology Unit, CREAF- CSIC-UAB, Barcelona, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| |
Collapse
|
41
|
Högfors-Rönnholm E, Christel S, Engblom S, Dopson M. Indirect DNA extraction method suitable for acidic soil with high clay content. MethodsX 2018; 5:136-140. [PMID: 30622912 PMCID: PMC6314954 DOI: 10.1016/j.mex.2018.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 02/18/2018] [Indexed: 12/02/2022] Open
Abstract
DNA extraction is an essential procedure when investigating microbial communities in environmental samples by sequencing technologies. High clay soils can be problematic as DNA adsorbs to the clay particles and can thereby be preserved from lysed, non-viable cells for a substantial period of time. In order to accurately estimate the intact and living microbial community in the soil, extracellular DNA from dead, remnant bacterial cells needs to be removed prior to DNA extraction. One possibility is to use a sodium phosphate buffer to release both extracellular DNA and bacterial cells from the clay particles. After removing the extracellular DNA by centrifugation, the remaining viable cells can be harvested and DNA extracted. The described method is a modification of a procedure for separating extracellular DNA and bacterial cells from acidic clay soils. The modified method increases bacterial cell yields from acidic clay soils, such as acid sulfate soil. The modified method eliminates some steps from the original method, as only DNA from intact bacterial cells is required. The indirect DNA extraction method increases the workload compared to standard direct extraction methods, but subsequent downstream analyses will give a more representative picture of the viable microbial community composition in the soil.
Collapse
Affiliation(s)
- Eva Högfors-Rönnholm
- Research and Development, Novia University of Applied Sciences, Vaasa, Finland
- Corresponding author.
| | - Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Sten Engblom
- Research and Development, Novia University of Applied Sciences, Vaasa, Finland
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| |
Collapse
|
42
|
The use of extracellular DNA as a proxy for specific microbial activity. Appl Microbiol Biotechnol 2018; 102:2885-2898. [PMID: 29423636 PMCID: PMC5847193 DOI: 10.1007/s00253-018-8786-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/11/2018] [Accepted: 01/14/2018] [Indexed: 02/07/2023]
Abstract
The ubiquity and relevance of extracellular DNA (exDNA) are well-known and increasingly gaining importance in many fields of application such as medicine and environmental microbiology. Although sources and types of exDNA are manifold, ratios of specific DNA-molecules inside and outside of living cells can give reliable information about the activity of entire systems and of specific microbial groups or species. Here, we introduce a method to discriminate between internal (iDNA), as well as bound and free exDNA, and evaluate various DNA fractions and related ratios (ex:iDNA) regarding their applicability to be used as a fast, convenient, and reliable alternative to more tedious RNA-based activity measurements. In order to deal with microbial consortia that can be regulated regarding their activity, we tested and evaluated the proposed method in comparison to sophisticated dehydrogenase- and RNA-based activity measurements with two anaerobic microbial consortia (anaerobic fungi and syntrophic archaea and a microbial rumen consortium) and three levels of resolution (overall activity, total bacteria, methanogenic archaea). Furthermore, we introduce a 28S rRNA gene-specific primer set and qPCR protocol, targeting anaerobic fungi (Neocallimastigomycota). Our findings show that the amount of actively released free exDNA (fDNA) strongly correlates with different activity measurements and is thus suggested to serve as a proxy for microbial activity.
Collapse
|
43
|
Guo XP, Yang Y, Lu DP, Niu ZS, Feng JN, Chen YR, Tou FY, Garner E, Xu J, Liu M, Hochella MF. Biofilms as a sink for antibiotic resistance genes (ARGs) in the Yangtze Estuary. WATER RESEARCH 2018; 129:277-286. [PMID: 29156392 DOI: 10.1016/j.watres.2017.11.029] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/09/2017] [Accepted: 11/11/2017] [Indexed: 06/07/2023]
Abstract
Biofilms are ubiquitous throughout aquatic environments and they are thought to promote the acquisition and dissemination of antibiotic resistant genes (ARGs). This study focused on the occurrence and distribution of five types of ARG in naturally-occurring biofilms, in comparison to associated sediment and water samples, from the Yangtze Estuary, which borders the meta-city of Shanghai, China. The detection frequency and abundances of most ARGs showed the following order: biofilm > sediment > water, which can be attributed to a high level of antibiotics and metals that can accelerate the generation and propagation of ARGs in biofilms. Most of ARG abundances were contributed by extracellular DNA (eDNA) in biofilm and sediment samples. ARGs (sul1, sul2, tetA and tetW) in eDNA were significantly correlated with TOC in both biofilm and sediment samples. Furthermore, both intracellular DNA-associated ARGs per gram of microbial biomass carbon (MBC) and eDNA-associated ARGs per gram of non-MBC and were higher in biofilms than sediments, and the partitioning coefficients of ARGs in eDNA between biofilm and water were higher than those between sediment and water. Our results provide new insight for evaluating the occurrence and abundance of ARGs in aquatic environments, confirming that biofilms are a significant sink for ARGs in the estuarine environment.
Collapse
Affiliation(s)
- Xing-Pan Guo
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
| | - Da-Pei Lu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zuo-Shun Niu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jing-Nan Feng
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yu-Ru Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Fei-Yun Tou
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Emily Garner
- Charles E. Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, 418 Durham Hall, Blacksburg, VA 24061, USA
| | - Jiang Xu
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh 15213, USA
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Michael F Hochella
- The Center for NanoBioEarth, Department of Geosciences, Virginia Tech, Blacksburg, VA 24061, USA; Geosciences Group, Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| |
Collapse
|
44
|
Mantha S, Anderson A, Acharya SP, Harwood VJ, Weidhaas J. Transport and attenuation of Salmonella enterica, fecal indicator bacteria and a poultry litter marker gene are correlated in soil columns. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 598:204-212. [PMID: 28441599 DOI: 10.1016/j.scitotenv.2017.04.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
Millions of tons of fecal-contaminated poultry litter are applied to U.S. agricultural fields annually. Precipitation and irrigation facilitate transport of fecal-derived pathogens and fecal indicator bacteria (FIB) to groundwater. The goal of this study was to compare transport of pathogens, FIB, and a microbial source tracking marker gene for poultry litter (LA35) in a simulated soil-to-groundwater system. Nine laboratory soil columns containing four different soil types were used to evaluate microbial transport to groundwater via infiltration. Quantitative polymerase chain reaction was used to monitor Salmonella enterica Typhimurium, Escherichia coli, Enterococcus spp., Brevibacterium sp. LA35 and Bacteroidales leached from soil columns inoculated with poultry litter. S. enterica was correlated with LA35 poultry litter marker gene and FIB concentrations in column soils containing organic matter, but not in acid washed sands. In contrast, S. enterica was found to correlate with LA35 and FIB in the leachate from columns containing sand, but not with leachate from organic soil columns. The majority of recovered DNA was found in leachate of predominately sandy soil columns, and in the soil of loamy columns. At least 90% of the DNA retained in soils for each microbial target was found in the top 3cm of the column. These studies suggest that poultry litter associated pathogens and FIB are rapidly released from litter, but are influenced by complex attenuation mechanisms during infiltration, including soil type. This study advances our understanding of the potential for subsurface transport of poultry litter associated pathogens and FIB, and support the use of the LA35 marker gene for evaluating poultry litter impacts on groundwater.
Collapse
Affiliation(s)
- Sirisha Mantha
- Civil and Environmental Engineering, West Virginia University, United States
| | - Angela Anderson
- Civil and Environmental Engineering, West Virginia University, United States
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, United States
| | - Jennifer Weidhaas
- Civil and Environmental Engineering, University of Utah, 110 Central Campus Drive, Salt Lake City, UT 84112, United States.
| |
Collapse
|
45
|
|
46
|
Schmidt MP, Martínez CE. Ironing Out Genes in the Environment: An Experimental Study of the DNA-Goethite Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:8525-8532. [PMID: 28732154 DOI: 10.1021/acs.langmuir.7b01911] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
DNA fate in soil plays an important role in the cycling of genetic information in the environment. Adsorption onto mineral surfaces has great impact on this function. This study probes the kinetics, equilibrium behavior and bonding mechanisms associated with adsorption of DNA onto goethite, a common soil mineral. Surface sensitive ATR-FTIR and XPS approaches are applied to directly characterize the DNA-goethite interface. Adsorption kinetics follow a pseudo-first-order model, suggesting adsorption rate is surface limited. Adsorption rate constants increase with DNA concentration, ranging from 3.29 × 10-3 to 3.55 × 10-1 min-1. Equilibrium adsorption, as monitored by ATR-FTIR and XPS, follows the Langmuir model, with a high affinity of DNA for goethite observed (K = 1.25 × 103 and 9.48 × 102 mL/mg for ATR-FTIR and XPS, respectively). ATR-FTIR and XPS characterization of the structure of surface adsorbed DNA demonstrates inner-sphere coordination between backbone phosphate groups of DNA and goethite. Furthermore, adsorbed DNA retains a B-form, suggesting the DNA helix adsorbs on goethite without degradation or alteration to helical structure, despite binding of backbone phosphate groups. This work advances our understanding of the environmental behavior of DNA by characterizing the mechanism of adsorption onto a prominent soil mineral.
Collapse
Affiliation(s)
- Michael P Schmidt
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University , Ithaca, New York 14853, United States
| | - Carmen E Martínez
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University , Ithaca, New York 14853, United States
| |
Collapse
|
47
|
Han D, Nam SI, Kim JH, Stein R, Niessen F, Joe YJ, Park YH, Hur HG. Inference on Paleoclimate Change Using Microbial Habitat Preference in Arctic Holocene Sediments. Sci Rep 2017; 7:9652. [PMID: 28851886 PMCID: PMC5575242 DOI: 10.1038/s41598-017-08757-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/19/2017] [Indexed: 12/11/2022] Open
Abstract
The present study combines data of microbial assemblages with high-resolution paleoceanographic records from Core GC1 recovered in the Chukchi Sea. For the first time, we have demonstrated that microbial habitat preferences are closely linked to Holocene paleoclimate records, and found geological, geochemical, and microbiological evidence for the inference of the sulphate-methane transition zone (SMTZ) in the Chukchi Sea. In Core GC1, the layer of maximum crenarchaeol concentration was localized surrounding the SMTZ. The vertically distributed predominant populations of Gammaproteobacteria and Marine Group II Euryarchaeota (MG-II) were consistent with patterns of the known global SMTZs. MG-II was the most prominent archaeal group, even within the layer of elevated concentrations of crenarchaeol, an archaeal lipid biomarker most commonly used for Marine Group I Thaumarchaeota (MG-I). The distribution of MG-I and MG-II in Core GC1, as opposed to the potential contribution of MG-I to the marine tetraether lipid pool, suggests that the application of glycerol dibiphytanyl glycerol tetraethers (GDGT)-based proxies needs to be carefully considered in the subsurface sediments owing to the many unknowns of crenarchaeol. In conclusion, microbiological profiles integrated with geological records seem to be useful for tracking microbial habitat preference, which reflect climate-triggered changes from the paleodepositional environment.
Collapse
Affiliation(s)
- Dukki Han
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Seung-Il Nam
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
| | - Ji-Hoon Kim
- Petroleum and Marine Research Division, Korea Institute of Geosciences and Mineral Resources, 124 Gwahang-no Yuseong-gu, Daejeon, 34131, Republic of Korea
| | - Ruediger Stein
- Alfred Wegener Institute (AWI) Helmholtz Centre for Polar and Marine Research, Am Alten Hafen 26, Bremerhaven, 27568, Germany.,Department of Geosciences (FB5), Klagenfurter Str. 4, University of Bremen, 28359, Bremen, Germany
| | - Frank Niessen
- Alfred Wegener Institute (AWI) Helmholtz Centre for Polar and Marine Research, Am Alten Hafen 26, Bremerhaven, 27568, Germany
| | - Young Jin Joe
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Yu-Hyeon Park
- Division of Earth Environmental System, Pusan National University, Busan, 609-735, Republic of Korea
| | - Hor-Gil Hur
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.
| |
Collapse
|
48
|
Highmore CJ, Rothwell SD, Keevil CW. Improved sample preparation for direct quantitative detection of Escherichia coli O157 in soil using qPCR without pre-enrichment. Microb Biotechnol 2017; 10:969-976. [PMID: 28585286 PMCID: PMC5481516 DOI: 10.1111/1751-7915.12737] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 04/29/2017] [Indexed: 12/01/2022] Open
Abstract
The prominence of fresh produce as a vehicle for foodborne pathogens such as enterohaemorrhagic Escherichia coli (EHEC) O157 is rising, where disease cases can cause hospitalization and in some cases death. This rise emphasises the necessity for accurate and sensitive methods for detection of pathogens in soil, potential sources of contamination of fresh produce. The complexity of the soil matrix has previously proven prohibitive to pathogen detection via molecular methods without the use of a culture enrichment step, thereby excluding the detection of viable but non-culturable cells. Here, a sample preparation procedure to facilitate a direct qPCR assay is developed for the detection of E. coli O157 in soil, bypassing culture steps in favour of sample separation through pulsification release and filtration. In sand and peat-based compost, the method is sensitive to 10 CFU g-1 soil. When testing soils from agricultural sites, it was found that several were qPCR positive for E. coli O157 while being culture-negative, with peat-based compost possessing a concentration of 200 tir gene copies per gram. This procedure offers a rapid, quantitative assessment of the potential presence of E. coli O157 in soils which can act as a prescreen of their suitability to grow fresh produce safely.
Collapse
Affiliation(s)
- Callum J Highmore
- Environmental Healthcare Unit, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton, UK, SO17 1BJ
| | - Steve D Rothwell
- Vitacress Salads Ltd, Lower Link Farm, St Mary Bourne, Andover, UK, SP11 6DB
| | - Charles W Keevil
- Environmental Healthcare Unit, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton, UK, SO17 1BJ
| |
Collapse
|
49
|
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.
Collapse
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.
| |
Collapse
|
50
|
Nguyen D, Boberg J, Ihrmark K, Stenström E, Stenlid J. Do foliar fungal communities of Norway spruce shift along a tree species diversity gradient in mature European forests? FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|