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Pei Y, Sun M, Zhang J, Lei A, Chen H, Kang X, Ni H, Yang S. Comparative Metagenomic and Metatranscriptomic Analyses Reveal the Response of Black Soldier Fly ( Hermetia illucens) Larvae Intestinal Microbes and Reduction Mechanisms to High Concentrations of Tetracycline. TOXICS 2023; 11:611. [PMID: 37505576 PMCID: PMC10386730 DOI: 10.3390/toxics11070611] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023]
Abstract
Black soldier fly (Hermetia illucens L) larvae (BSFL) possess remarkable antibiotic degradation abilities due to their robust intestinal microbiota. However, the response mechanism of BSFL intestinal microbes to the high concentration of antibiotic stress remains unclear. In this study, we investigated the shift in BSFL gut microbiome and the functional genes that respond to 1250 mg/kg of tetracycline via metagenomic and metatranscriptomic analysis, respectively. The bio-physiological phenotypes showed that the survival rate of BSFL was not affected by tetracycline, while the biomass and substrate consumption of BSFL was slightly reduced. Natural BSFL achieved a 20% higher tetracycline degradation rate than the germ-free BSFL after 8 days of rearing. Metagenomic and metatranscriptomic sequencing results revealed the differences between the entire and active microbiome. Metatranscriptomic analysis indicated that Enterococcus, Vagococcus, Providencia, and Paenalcaligenes were the active genera that responded to tetracycline. Furthermore, based on the active functional genes that responded to tetracycline pressure, the response mechanisms of BSFL intestinal microbes were speculated as follows: the Tet family that mediates the expression of efflux pumps expel tetracycline out of the microbes, while tetM and tetW release it from the ribosome. Eventually, tetracycline was degraded by deacetylases and novel enzymes. Overall, this study provides novel insights about the active intestinal microbes and their functional genes in insects responding to the high concentration of antibiotics.
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Affiliation(s)
- Yaxin Pei
- Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Mengxiao Sun
- Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Jiran Zhang
- Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Aojie Lei
- Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Hongge Chen
- Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiangtao Kang
- Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Hongyuhang Ni
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Sen Yang
- Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
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Lachka M, Soltisova K, Nosalova L, Timkova I, Pevna V, Willner J, Janakova I, Luptakova A, Sedlakova-Kadukova J. Metal-containing landfills as a source of antibiotic tolerance. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:262. [PMID: 36600113 DOI: 10.1007/s10661-022-10873-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
To unveil the potential effect of metal presence to antibiotic tolerance proliferation, four sites of surface landfills containing tailings from metal processing in Slovakia (Hnúšťa, Hodruša, Košice) and Poland (Tarnowskie Góry) were investigated. Tolerance and multitolerance to selected metals (Cu, Ni, Pb, Fe, Zn, Cd) and antibiotics (ampicillin, tetracycline, chloramphenicol, and kanamycin) and interrelationships between them were evaluated. A low bacterial diversity (Shannon-Wiener index from 0.83 to 2.263) was detected in all sampling sites. Gram-positive bacteria, mostly belonging to the phylum Actinobacteria, dominated in three of the four sampling sites. The recorded percentages of tolerant bacterial isolates varied considerably for antibiotics and metals from 0 to 57% and 0.8 to 47%, respectively, among the sampling sites. Tolerances to chloramphenicol (45-57%) and kanamycin (32-45%) were found in three sites. Multitolerance to several metals and antibiotics in the range of 24 to 48% was recorded for three sites. A significant positive correlation (p < 0.05) for the co-occurrence of tolerance to each studied metal and at least one of the antibiotics was observed. Exposure time to the metal (landfill duration) was an important factor for the development of metal- as well as antibiotic-tolerant isolates. The results show that metal-contaminated sites represent a significant threat for human health not only for their toxic effects but also for their pressure to antibiotic tolerance spread in the environment.
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Affiliation(s)
- M Lachka
- Faculty of Natural Science, University of Ss. Cyril and Methodius in Trnava, Nam. J. Herdu 2, 917 01, Trnava, Slovakia
| | - K Soltisova
- Faculty of Natural Science, Pavol Jozef Safarik University in Kosice, Srobarova 2, 041 54, Košice, Slovakia
| | - L Nosalova
- Faculty of Natural Science, Pavol Jozef Safarik University in Kosice, Srobarova 2, 041 54, Košice, Slovakia
| | - I Timkova
- Faculty of Natural Science, Pavol Jozef Safarik University in Kosice, Srobarova 2, 041 54, Košice, Slovakia
| | - V Pevna
- Faculty of Natural Science, Pavol Jozef Safarik University in Kosice, Srobarova 2, 041 54, Košice, Slovakia
| | - J Willner
- Faculty of Materials Engineering, Silesian University of Technology, Ul. Akademicka 2A, 44 100, Gliwice, Poland
| | - I Janakova
- Faculty of Mining and Geology, VSB Technical University of Ostrava, 17. Listopadu 15, 708 00, Poruba, Ostrava, Czech Republic
| | - A Luptakova
- Institute of Geotechnics, Slovak Academy of Sciences, Watsonova 45, 040 01, Košice, Slovakia
| | - J Sedlakova-Kadukova
- Faculty of Natural Science, University of Ss. Cyril and Methodius in Trnava, Nam. J. Herdu 2, 917 01, Trnava, Slovakia.
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Xu Y, Li H, Tan L, Li Q, Liu W, Zhang C, Gao Y, Wei X, Gong Q, Zheng X. What role does organic fertilizer actually play in the fate of antibiotic resistome and pathogenic bacteria in planting soil? JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 317:115382. [PMID: 35623127 DOI: 10.1016/j.jenvman.2022.115382] [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: 03/30/2022] [Revised: 05/08/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Organic fertilizer increase antibiotic resistance genes (ARGs) and bacterial pathogens have widely documented. However, how organic fertilizer is involved in changing soil ARGs and pathogenic bacteria after long-term (≥5 years) application remains unclear. Herein, the ARGs and pathogenic bacteria were compared in organic fertilized soils (AF) and non-fertilized soils (NF), and the contribution of input sources (organic fertilizer, irrigation water, air and background soil) on soil ARGs also was determined in this study. Results showed that the abundances of some ARGs, such as vanR and aac(6')-I in AF, were significantly higher than these of NF (p < 0.05). And a relatively higher abundance of potential pathogens, especially, Salmonella enterica and Stenotrophomonas maltophilia, in AF was observed. This indicated that organic fertilizer application can maintain a high level of some soil ARGs and pathogenic bacteria for at least 5 years. Traceability analysis unearthed that organic fertilizer application mainly increased its own contribution to soil ARGs from 1.16% to 9.05%, as well reduced the contribution of background soil, suggesting that the increase in soil ARGs may be partly attributable to organic fertilizer inputs. Notably, organic fertilizer application did not significantly alter the contribution ratio of input sources to microorganisms, but there was a clear change in the composition of soil microorganisms, which meant that the effect of the input source on the microorganism may emanate from other factors, rather than direct inputs. Subsequent structural equation demonstrated that organic fertilizer application significantly enhanced the effect of environmental factors on ARGs, and also indirectly increased the influence of communities on ARGs. Collectively, under the long-term fertilization, the role of organic fertilizers on soil ARGs not just stems from its own input, and also dominates the influence of environmental factors on ARGs. This study elucidates main causes for the difference in ARGs in AF vs. NF and enlightens actual role of organic fertilizer in them.
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Affiliation(s)
- Yan Xu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, 300191, China; Department F.A. Forel for Environmental and Aquatic Sciences, Section of Earth and Environmental Sciences and Institute for Environmental Sciences, University of Geneva, Switzerland
| | - Houyu Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, 300191, China
| | - Lu Tan
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, 300191, China
| | - Qian Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, 300191, China
| | - Wei Liu
- Department F.A. Forel for Environmental and Aquatic Sciences, Section of Earth and Environmental Sciences and Institute for Environmental Sciences, University of Geneva, Switzerland
| | - Chunxue Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, 300191, China
| | - Yi Gao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, 300191, China
| | - Xiaocheng Wei
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, 300191, China
| | - Qiong Gong
- Shangrao Normal University, Jiangxi, 334001, China
| | - Xiangqun Zheng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, 300191, China.
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Qing L, Qigen D, Jian H, Hongjun W, Jingdu C. Profiles of tetracycline resistance genes in paddy soils with three different organic fertilizer applications. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119368. [PMID: 35489540 DOI: 10.1016/j.envpol.2022.119368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/01/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
The rapid expansion of organic rice cultivation areas have been accompanied by increased application of organic fertilizers. The high prevalence of soil antibiotic resistance caused by organic fertilizer application poses a severe threat to the agricultural and soil ecosystems. To date, research efforts and understanding of the effects and mechanism of action of the various organic fertilizers on antibiotic resistance in paddy soils remain poorly investigated. Tetracycline resistance genes (TRGs, including tetB, tetC, tetL, tetZ, tetM, tetO, tetT, and tetX), class 1 integron-integrase gene (intI1) and bacterial communities were characterized using quantitative-PCR and Illumina MiSeq sequencing, in paddy soils exposed to inorganic fertilizer (NPK), animal-derived organic fertilizer (AOF, composted swine and/or chicken manure), plant-derived organic fertilizer (POF, rapeseed cake and/or astragalus) and commercial organic fertilizer (COF, composted of animal manure mix with crop residues) applications. Compared with NPK, AOF applications significantly increased the relative abundance of TRGs, which was predominantly expressed in the increase of the relative abundance of tetC, tetM, tetO, tetT, and tetX, while POF and COF had no significant effect on the relative abundance of TRGs. Principal coordinate analysis revealed that AOF and POF significantly altered bacterial communities in paddy soils relative to NPK, while COF had no significant change of bacterial communities. Variation partitioning analysis indicated that soil physicochemical properties were the decisive factors for the changes of TRGs in organic paddy fields. Furthermore, redundancy analysis and the Mantel test showed that TRG profiles in AOF applied paddy soils were strongly influenced by electrical conductivity (EC). Total nitrogen (TN) and organic matter (OM) affected the distribution of TRGs in COF and POF applied paddy soils through a different mechanism. This study provides insights into the impacts of different types of organic fertilizer on the profiles of TRGs in paddy soils.
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Affiliation(s)
- Li Qing
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China
| | - Dai Qigen
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Hu Jian
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Wu Hongjun
- Yangzhou Supervision & Inspection Center for Agri-products, Yangzhou, 225101, China
| | - Chen Jingdu
- Yangzhou Municipal Bureau of Agriculture and Rural Affairs, Yangzhou, 225000, China
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Profile of Bacterial Community and Antibiotic Resistance Genes in Typical Vegetable Greenhouse Soil. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19137742. [PMID: 35805398 PMCID: PMC9265268 DOI: 10.3390/ijerph19137742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 12/10/2022]
Abstract
The use of vegetable greenhouse production systems has increased rapidly because of the increasing demand for food materials. The vegetable greenhouse production industry is confronted with serious environmental problems, due to their high agrochemical inputs and intensive utilization. Besides this, antibiotic-resistant bacteria, carrying antibiotic-resistance genes (ARGs), may enter into a vegetable greenhouse with the application of animal manure. Bacterial communities and ARGs were investigated in two typical vegetable-greenhouse-using counties with long histories of vegetable cultivation. The results showed that Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi, and Gemmatimonadetes were the dominant phyla, while aadA, tetL, sul1, and sul2 were the most common ARGs in greenhouse vegetable soil. Heatmap and principal coordinate analysis (PCoA) demonstrated that the differences between two counties were more significant than those among soils with different cultivation histories in the same county, suggesting that more effects on bacterial communities and ARGs were caused by soil type and manure type than by the accumulation of cultivation years. The positive correlation between the abundance of the intI gene with specific ARGs highlights the horizontal transfer potential of these ARGs. A total of 11 phyla were identified as the potential hosts of specific ARGs. Based on redundancy analysis (RDA), Ni and pH were the most potent factors determining the bacterial communities, and Cr was the top factor affecting the relative abundance of the ARGs. These results might be helpful in drawing more attention to the risk of manure recycling in the vegetable greenhouse, and further developing a strategy for practical manure application and sustainable production of vegetable greenhouses.
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Kang Y, Xu W, Zhang Y, Tang X, Bai Y, Hu J. Bloom of tetracycline resistance genes in mudflats following fertilization is attributed to the increases in the shared potential hosts between soil and organic fertilizers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:13292-13304. [PMID: 34585344 DOI: 10.1007/s11356-021-16676-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
A field experiment was carried out in mudflats adjacent to the Yellow Sea, China, amended with sewage sludge and vermicompost by one-time input at different rates to reveal the fates of tetracycline resistance genes (TRGs) and their potential hosts in the soils. Quantitative PCR results showed that soils added with either sludge or vermicompost had more abundant TRGs compared with the non-fertilized soil. This situation was more obvious in sludge fertilized soils especially at high application rates. Vermicompost exhibited a promising outlook for improvement of the mudflats. The abundances of intI1 in the non-fertilized soils were significantly higher than those in fertilizers and fertilized soils. The potential hosts for intI1 were not shared with other TRGs-contained hosts, indicating that intI1 had little effects on the dissemination of TRGs in the mudflats. Moreover, the exclusive hosts for TRGs in fertilizers were not higher than those in the non-fertilized soils, illustrating little effects of fertilization on the introduction of exogenous TRGs into soil. The shared hosts between soil and fertilizers were highest among four possible sources, contributing vastly to the bloom of TRGs following fertilization. It was also shown that different organic fertilizers caused distinct categories of shared potential hosts for TRGs. RDA analysis further indicated that the abundances of the shared potential hosts were affected by soil nutrients. These results suggested that the development of TRGs in soil following fertilization depended on the shared potential hosts with similar ecological niches between soil and fertilizers.
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Affiliation(s)
- Yijun Kang
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, People's Republic of China
| | - Wenjie Xu
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Yang Zhang
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Xingyao Tang
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, People's Republic of China
| | - Yanchao Bai
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Jian Hu
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.
- Yancheng Teachers University, 2 South Hope Avenue, Yancheng, Jiangsu, People's Republic of China, 224007.
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Peng S, Wang Y, Chen R, Lin X. Chicken Manure and Mushroom Residues Affect Soil Bacterial Community Structure but Not the Bacterial Resistome When Applied at the Same Rate of Nitrogen for 3 Years. Front Microbiol 2021; 12:618693. [PMID: 34093457 PMCID: PMC8177108 DOI: 10.3389/fmicb.2021.618693] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 04/19/2021] [Indexed: 01/17/2023] Open
Abstract
Animal manure is a reservoir of antibiotic resistance genes (ARGs), and direct application of the manure will lead to spread of ARGs in farmland. Here, we explored the impacts of chicken manure and heat-treated chicken manure on the patterns of soil resistome after 3 years’ application, with mushroom residues set as the plant-derived organic manure treatment. A total of 262 ARG subtypes were detected in chicken manure using high-throughput qPCR, and heat treatment can effectively remove 50 types of ARGs. Although ARG subtypes and abundance were both higher in chicken manure, there was no significant difference in the ARG profiles and total ARG abundance among three manure-treated soils. Soil bacteria community compositions were significantly different among manure-treated soils, but they were not significantly correlated with soil ARG profiles. Fast expectation–maximization microbial source tracking (FEAST) was used for quantifying the contributions of the potential sources to microbial taxa and ARGs in manure-fertilized soil. Results revealed that only 0.2% of the chicken manure-derived bacterial communities survived in soil, and intrinsic ARGs were the largest contributor of soil ARGs (95.8–99.7%); ARGs from chicken manure only contributed 0.4%. The total ARG abundance in the heat-treated chicken manure-amended soils was similar to that in the mushroom residue-treated soils, while it was 1.41 times higher in chicken manure-treated soils. Thus, heat treatment of chicken manure may efficiently reduce ARGs introduced into soil and decrease the risk of dissemination of ARGs.
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Affiliation(s)
- Shuang Peng
- College of Environment and Ecology, Jiangsu Open University, Nanjing, China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yiming Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China
| | - Ruirui Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Sabri NA, van Holst S, Schmitt H, van der Zaan BM, Gerritsen HW, Rijnaarts HHM, Langenhoff AAM. Fate of antibiotics and antibiotic resistance genes during conventional and additional treatment technologies in wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 741:140199. [PMID: 32615424 DOI: 10.1016/j.scitotenv.2020.140199] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/11/2020] [Accepted: 06/11/2020] [Indexed: 05/23/2023]
Abstract
Information on the removal of antibiotics and ARGs in full-scale WWTPs (with or without additional treatment technology) is limited. However, it is important to understand the efficiency of full-scale treatment technologies in removing antibiotics and ARGs under a variety of conditions relevant for practice to reduce their environmental spreading. Therefore, this study was performed to evaluate the removal of antibiotics and ARGs in a conventional wastewater treatment plant (WWTP A) and two full-scale combined with additional treatment technologies. WWTP B, a conventional activated sludge treatment followed by an activated carbon filtration step (1-STEP® filter) as a final treatment step. WWTP C, a treatment plant using aerobic granular sludge (NEREDA®) as an alternative to activated sludge treatment. Water and sludge were collected and analysed for 52 antibiotics from four target antibiotic groups (macrolides, sulfonamides, quinolones, tetracyclines) and four target ARGs (ermB, sul 1, sul 2 and tetW) and integrase gene class 1 (intI1). Despite the high removal percentages (79-88%) of the total load of antibiotics in all WWTPs, some antibiotics were detected in the various effluents. Additional treatment technology (WWTP C) showed antibiotics removal up to 99% (tetracyclines). For ARGs, WWTP C reduced 2.3 log followed by WWTP A with 2.0 log, and WWTP B with 1.3 log. This shows that full-scale WWTP with an additional treatment technology are promising solutions for reducing emissions of antibiotics and ARGs from wastewater treatment plants. However, total removal of the antibiotics and ARGS cannot be achieved for all types of antibiotics and ARGs. In addition, the ARGs were more abundant in the sludge compared to the wastewater effluent suggesting that sludge is an important reservoir representing a source for later ARG emissions upon reuse, i.e. as fertilizer in agriculture or as resource for bioplastics or bioflocculants. These aspects require further research.
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Affiliation(s)
- N A Sabri
- Department of Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - S van Holst
- Department of Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - H Schmitt
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - B M van der Zaan
- Deltares, Subsurface and Groundwater Systems, Daltonlaan 600, 3584 KB Utrecht, the Netherlands
| | - H W Gerritsen
- Wageningen Food Safety Research (WFSR), Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, the Netherlands
| | - H H M Rijnaarts
- Department of Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - A A M Langenhoff
- Department of Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands.
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Cuadrat RRC, Sorokina M, Andrade BG, Goris T, Dávila AMR. Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples. Gigascience 2020; 9:giaa046. [PMID: 32391909 PMCID: PMC7213576 DOI: 10.1093/gigascience/giaa046] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/13/2020] [Accepted: 04/16/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The rise of antibiotic resistance (AR) in clinical settings is of great concern. Therefore, the understanding of AR mechanisms, evolution, and global distribution is a priority for patient survival. Despite all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental microorganisms. We used 293 metagenomic samples from the TARA Oceans project to detect and quantify environmental antibiotic resistance genes (ARGs) using machine learning tools. RESULTS After manual curation of ARGs, their abundance and distribution in the global ocean are presented. Additionally, the potential of horizontal ARG transfer by plasmids and their correlation with environmental and geographical parameters is shown. A total of 99,205 environmental open reading frames (ORFs) were classified as 1 of 560 different ARGs conferring resistance to 26 antibiotic classes. We found 24,567 ORFs in putative plasmid sequences, suggesting the importance of mobile genetic elements in the dynamics of environmental ARG transmission. Moreover, 4,804 contigs with >=2 putative ARGs were found, including 2 plasmid-like contigs with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in the natural ocean environment. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs similar to mobilized colistin resistance genes (mcr) with high abundance on polar biomes. Of these, 5 are assigned to Psychrobacter, a genus including opportunistic human pathogens. CONCLUSIONS This study uncovers the diversity and abundance of ARGs in the global ocean metagenome. Our results are available on Zenodo in MySQL database dump format, and all the code used for the analyses, including a Jupyter notebook js avaliable on Github. We also developed a dashboard web application (http://www.resistomedb.com) for data visualization.
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Affiliation(s)
- Rafael R C Cuadrat
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke - DIfE, Arthur-Scheunert-Allee 114–116, 14558 Nuthetal, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Lessingstrasse 8, 07743 Jena, Germany
| | - Bruno G Andrade
- Animal Biotechnology Laboratory, Embrapa Southeast Livestock, EMBRAPA, Rodovia Washington Luiz, Km 234 s/n°, 13560-970 São Carlos, SP, Brazil
| | - Tobias Goris
- Department of Molecular Toxicology, Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke - DIfE, Arthur-Scheunert-Allee 114–116, 14558 Nuthetal, Germany
| | - Alberto M R Dávila
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Av Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil
- Graduate Program in Biodiversity and Health, Oswaldo Cruz Institute, FIOCRUZ, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil
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