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Wang H, Feng Y, Zhang Q, Zou M, Li T, Ai L, Wang H. Urban greenspace types and climate factors jointly drive the microbial community structure and co-occurrence network. Sci Rep 2024; 14:16042. [PMID: 38992141 DOI: 10.1038/s41598-024-66588-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024] Open
Abstract
The benefits of urban green space are socially widely recognized as a direct link between plant-microbe interactions and the maintenance of biodiversity, community stability, and ecosystem functioning. Nevertheless, there is a lack of knowledge about the factors influencing microbial communities in urban green spaces, especially those related to phyllosphere epiphytes and stem epiphytes. In this study, we analyzed the microbial community assembly in leaf and stem bark samples collected from Square, Road, Campus, and Park. Illumina sequecing of 16S amplicons was performed to characterize microbial diversity and composition. The α-diversity was significantly higher in the bark epiphytic community, compared to the phyllosphere. Moreover, urban greenspaces'type altered the way communities gathered. The main soil and air properties factors of the urban greenhouse (e.g. soil temperature, atmospheric moisture, air temperature) were shaping the characteristics of bacterial communities on the leaf surface and bark epiphytic. In addition, in the co-occurrence network analysis, keystone taxa were not mostly observed in abundant species, which may be necessary to maintain ecosystem functions. Finally, our findings provide a deeper understanding of the ecological dynamics and microbial interactions within plant phyllosphere and stem epiphytes microbiomes.
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Affiliation(s)
- Huan Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400718, China
- Chongqing Landscape and Gardening Research Institute, Chongqing, 401329, China
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, 401329, China
| | - Yilong Feng
- Chongqing Landscape and Gardening Research Institute, Chongqing, 401329, China
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, 401329, China
| | - Qiaoyong Zhang
- Chongqing Landscape and Gardening Research Institute, Chongqing, 401329, China
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, 401329, China
| | - Min Zou
- Chongqing Landscape and Gardening Research Institute, Chongqing, 401329, China
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, 401329, China
| | - Ting Li
- Chongqing Landscape and Gardening Research Institute, Chongqing, 401329, China
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, 401329, China
| | - Lijiao Ai
- Chongqing Landscape and Gardening Research Institute, Chongqing, 401329, China.
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, 401329, China.
| | - Haiyang Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400718, China.
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Zhang Y, Ji Y, Tang X, Chen M, Su J. Spread of plasmids carrying antibiotic resistance genes in soil-lettuce-snail food chain. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:34295-34308. [PMID: 38700770 DOI: 10.1007/s11356-024-33509-1] [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: 09/18/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024]
Abstract
Fertilization can change the composition of antibiotic resistance genes(ARGs) and their host bacteria in agricultural fields, while complex microbial activities help ARGs into crops and transmit them to humans through agricultural products.Therefore, this study constructed a farmland food chain with soil-lettuce-snail as a typical structure, added genetically engineered Pseudomonas fluorescens containing multidrug-resistant plasmid RP4 to track its spread in the farmland food chain, and used different fertilization methods to explore its influence on the spread and diffusion of ARGs and intl1 in the farmland food chain. It was found that exogenous Pseudomonas can enter plants from soil and pass into snails' intestines, and there is horizontal gene transfer phenomenon of RP4 plasmid in bacteria. At different interfaces of the constructed food chain, the addition of exogenous drug-resistant bacteria had different effects on the total abundance of ARGs and intl1. Fertilization, especially manure, not only promoted the spread of Pseudomonas aeruginosa and the transfer of RP4 plasmid levels, but also significantly increased the total abundance of ARGs and intl1 at all interfaces of the constructed food chain. The main ARGs host bacteria in the constructed food chain include Proteobacteria, Bacteroides, and Firmicutes, while Flavobacterium of Bacteroides is the unique potential host bacteria of RP4 plasmid. In conclusion, this study provides a reference for the risk assessment of ARGs transmitted to the human body through the food chain, and has important practical significance to reduce the antibiotic resistance contamination of agricultural products and ensure the safety of vegetable basket.
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Affiliation(s)
- Yuan Zhang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
| | - Yan Ji
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Xinyue Tang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Minglong Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Jianqiang Su
- Key Laboratory of Urban Pollutant Conversion, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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3
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Wen X, Xu J, Wang Y, Yang X, Peng G, Li S, Ma B, Zou Y, Liao X, Wang Y, Worrich A, Wu Y. Community coalescence and plant host filtering determine the spread of tetracycline resistance genes from pig manure into the microbiome continuum of the soil-plant system. Microbiol Res 2024; 284:127734. [PMID: 38670037 DOI: 10.1016/j.micres.2024.127734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/27/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
The spread of livestock manure-borne antibiotic resistance genes (ARGs) into agroecosystems through manure application poses a potential threat to human health. However, there is still a knowledge gap concerning ARG dissemination in coalescing manure, soil and plant microbiomes. Here, we examined the fate of tetracycline resistance genes (TRGs) originating from pig manure microbiomes and spread in the soil-A thaliana system and explored the effects of microbial functions on TRGs spread at different interfaces. Our results indicate that the TRGs abundances in all microbiome continuum of the soil-A. thaliana system were significantly increased with the application of a living manure microbiome, although the addition of manure with both an active and inactive microbiome caused a shift in the microbial community composition. This was attributed to the increasing relative abundances of tetA, tetL, tetM, tetO, tetW and tolC in the system. The application of living manure with DOX residues resulted in the highest relative abundance of total TRGs (3.30×10-3 copies/16S rRNA gene copies) in the rhizosphere soil samples. Community coalescence of the manure and soil microbiomes increased the abundance of Firmicutes in the soil and root microbiome, which directly explains the increase in TRG abundance observed in these interfaces. In contrast, the leaf microbiome differed markedly from that of the remaining samples, indicating strong plant host filtering effects on Firmicutes and TRGs from pig manure. The random forest machine learning model revealed microbial functions and their significant positive correlation with TRG abundance in the microbiome continuum of the system. Our findings revealed that community coalescence is the main driver of TRG spread from manure to the soil and root microbiomes. Plant host filtering effects play a crucial role in allowing certain microbial groups to occupy ecological niches in the leaves, thereby limiting the establishment of manure-borne TRGs in aboveground plant tissues.
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Affiliation(s)
- Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China; Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany
| | - Jiaojiao Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yiting Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xin Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Guoliang Peng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China
| | - Siming Li
- Shimadzu (China) Co., LTD. Guangzhou Branch, Guangzhou 510656, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany.
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 525000, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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Rojas-Sánchez B, Castelán-Sánchez H, Garfias-Zamora EY, Santoyo G. Diversity of the Maize Root Endosphere and Rhizosphere Microbiomes Modulated by the Inoculation with Pseudomonas fluorescens UM270 in a Milpa System. PLANTS (BASEL, SWITZERLAND) 2024; 13:954. [PMID: 38611483 PMCID: PMC11013257 DOI: 10.3390/plants13070954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/11/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
Milpa is an agroecological production system based on the polyculture of plant species, with corn featuring as a central component. Traditionally, the milpa system does not require the application of chemicals, and so pest attacks and poor growth in poor soils can have adverse effects on its production. Therefore, the application of bioinoculants could be a strategy for improving crop growth and health; however, the effect of external inoculant agents on the endemic microbiota associated with corn has not been extensively studied. Here, the objective of this work was to fertilize a maize crop under a milpa agrosystem with the PGPR Pseudomonas fluorescens UM270, evaluating its impact on the diversity of the rhizosphere (rhizobiome) and root endophytic (root endobiome) microbiomes of maize plants. The endobiome of maize roots was evaluated by 16S rRNA and internal transcribed spacer region (ITS) sequencing, and the rhizobiome was assessed by metagenomic sequencing upon inoculation with the strain UM270. The results showed that UM270 inoculation of the rhizosphere of P. fluorescens UM270 did not increase alpha diversity in either the monoculture or milpa, but it did alter the endophytic microbiome of maize plant roots by stimulating the presence of bacterial operational taxonomic units (OTUs) of the genera Burkholderia and Pseudomonas (in a monoculture), whereas, in the milpa system, the PGPR stimulated greater endophytic diversity and the presence of genera such as Burkholderia, Variovorax, and N-fixing rhizobia genera, including Rhizobium, Mesorhizobium, and Bradyrhizobium. No clear association was found between fungal diversity and the presence of strain UM270, but beneficial fungi, such as Rizophagus irregularis and Exophiala pisciphila, were detected in the Milpa system. In addition, network analysis revealed unique interactions with species such as Stenotrophomonas sp., Burkholderia xenovorans, and Sphingobium yanoikuyae, which could potentially play beneficial roles in the plant. Finally, the UM270 strain does not seem to have a strong impact on the microbial diversity of the rhizosphere, but it does have a strong impact on some functions, such as trehalose synthesis, ammonium assimilation, and polyamine metabolism. The inoculation of UM270 biofertilizer in maize plants modifies the rhizo- and endophytic microbiomes with a high potential for stimulating plant growth and health in agroecological crop models.
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Affiliation(s)
- Blanca Rojas-Sánchez
- Genomic Diversity Lab, Institute of Chemical and Biological Research, Universidad Michoacana de San Nicolas de Hidalgo, Morelia 58030, Mexico; (B.R.-S.); (E.Y.G.-Z.)
| | - Hugo Castelán-Sánchez
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
| | - Esmeralda Y. Garfias-Zamora
- Genomic Diversity Lab, Institute of Chemical and Biological Research, Universidad Michoacana de San Nicolas de Hidalgo, Morelia 58030, Mexico; (B.R.-S.); (E.Y.G.-Z.)
| | - Gustavo Santoyo
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
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5
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Zhuang X, Fan H, Li X, Dong Y, Wang S, Zhao B, Wu S. Transfer and accumulation of antibiotic resistance genes and bacterial pathogens in the mice gut due to consumption of organic foods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:169842. [PMID: 38215844 DOI: 10.1016/j.scitotenv.2023.169842] [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: 09/19/2023] [Revised: 11/27/2023] [Accepted: 12/30/2023] [Indexed: 01/14/2024]
Abstract
Over the last few decades, organic food demand has grown largely because of increasing personal health concerns. Organic farming introduces antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) into foods. However, potential effects of organic foods on the gut microbiome and ARGs have been overlooked. Using high-throughput quantitative PCR and 16S rRNA high-throughput sequencing technology, we examined 132 ARGs from major classes, eight transposase genes, universal class I integron-integrase gene (intI), clinical class I integron-integrase gene (cintI), and the bacterial community in mouse gut after 8 weeks with an either organic or inorganic lettuce and wheat diet. A total of 8 types of major ARGs and 10 mobile genetic elements (MGEs) were detected in mice gut, including tetracycline, multidrug, sulfonamide, aminoglycoside, beta-lactamase, chloramphenicol, MLSB and vancomycin resistance genes. We found that abundance and diversity of ARGs, mobile gene elements, and potential ARB in the gut increased with time after consumption of organic foods, whereas no significant changes were observed in inorganic treated groups. Moreover, MGEs, including IS613, Tp614 and tnpA_03 were found to play an important role in regulating ARG profiles in the gut microbiome following consumption of organic foods. Importantly, feeding organic food increased the relative abundance of the potentially antibiotic-resistant pathogens, Bacteroides and Streptococcus. Our results confirm that there is an increasing risk of ARGs and ARB in the gut microbiome, which highlights the importance of organic food industries taking into account the potential accumulation and transmission of ARGs as a risk factor.
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Affiliation(s)
- Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Zhao
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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Zhao J, Duan G, Zhu D, Li J, Zhu Y. Microbial-influenced pesticide removal co-occurs with antibiotic resistance gene variation in soil-earthworm-maize system. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 342:123010. [PMID: 38012967 DOI: 10.1016/j.envpol.2023.123010] [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: 08/21/2023] [Revised: 11/01/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
Within human-influenced landscapes, pesticides cooccur with a variety of antibiotic stressors. However, the relationship between pesticides removal process and antibiotic resistance gene variation are not well understood. This study explored pesticide (topramezone, TPZ) and antibiotic (polymyxin E, PME) co-contamination using liquid chromatography-tandem mass spectrometry (LC-MS/MS), bacterial-16 S rRNA sequencing and high-throughput quantitative polymerase chain reaction (HT-qPCR) in a soil-earthworm-maize system. After incubating soil for 28 days with TPZ and PME (10 mg kg-1 dry weight), earthworm weight-gain, mortality rates, and maize plant weight-gain only differed slightly, but height-gain significantly decreased. PME significantly increased TPZ-removal in the soil. Accumulation of TPZ in earthworm's tissues may pose potential risks in the food chain. Combined pollution altered the microbial community structure and increased the abundance of functional microorganisms involved in aromatic compound degradation. Furthermore, maize rhizosphere can raise resistance genes, however earthworms can reduce resistance genes. Co-contamination increased absolute abundance of mobile genetic elements (MGEs) in bulk-soil samples, antibiotic resistance genes (ARGs) in skin samples and number of ARGs in bulk-soil samples, while decreased absolute abundance of transposase gene in bulk-soil samples and number of ARGs in rhizosphere-soil samples. Potential hosts harbouring ARGs may be associated with the antagonistic effect during resistance and detoxification of TPZ and PMB co-occurrence. These findings provide insights into the mechanism underlining pesticide removal regarding occurrence of ARGs in maize agroecosystem.
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Affiliation(s)
- Jun Zhao
- Laboratory for Chemical Environmental Risk Assessment, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Guilan Duan
- University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Dong Zhu
- University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Jianzhong Li
- Laboratory for Chemical Environmental Risk Assessment, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yongguan Zhu
- University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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7
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Kang Y, Zhao S, Cheng H, Xu W, You R, Hu J. The distribution profiles of tetracycline resistance genes in rice: Comparisons using four genotypes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168359. [PMID: 37951253 DOI: 10.1016/j.scitotenv.2023.168359] [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: 09/24/2023] [Revised: 10/27/2023] [Accepted: 11/03/2023] [Indexed: 11/13/2023]
Abstract
The potential transmission of antibiotic resistance genes (ARGs) from the rhizosphere to plants and humans poses a significant concern. This study aims to investigate the distribution of tetracycline resistance genes (TRGs) in rice using four genotypes and identify the primary source of TRGs in grains. Quantitative polymerase chain reaction (qPCR) was employed to determine the abundance of seven TRGs and intI1 in four rice varieties and three partitions during the jointing and heading stages, respectively. The analysis of the bacterial community was conducted to elucidate the underlying mechanism of the profiles of TRGs. It was observed that tetZ was predominantly present in the rhizosphere and endoroot, whereas tetX became dominant in grains. The relative abundances of TRGs and intI1 exhibited significant variations across both the variety and partition. However, no significant differences were observed in grains, where the abundances of TRGs were several orders of magnitude lower compared to those in the rhizosphere. Nevertheless, the potential risk of the dissemination of TRGs to humans, particularly those carried by potential pathogens in grains, warrants attention. The increased likelihood of TRGs accumulation in the rhizosphere and endoroot of hybrid rice varieties, as opposed to japonica varieties, may be attributed to the heightened metabolic activities of their roots. The significant associations observed between intI1 and TRGs, coupled with the substantial alterations in potential hosts for intI1 across various treatments, indicate that intI1-mediated horizontal gene transfer plays a role in the diverse range of bacterial hosts for TRGs. The study also revealed that rhizosphere bacteria during the jointing stage serve as the primary contributors of TRGs in grains through the endoroot junction. The findings indicate that Japonica rice varieties exhibit superior control over TRGs compared to hybrid varieties, emphasizing the need for early interventions throughout the entire growth period of rice.
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Affiliation(s)
- Yijun Kang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China; Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University, Yancheng, Jiangsu, China; Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng Teachers University, Yancheng, Jiangsu, China.
| | - Sumeng Zhao
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Haoyang Cheng
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Wenjie Xu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Ruiqiang You
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China.
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Song J, Chen Y, Mi H, Xu R, Zhang W, Wang C, Rensing C, Wang Y. Prevalence of antibiotic and metal resistance genes in phytoremediated cadmium and zinc contaminated soil assisted by chitosan and Trichoderma harzianum. ENVIRONMENT INTERNATIONAL 2024; 183:108394. [PMID: 38128385 DOI: 10.1016/j.envint.2023.108394] [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: 09/18/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Heavy metal in soil have been shown to be toxic with high concentrations and acts as selective pressure on both bacterial metal and antibiotic resistance determinants, posing a serious risk to public health. In cadmium (Cd) and zinc (Zn) contaminated soil, chitosan (Chi) and Trichoderma harzianum (Tri) were applied alone and in combination to assist phytoremediation by Amaranthus hypochondriacus L. Prevalence of antibiotic and metal resistance genes (ARGs and MRGs) in the soil was also evaluated using metagenomic approach. Results indicated that the phytoremediation of Cd and Zn contaminated soil was promoted by Chi, and Tri further reinforced this effect, along with the increased availability of Cd and Zn in soil. Meanwhile, combination of Chi and Tri enhanced the prevalence of ARGs (e.g., multidrug and β-lactam resistance genes) and maintained a high level of MRGs (e.g., chromium, copper) in soil. Soil available Zn and Cd fractions were the main factors contributing to ARGs profile by co-selection, while boosted bacterial hosts (e.g., Mitsuaria, Solirubrobacter, Ramlibacter) contributed to prevalence of most MRGs (e.g., Cd). These findings indicate the potential risk of ARGs and MRGs propagation in phytoremediation of metal contaminated soils assisted by organic and biological agents.
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Affiliation(s)
- Jianxiao Song
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China; Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, Xi'an 710000, Shaanxi, PR China
| | - Yanlong Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China; Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, Xi'an 710000, Shaanxi, PR China.
| | - Huizi Mi
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China
| | - Risheng Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China; Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, Xi'an 710000, Shaanxi, PR China
| | - Wenshuang Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China
| | - Chao Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China; Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, Xi'an 710000, Shaanxi, PR China
| | - Christopher Rensing
- Institute of Environmental Microbiology, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Yuheng Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China; Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, Xi'an 710000, Shaanxi, PR China
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Li XY, Wu WF, Wu CY, Hu Y, Xiang Q, Li G, Lin XY, Zhu YG. Seeds Act as Vectors for Antibiotic Resistance Gene Dissemination in a Soil-Plant Continuum. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21358-21369. [PMID: 38078407 DOI: 10.1021/acs.est.3c05678] [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: 12/20/2023]
Abstract
Though the evidence for antibiotic resistance spread via plant microbiome is mounting, studies regarding antibiotic resistome in the plant seed, a reproductive organ and important food resource, are still in their infancy. This study investigated the effects of long-term organic fertilization on seed bacterial endophytes, resistome, and their intergenerational transfer in the microcosm. A total of 99 antibiotic resistance genes (ARGs) and 26 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR. The amount of organic fertilizer applied was positively correlated to the number and relative abundance of seed-associated ARGs and MGEs. Moreover, the transmission of ARGs from the rhizosphere to the seed was mainly mediated by the shared bacteria and MGEs. Notably, the rhizosphere of progeny seedlings derived from seeds harboring abundant ARGs was found to have a higher relative abundance of ARGs. Using structural equation models, we further revealed that seed resistome and MGEs were key factors affecting the ARGs in the progeny rhizosphere, implying the seed was a potential resistome reservoir for rhizosphere soil. This study highlights the overlooked role of seed endophytes in the dissemination of resistome in the soil-plant continuum, and more attention should be paid to plant seeds as vectors of ARGs within the "One-Health" framework.
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Affiliation(s)
- Xin-Yuan Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Wei-Feng Wu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Chun-Yan Wu
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Yan Hu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Qian Xiang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Xian-Yong Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yong-Guan Zhu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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10
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Wu D, Ma X, Meng Y, Cai R, Zhang X, Liu L, Deng L, Chen C, Wang F, Xu Q, He B, He M, Hu R, Zhen J, Han Y, He S, Xu L. Impact of nitrogen application and crop stage on epiphytic microbial communities on silage maize leaf surfaces. PeerJ 2023; 11:e16386. [PMID: 38025755 PMCID: PMC10656910 DOI: 10.7717/peerj.16386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
This study aimed to examine the impact of nitrogen (N) fertilization on phyllosphere microorganisms in silage maize (Zea mays) to enhance the production of high-quality silage. The effects of different N application rates (160, 240, and 320 kg ha-1) and maturity stages (flowering and dough stages) on microbial diversity, abundance and physiochemical properties of the leaf surfaces were evaluated in a field experiment. The results showed that N application rates did not significantly impact the abundance of lactic acid bacteria (LAB), aerobic bacteria (AB), yeasts, or molds on the leaf surfaces. However, these microbes were more abundant during the flowering stage compared to the dough stage. Furthermore, the N application rate had no significant impact on inorganic phosphorus, soluble sugar, free amino acids, total phenolic content, and soluble protein concentrations, or pH levels on the leaf surfaces. Notably, these chemical indices were lower during the dough stage. The abundance of Pantoea decreased with higher N application rates, while that of other microorganisms did not changes significantly. The abundance of AB, LAB, yeasts, and molds were positively correlated with soluble sugar, soluble protein, inorganic phosphorus, free amino acids, and total phenolic concentrations on leaf surfaces. Moreover, water loss was negatively correlated with the abundance of AB, LAB, yeasts, and molds, whereas water retention capacity and stomatal density were positively correlated with microbial abundance. We recommend applying an optimal N rate of 160 kg ha-1 to silage maize and harvesting at the flowering stage is recommended.
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Affiliation(s)
- Dan Wu
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Xueling Ma
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Yuanyan Meng
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Rongjin Cai
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Xiaolong Zhang
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Li Liu
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Lianping Deng
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Changjing Chen
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Fang Wang
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Qingbiao Xu
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Bin He
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Mingzhu He
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Rensheng Hu
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Jinjing Zhen
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Yan Han
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Shaoshen He
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
| | - Liuxing Xu
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, China
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11
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Seyoum MM, Ashworth AJ, Feye KM, Ricke SC, Owens PR, Moore PA, Savin M. Long-term impacts of conservation pasture management in manuresheds on system-level microbiome and antibiotic resistance genes. Front Microbiol 2023; 14:1227006. [PMID: 37886073 PMCID: PMC10598662 DOI: 10.3389/fmicb.2023.1227006] [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: 05/25/2023] [Accepted: 09/13/2023] [Indexed: 10/28/2023] Open
Abstract
Animal manure improves soil fertility and organic carbon, but long-term deposition may contribute to antibiotic resistance genes (ARGs) entering the soil-water environment. Additionally, long-term impacts of applying animal manure to soil on the soil-water microbiome, a crucial factor in soil health and fertility, are not well understood. The aim of this study is to assess: (1) impacts of long-term conservation practices on the distribution of ARGs and microbial dynamics in soil, and runoff; and (2) associations between bacterial taxa, heavy metals, soil health indicators, and ARGs in manures, soils, and surface runoff in a study following 15 years of continuous management. This management strategy consists of two conventional and three conservation systems, all receiving annual poultry litter. High throughput sequencing of the 16S ribosomal RNA was carried out on samples of cattle manure, poultry litter, soil, and runoff collected from each manureshed. In addition, four representative ARGs (intl1, sul1, ermB, and blactx-m-32) were quantified from manures, soil, and runoff using quantitative PCR. Results revealed that conventional practice increased soil ARGs, and microbial diversity compared to conservation systems. Further, ARGs were strongly correlated with each other in cattle manure and soil, but not in runoff. After 15-years of conservation practices, relationships existed between heavy metals and ARGs. In the soil, Cu, Fe and Mn were positively linked to intl1, sul1, and ermB, but trends varied in runoff. These findings were further supported by network analyses that indicated complex co-occurrence patterns between bacteria taxa, ARGs, and physicochemical parameters. Overall, this study provides system-level linkages of microbial communities, ARGs, and physicochemical conditions based on long-term conservation practices at the soil-water-animal nexus.
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Affiliation(s)
- Mitiku Mihiret Seyoum
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Amanda J. Ashworth
- USDA-ARS, Poultry Production and Product Safety Research Unit, Fayetteville, AR, United States
| | - Kristina M. Feye
- Cellular and Molecular Biology, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science & Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Phillip R. Owens
- USDA-ARS, Dale Bumpers Small Farms Research Center, Booneville, AR, United States
| | - Philip A. Moore
- USDA-ARS, Poultry Production and Product Safety Research Unit, Fayetteville, AR, United States
| | - Mary Savin
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
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12
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Zhang L, Bai J, Zhai Y, Zhang K, Wang Y, Xiao R, Jorquera MA. Effects of antibiotics on the endophyte and phyllosphere bacterial communities of lotus from above and below surface water in a typical shallow lake. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107812. [PMID: 37343440 DOI: 10.1016/j.plaphy.2023.107812] [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: 02/28/2023] [Revised: 05/21/2023] [Accepted: 05/31/2023] [Indexed: 06/23/2023]
Abstract
Antibiotics are ubiquitous pollutants that are widely found in aquatic ecosystems, where the bacterial community of aquatic plants is influenced by antibiotics. However, differences between endophyte and phyllosphere bacteria of Lotus from above and below surface water remains unclear. Lotus samples from above and below the surface water were collected to investigate the differences in endophyte and phyllosphere bacteria and dominant environmental factors in regions with low (L-) and high (H-) total antibiotic levels. There were significant differences in Shannon diversity between endophyte and phyllosphere bacteria except between the below-surface water phyllosphere bacteria and below-surface water endophytes in both L-antibiotic and H-antibiotic regions, with higher values for phyllosphere bacteria. The dominant phylum in all phyllosphere samples was Proteobacteria (76.1%-92.5%), while Cyanobacteria (47.8%-81.1%) was dominant in all endophyte samples. The dominant source of above-surface water endophytes was below-surface water endophytes (83.68-91.25%), below-surface water phyllosphere bacteria (48.43-55.91%) for above-surface water phyllosphere bacteria, and above-surface water endophytes (53.83-61.80%) for below-surface water endophytes, while the dominant contributor to the below-surface water phyllosphere bacteria was also below-surface water endophytes (52.96-61.00%) in two regions, indicating that antibiotic stress changed the sink‒source relationship between endophytes and phyllosphere bacteria. The physical-chemical properties of surface water and sediments could be responsible for the variations in the above- and below-surface water endophytes and phyllosphere bacteria in both regions. It is suggested that antibiotics may have a substantial effect on endophyte and phyllosphere bacterial community.
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Affiliation(s)
- Ling Zhang
- School of Environment, Beijing Normal University, Beijing, 100875, China; School of Chemistry and Chemical Engineering, Qinghai Normal University, Xining, 810008, China
| | - Junhong Bai
- School of Environment, Beijing Normal University, Beijing, 100875, China; Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou, 256600, China.
| | - Yujia Zhai
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Kegang Zhang
- Department of Environmental Engineering and Science, North China Electric Power University, Baoding, China
| | - Yaqi Wang
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Rong Xiao
- College of Environment & Safety Engineering, FuZhou University, Fuzhou, China
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
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13
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Zhang Y, Zhao J, Chen M, Tang X, Wang Y, Zou Y. Fecal antibiotic resistance genes were transferred through the distribution of soil-lettuce-snail food chain. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:87793-87809. [PMID: 37434056 DOI: 10.1007/s11356-023-28606-6] [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: 03/21/2023] [Accepted: 07/01/2023] [Indexed: 07/13/2023]
Abstract
Massive antibiotic resistance genes (ARG) were detected in the soil modified by manure, which may affect human life safety through the food chain. However, the transmission of ARGs through the soil-plant-animal food chain is still unclear. Therefore, this study used high-throughput quantitative PCR technology to explore the effects of pig manure application on ARGs and bacterial communities in soil, lettuce phyllosphere, and snail excrement. The results showed that a total of 384 ARGs and 48 MEGs were detected in all samples after 75 days of incubation. The diversity of ARGs and MGEs in soil components increased significantly by 87.04% and 40% with the addition of pig manure. The absolute abundance of ARGs in the phyllosphere of lettuce was significantly higher than that of the control group, with a growth rate of 212.5%. Six common ARGs were detected between the three components of the fertilization group, indicating that there was internal transmission of fecal ARGs between the trophic levels of the food chain. Firmicutes and Proteobacteria were identified as the dominant host bacteria in the food chain system, which were more likely to be used as carriers of ARGs to promote the spread of resistance in the food chain. The results were used to assess the potential ecological risks of livestock and poultry manure. It provides theoretical basis and scientific support for the formulation of ARG prevention and control policies.
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Affiliation(s)
- Yuan Zhang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
| | - Jiayi Zhao
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Minglong Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Xinyue Tang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Yijia Wang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Yun Zou
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
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14
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Wang J, Xu S, Zhao K, Song G, Zhao S, Liu R. Risk control of antibiotics, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) during sewage sludge treatment and disposal: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162772. [PMID: 36933744 DOI: 10.1016/j.scitotenv.2023.162772] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/14/2023] [Accepted: 03/06/2023] [Indexed: 05/06/2023]
Abstract
Sewage sludge is an important reservoir of antibiotics, antibiotic resistance genes (ARGs), and antibiotic resistant bacteria (ARB) in wastewater treatment plants (WWTPs), and the reclamation of sewage sludge potentially threats human health and environmental safety. Sludge treatment and disposal are expected to control these risks, and this review summarizes the fate and controlling efficiency of antibiotics, ARGs, and ARB in sludge involved in different processes, i.e., disintegration, anaerobic digestion, aerobic composting, drying, pyrolysis, constructed wetland, and land application. Additionally, the analysis and characterization methods of antibiotics, ARGs, and ARB in complicate sludge are reviewed, and the quantitative risk assessment approaches involved in land application are comprehensively discussed. This review benefits process optimization of sludge treatment and disposal, with regard to environmental risks control of antibiotics, ARGs, and ARB in sludge. Furthermore, current research limitations and gaps, e.g., the antibiotic resistance risk assessment in sludge-amended soil, are proposed to advance the future studies.
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Affiliation(s)
- Jiaqi Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Yangze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siqi Xu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Kai Zhao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ge Song
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shunan Zhao
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruiping Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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15
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Xu L, Wang R, Jin B, Chen J, Jiang T, Ali W, Tian S, Lu L. Cadmium inhibits powdery mildew colonization and reconstructs microbial community in leaves of the hyperaccumulator plant Sedum alfredii. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 260:115076. [PMID: 37257346 DOI: 10.1016/j.ecoenv.2023.115076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/27/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
Understanding the influence of the heavy metal cadmium (Cd) on the phyllosphere microbiome of hyperaccumulator plants is crucial for enhancing phytoremediation. The characteristics of the phyllosphere of Sedum alfredii Hance, a hyperaccumulator plant, were investigated using 16S rRNA and internal transcribed spacer amplicon sequencing of powdery mildew-infected leaves treated or untreated with Cd. The results showed that the colonization of powdery mildew caused severe chlorosis and necrosis in S. alfredii leaves, and the relative abundance of Leotiomycetes in infected leaves increased dramatically and significantly decreased phyllosphere microbiome diversity. However, S. alfredii preferentially accumulated higher concentrations of Cd in the leaves of infected plants than in uninfected plants by powdery mildew, which in turn significantly inhibited powdery mildew colonization in leaves; the relative abundance of the fungal class Leotiomycetes in infected leaves decreased, and alpha and beta diversities of the phyllosphere microbiome significantly increased with Cd treatment in the infected plants. In addition, the inter-kingdom networks in the microbiota of the infected leaves treated with Cd presented many nodes and edges, and the highest inter-kingdom modularity compared to the untreated infected leaves, indicating a highly connected microbial community. These results suggest that Cd significantly inhibits powdery mildew colonization by altering the composition of the phyllosphere microbiome in S. alfredii leaves, paving the way for efficient heavy metal phytoremediation and providing a new perspective on defense strategies against heavy metals.
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Affiliation(s)
- Lingling Xu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Runze Wang
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bingjie Jin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiuzhou Chen
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tianchi Jiang
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Waqar Ali
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Science's, Guiyang 550081, China
| | - Shengke Tian
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lingli Lu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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16
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Chen P, Yu K, He Y. The dynamics and transmission of antibiotic resistance associated with plant microbiomes. ENVIRONMENT INTERNATIONAL 2023; 176:107986. [PMID: 37257204 DOI: 10.1016/j.envint.2023.107986] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.
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Affiliation(s)
- Ping Chen
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Kaifeng Yu
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yiliang He
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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17
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Xiao R, Huang D, Du L, Song B, Yin L, Chen Y, Gao L, Li R, Huang H, Zeng G. Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161855. [PMID: 36708845 DOI: 10.1016/j.scitotenv.2023.161855] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/14/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.
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Affiliation(s)
- Ruihao Xiao
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Danlian Huang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China.
| | - Li Du
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Lingshi Yin
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Yashi Chen
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Lan Gao
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Ruijin Li
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Hai Huang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China.
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18
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Zhao H, Liu X, Sun Y, Liu J, Waigi MG. Effects and mechanisms of plant growth regulators on horizontal transfer of antibiotic resistance genes through plasmid-mediated conjugation. CHEMOSPHERE 2023; 318:137997. [PMID: 36720410 DOI: 10.1016/j.chemosphere.2023.137997] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/02/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
A vast number of bacteria occur in both soil and plants, with some of them harboring antibiotic resistance genes (ARGs). When bacteria congregate on the interface of soil particles or on plant root surfaces, these ARGs can be transferred between bacteria via conjugation, leading to the formation of antibiotic-resistant pathogens that threaten human health. Plant growth regulators (PGRs) are widely used in agricultural production, promoting plant growth and increasing crop yields. However, until now, little information has been known about the effects of PGRs on the horizontal gene transfer (HGT) of ARGs. In this study, with Escherichia coli DH5α (carrying RP4 plasmid with TetR, AmpR, KanR) as the donor and E. coli HB101 as the recipient, a series of diparental conjugation experiments were conducted to investigate the effects of indoleacetic acid (IAA), ethel (ETH) and gibberellin (GA3) on HGT of ARGs via plasmid-mediated conjugation. Furthermore, the mechanisms involved were also clarified. The results showed that all three PGRs affected the ARG transfer frequency by inducing the intracellular reactive oxygen species (ROS) formation, changing the cell membrane permeability, and regulating the gene transcription of traA, traL, trfAp, trbBp, kilA, and korA in plasmid RP4. In detail, 50-100 mg⋅L-1 IAA, 20-50 mg⋅L-1 ETH and 1500-2500 mg⋅L-1 GA3 all significantly promoted the ARG conjugation. This study indicated that widespread use of PGRs in agricultural production could affect the HGT of ARGs via plasmid-mediated conjugation, and the application of reasonable concentrations of PGRs could reduce the ARG transmission in both soil environments and plants.
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Affiliation(s)
- Hui Zhao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xiangyu Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yulong Sun
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Juan Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR 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
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19
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Li X, Tseng HT, Hemmings G, Omolehin O, Taylor C, Taylor A, Kong P, Daughtrey M, Gouker F, Hong C. Characterization of Boxwood Shoot Bacterial Communities and Potential Impact from Fungicide Treatments. Microbiol Spectr 2023; 11:e0416322. [PMID: 36853063 PMCID: PMC10100737 DOI: 10.1128/spectrum.04163-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
Phyllosphere bacterial communities play important roles in plant fitness and growth. The objective of this study was to characterize the epiphytic and endophytic bacterial communities of boxwood shoots and determine how they may respond to commonly used fungicides. In early summer and early fall, shoot samples were collected immediately before and 1, 7, and 14 days after three fungicides containing chlorothalonil and/or propiconazole were applied to the canopy. Total genomic DNA from shoot surface washings and surface-sterilized shoot tissues was used as the template for 16S rRNA metabarcoding, and the amplicons were sequenced on a Nanopore MinION sequencer to characterize the epiphytic and endophytic communities. The bacterial communities were phylogenetically more diverse on the boxwood shoot surface than in the internal tissue, although the two communities shared 12.7% of the total 1,649 identified genera. The most abundant epiphytes were Methylobacterium and Pantoea, while Stenotrophomonas and Brevundimonas were the dominant endophytes. Fungicide treatments had strong impacts on epiphytic bacterial community structure and composition. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) and analysis of variance (ANOVA)-like differential expression (ALDEx2) together identified 312 and 1,362 epiphytes changed in abundance due to fungicide treatments in early summer and early fall, respectively, and over 50% of these epiphytes were negatively impacted by fungicide. The two chlorothalonil-based contact fungicides demonstrated more marked effects than the propiconazole-based systemic fungicide. These results are foundational for exploring and utilizing the full potential of the microbiome and fungicide applications and developing a systems approach to boxwood health and production. IMPORTANCE Agrochemicals are important tools for safeguarding plants from invasive pathogens, insects, mites, and weeds. How they may affect the plant microbiome, a critical component of crop health and production, was poorly understood. Here, we used boxwood, an iconic low-maintenance landscape plant, to characterize shoot epiphytic and endophytic bacterial communities and their responses to contact and systemic fungicides. This study expanded our understanding of the above-ground microbiome in ornamental plants and is foundational for utilizing the full benefits of the microbiome in concert with different fungicide chemistries to improve boxwood health. This study also sets an example for a more thorough evaluation of these and other agrochemicals for their effects on boxwood microbiomes during production and offers an expanded systems approach that could be used with other crops for enhanced integrated pest management.
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Affiliation(s)
- Xiaoping Li
- Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Virginia Beach, Virginia, USA
| | - Hsien Tzer Tseng
- North Carolina Department of Agriculture and Consumer Services, Plant Industry Division, Raleigh, North Carolina, USA
| | - Ginger Hemmings
- North Carolina Department of Agriculture and Consumer Services, Plant Industry Division, Dobson, North Carolina, USA
| | - Olanike Omolehin
- Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Virginia Beach, Virginia, USA
| | - Chad Taylor
- North Carolina Department of Agriculture and Consumer Services, Plant Industry Division, Boone, North Carolina, USA
| | - Amanda Taylor
- North Carolina University Cooperative Extension, Morganton, North Carolina, USA
| | - Ping Kong
- Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Virginia Beach, Virginia, USA
| | - Margery Daughtrey
- Long Island Horticultural Research and Extension Center, Cornell University, Riverhead, New York, USA
| | - Fred Gouker
- USDA-ARS, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, Maryland, USA
| | - Chuanxue Hong
- Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Virginia Beach, Virginia, USA
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20
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Pham DN, Wu Q, Li M. Global profiling of antibiotic resistomes in maize rhizospheres. Arch Microbiol 2023; 205:89. [PMID: 36781495 DOI: 10.1007/s00203-023-03424-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 02/15/2023]
Abstract
The spreading of antimicrobial resistance (AMR) in crops and food products represents a global concern. In this study, we conducted a survey of resistomes in maize rhizosphere from Michigan, California, the Netherlands, and South Africa, and investigated potential associations with host bacteria and soil management practices in the crop field. For comparison, relative abundance of antibiotic resistance genes (ARGs) is normalized to the size of individual metagenomes. Michigan maize rhizosphere metagenomes showed the highest abundance and diversity of ARGs, with the detection of blaTEM-116, blaACT-4/-6, and FosA2, exhibiting high similarity (≥ 99.0%) to those in animal and human pathogens. This was probably related to the decade-long application of manure/composted manure from antibiotic-treated animals. Moreover, RbpA, vanRO, mtrA, and dfrB were prevalently found across most studied regions, implying their intrinsic origins. Further analysis revealed that RbpA, vanRO, and mtrA are mainly harbored by native Actinobacteria with low mobility since mobile genetic elements were rarely found in their flanking regions. Notably, a group of dfrB genes are adjacent to the recombination binding sites (attC), which together constitute mobile gene cassettes, promoting the transmission from soil bacteria to human pathogens. These results suggest that maize rhizosphere resistomes can be distinctive and affected by many factors, particularly those relevant to agricultural practices.
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Affiliation(s)
- Dung Ngoc Pham
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Qiong Wu
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
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21
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Yu Y, Zhang Q, Zhang Z, Zhou S, Jin M, Zhu D, Yang X, Qian H, Lu T. Plants select antibiotic resistome in rhizosphere in early stage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159847. [PMID: 36461576 DOI: 10.1016/j.scitotenv.2022.159847] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Knowledge of the dissemination and emergence of antibiotic resistance genes (ARGs) in the plant rhizosphere is essential for evaluating the risk of the modern ARGs in soil planetary health. However, little is known about the selection mechanism in the plant rhizosphere. Here, we firstly analyzed the dynamic changes in the rhizosphere antibiotic resistome during the process of three passage enrichment of the rhizosphere microbiome in Arabidopsis thaliana (Col-0) and found evidence that plants directionally enriched levels of beneficial functional bacteria with many ARGs. Using the metagenome, we next evaluated the enrichment potential of the resistome in four common crops (barley, indica rice, japonica rice, and wheat) and found that the wheat rhizosphere harbored more abundant ARGs. Therefore, we finally cultivated the rhizosphere microbiome of wheat for three generations and found that approximately 60 % of ARGs were associated with beneficial bacteria enriched in the wheat rhizosphere, which might enter the soil food web and threaten human health, despite also performing beneficial functions in the plant rhizosphere. Our study provides new insights into the dissemination of ARGs in the plant rhizosphere, and the obtained data may be useful for sustainable and ecologically safe agricultural development.
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Affiliation(s)
- Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Shuyidan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Mingkang Jin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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22
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Wei M, Wang X, Zhou K, Yang R. Binary Adsorption and Migration Simulation of Levofloxacin with zinc at Concentrations Simulating Wastewater on Silty Clay and The Potential Environmental Risk in Groundwater. CHEMOSPHERE 2023; 311:136878. [PMID: 36419267 DOI: 10.1016/j.chemosphere.2022.136878] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/28/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Migration of soil pollutants can cause groundwater pollution, which is dominated by the soil adsorption of pollutants. Heavy metals and fluoroquinolone antibiotics exist in the soil and form compound pollution, with different adsorption behaviors in the soil. It may make the levofloxacin (LVFX) migration and potential risk of LVFX to groundwater change. Therefore, this research on Zinc (Zn/Zn2+) and LVFX studied the binary adsorption on silty clay in the vadose zone using the batch equilibrium adsorption method. Besides, Hydrus-1D simulate vertical migration. As the results show: (1) Silty clay has excellent storage capacity (adsorption rate>90%) for LVFX and is a natural barrier to reducing groundwater risk; (2) Binary adsorption of LVFX with Zn on silty clay had could be influenced by metallic oxide, pH value, and cation species. The metallic oxides adsorption rate decreased by 10.3%; Compared with single adsorption, Zn2+ promoted the adsorption of LVFX on silty clay, with the exception that the pH value was 2.0; Based on the simulated migration, subtle changes in adsorption may lead to a significant difference in migration and impact on the environmental risk of LVFX to groundwater. This paper proposed three aspects of the research should be strengthened to further develop the potential of silty clay in the prevention and control of groundwater pollution.
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Affiliation(s)
- Mengxian Wei
- China University of Geosciences (Beijing), Beijing, 450003, China.
| | - Xueshuang Wang
- Northwest Engineering Corporation Limited, Xi'an, Shan Xi Province, 710065, China
| | - Kai Zhou
- Subterranean Hydrology, WuHan University, Wuhan, Hubei Province, 430072, China
| | - Rui Yang
- MCC HuaTian Engineering & Technology corporation, Nanjing, Jiangsu Province, 210000, China
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23
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Runge P, Ventura F, Kemen E, Stam R. Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru upon Dysbiosis. MICROBIAL ECOLOGY 2023; 85:168-183. [PMID: 35041070 PMCID: PMC9849306 DOI: 10.1007/s00248-021-01947-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness, and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops, and trees under controlled and natural conditions. Tomato is one of the world's most important vegetable crops; however, little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum, and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over 2 consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi, and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa, and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner. Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves.Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype, and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes.
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Affiliation(s)
- Paul Runge
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Köln, Germany
| | - Freddy Ventura
- Plant Pathology and Bacteriology, International Potato Centre, Avenida La Molina 1895, La Molina, Lima, Peru
| | - Eric Kemen
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Remco Stam
- Chair of Phytopathology, TUM School of Life Science, Emil-Ramann-Str. 2, 85354, Freising-Weihenstephan, Germany.
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24
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Chi S, Xu W, Han Y. ARGs distribution and high-risk ARGs identification based on continuous application of manure in purple soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158667. [PMID: 36096231 DOI: 10.1016/j.scitotenv.2022.158667] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Tetracyclines (TCs) are one of the most widely used antibiotics in livestock and poultry industry. Sichuan province and Chongqing city are the provinces and cities with the most concentrated purple soil distribution in China, as well as the largest livestock and poultry breeding scale. Purple soils with low organic carbon content and poor structure, and manure fertilizers were heavily applied to improve soil quality. However, the research on antibiotic resistance genes (ARGs) dispersal in purple soils is limited. Overall, 234 ARGs subtypes belonging to 15 types were detected in all soils. Long-term application of livestock manures significantly changed the characteristics of ARGs, mobile genetic elements (MGEs), pathogen species and bacterial communities in the soil, and increased by 103.2 %, 13.1 %, 188.6 % and 43.7 % in chicken manure treatments compared with the control, respectively. Partial equation PLS-PM analysis further reveals that the main driving factor of ARGs is bacterial abundance, while bacterial diversity has a negative effect on ARGs abundance. Through ANOVA and network analysis, it was found that 30 ARGs were significantly affected by manure, its relative abundance is 0.8-1.4 times that of the control treatment. The qPCR results also proved that the relative abundance of ARGs including sul2, etc. increased with the increase of manure application and these resistance genes in chicken manure treatments were higher than in pig manure treatments. These resistance genes pose a high risk to public health, and chicken manure application posed a higher risk than pig manure. The TC content in the 40-60 cm soil layer was higher in medium- and high-volume pig manure, which was at risk of being transported to groundwater. Our research results deepen the understanding of ARGs transmission in purple soil under agricultural activities and emphasize the species and distribution of antibiotic resistance genes may differ across soil and manure types.
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Affiliation(s)
- Sunlin Chi
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Weihong Xu
- College of Resources and Environment, Southwest University, Chongqing 400715, China.
| | - Yurou Han
- College of Resources and Environment, Southwest University, Chongqing 400715, China
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25
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Pillay S, Calderón-Franco D, Urhan A, Abeel T. Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings. Front Microbiol 2022; 13:1066995. [PMID: 36532424 PMCID: PMC9755710 DOI: 10.3389/fmicb.2022.1066995] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/09/2022] [Indexed: 08/12/2023] Open
Abstract
The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.
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Affiliation(s)
- Stephanie Pillay
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | | | - Aysun Urhan
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
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26
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Wang J, Xie J, Li L, Effah Z, Xie L, Luo Z, Zhou Y, Jiang Y. Fertilization treatments affect soil CO 2 emission through regulating soil bacterial community composition in the semiarid Loess Plateau. Sci Rep 2022; 12:20123. [PMID: 36418374 PMCID: PMC9684500 DOI: 10.1038/s41598-022-21108-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 09/22/2022] [Indexed: 11/24/2022] Open
Abstract
A growing body of literature have emphasized the effects of fertilization regimes on soil respiration and microbial community in the semiarid region, however, fertilization treatment effects on the soil CO2 emission, soil bacterial community, and their relationships from long-term experiments is lacking. In the present study, we investigated the effects of long-term fertilization regimes on soil bacterial community and thereafter on soil CO2 emission. A 9-year field experiment was conducted with five treatments, including no fertilizer (NA) and four fertilization treatments (inorganic fertilizer (CF), inorganic plus organic fertilizer (SC), organic fertilizer (SM), and maize straw (MS)) with equal N input as N 200 kg hm-2. The results indicated that CO2 emission was significantly increased under fertilization treatments compared to NA treatment. The bacterial abundance was higher under MS treatment than under NA treatment, while the Chao1 richness showed opposite trend. MS treatment significantly change soil bacterial community composition compared to NA treatment, the phyla (Alphaproteobacteria and Gammaproteobacteria) and potential keystone taxa (Nitrosomonadaceae and Beijerinckiaceae) were higher, while the Acidobacteriota was lower under MS treatment than under NA treatment. CO2 emission was positively correlated with the abundance of Alphaproteobacteria, Gammaproteobacteria, and keystone taxa, negatively correlated with these of Acidobacteriota. Random forest modeling and structural equation modeling determined soil organic carbon, total nitrogen, and the composition and network module III of the bacterial community are the main factors contribute to CO2 emission. In conclusion, our results suggest that the increased CO2 emission was affected by the varied of soil bacterial community composition derived from fertilization treatments, which was related to Alphaproteobacteria, Gammaproteobacteria, Acidobacteriota, and potential keystone taxa (Nitrosomonadaceae and Beijerinckiaceae), and highlight that the ecological importance of the bacterial community in mediating carbon cycling in the semiarid Loess Plateau.
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Affiliation(s)
- Jinbin Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Junhong Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lingling Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Zechariah Effah
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lihua Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhuzhu Luo
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Resource and Environment, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yongjie Zhou
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
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27
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Zhao Y, Lin H, Liu Y, Jiang Y, Zhang W. Abundant bacteria shaped by deterministic processes have a high abundance of potential antibiotic resistance genes in a plateau river sediment. Front Microbiol 2022; 13:977037. [DOI: 10.3389/fmicb.2022.977037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Recent research on abundant and rare bacteria has expanded our understanding of bacterial community assembly. However, the relationships of abundant and rare bacteria with antibiotic resistance genes (ARGs) remain largely unclear. Here, we investigated the biogeographical patterns and assembly processes of the abundant and rare bacteria from river sediment at high altitudes (Lhasa River, China) and their potential association with the ARGs. The results showed that the abundant bacteria were dominated by Proteobacteria (55.4%) and Cyanobacteria (13.9%), while the Proteobacteria (33.6%) and Bacteroidetes (18.8%) were the main components of rare bacteria. Rare bacteria with a large taxonomic pool can provide function insurance in bacterial communities. Spatial distribution of persistent abundant and rare bacteria also exhibited striking differences. Strong selection of environmental heterogeneity may lead to deterministic processes, which were the main assembly processes of abundant bacteria. In contrast, the assembly processes of rare bacteria affected by latitude were dominated by stochastic processes. Abundant bacteria had the highest abundance of metabolic pathways of potential drug resistance in all predicted functional genes and a high abundance of potential ARGs. There was a strong potential connection between these ARGs and mobile genetic elements, which could increase the ecological risk of abundant taxa and human disease. These results provide insights into sedimental bacterial communities and ARGs in river ecosystems.
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28
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Zeng J, Li Y, Jin G, Su JQ, Yao H. Short-Term Benzalkonium Chloride (C 12) Exposure Induced the Occurrence of Wide-Spectrum Antibiotic Resistance in Agricultural Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15054-15063. [PMID: 36069710 DOI: 10.1021/acs.est.2c04730] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance genes (ARGs) are global pollutants that pose a potential risk to human health. Benzalkonium chloride (C12) (BC) disinfectants are thought to exert selection pressure on antibiotic resistance. However, evidence of BC-induced changes in antibiotic resistance in the soil environment is lacking. Here, we established short-term soil microcosms to investigate ARG profile dynamics in agricultural soils amended with sulfamethazine (SMZ, 10 mg kg-1) and gradient concentrations of BC (0-100 mg kg-1), using high-throughput quantitative PCR and Illumina sequencing. With the increase in BC concentration, the number of ARGs detected in the soil increased, but the normalized ARG abundance decreased. The added SMZ had a limited impact on ARG profiles. Compared to broad-spectrum fungicidal BC, the specificity of SMZ significantly affected the microbial community. Network analysis found that low-medium BC exposure concentrations resulted in the formation of small but strong ARG co-occurrence clusters in the soil, while high BC exposure concentration led to a higher incidence of ARGs. Variation partitioning analysis suggested that BC stress was the major driver shaping the ARG profile. Overall, this study highlighted the emergence and spread of BC-induced ARGs, potentially leading to the antimicrobial resistance problem in agricultural soils.
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Affiliation(s)
- Jieyi Zeng
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Guoping Jin
- Ningbo No. 9 Hospital, Ningbo 315020, People's Republic of China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Huaiying Yao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
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29
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Zheng F, Zhou GW, Zhu D, Neilson R, Zhu YG, Chen B, Yang XR. Does Plant Identity Affect the Dispersal of Resistomes Above and Below Ground? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14904-14912. [PMID: 35917301 DOI: 10.1021/acs.est.1c08733] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Resistomes are ubiquitous in natural environments. Previous studies have shown that both the plant phyllosphere and soil-borne nematodes were reservoirs of above- and below-ground resistomes, respectively. However, the influence of plant identity on soil, nematode, and phyllosphere resistomes remains unclear. Here, a microcosm experiment was used to explore the characteristics of bacterial communities and resistomes in soil, nematode, and phyllosphere associated with six different plant identities (Lactuca sativa, Cichorium endivia, Allium fistulosum, Coriandrum sativum, Raphanus sativus, and Mesembryanthemum crystallinum). A total of 222 antibiotic resistance genes (ARGs) and 7 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR from all samples. Plant identity not only significantly affected the diversity of resistomes in soil, nematode, and phyllosphere but also influenced the abundance of resistomes in nematodes. Shared bacteria and resistomes indicated a possible pathway of resistomes transfer through the soil-nematode-phyllosphere system. Structural equation models revealed that plant identity had no direct effect on phyllosphere ARGs, but altered indirectly through complex above- and below-ground interactions (soil-plant-nematode trophic transfer). Results also showed that bacteria and MGEs were key factors driving the above- and below-ground flow of resistomes. The study extends our knowledge about the top-down and bottom-up dispersal patterns of resistomes.
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Affiliation(s)
- Fei Zheng
- School of Life Sciences, Hebei University, Baoding 071002, China
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guo-Wei Zhou
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, United Kingdom
| | - 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, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Bing Chen
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
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Zhang M, Hou L, Zhu Y, Zhang C, Li W, Lai X, Yang J, Li S, Shu H. Composition and distribution of bacterial communities and antibiotic resistance genes in fish of four mariculture systems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 311:119934. [PMID: 35973451 DOI: 10.1016/j.envpol.2022.119934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 06/15/2023]
Abstract
Fish-related antibiotic resistance genes (ARGs) have attracted attention for their potentially harmful effects on food safety and human health through the food chain transfer. However, the potential factors affecting these ARGs have not been fully explored. In this study, ARGs and bacterial communities in the fish gut, mucosal skin, and gill filaments in fish were comprehensively evaluated in four different mariculture systems formed by hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂), Gracilaria bailinae, and Litopenaeus vannamei using different combinations. The results showed that 9 ARGs were detected in the gut and mucosal skin and 6 ARGs in the gill filaments. The detection rate of aphA1 was the highest, and the abundance was 1.91 × 10-3 - 6.30 × 10-2 copies per 16 S rRNA gene. Transposase gene (tnpA-04) was detected in all samples with the abundance of 3.57 × 10-3 - 3.59 × 10-2 copies per 16 S rRNA gene, and was strongly correlated with multiple ARGs (e.g., aphA1, tet(34), mphA-02). Proteobacteria, Deinococcus-Thermus, Firmicutes, and Bacteroidetes were the dominant phyla in the four mariculture systems, accounting for 65.1%-96.2% of the total bacterial community. Notably, the high relative abundance of Stenotrophomonas, a potential human pathogen, was elevated by 20.5% in the hybrid grouper gut in the monoculture system. In addition, variation partitioning analysis (VPA) showed that the difference in bacterial communities between mariculture systems was the main driving factor of ARGs distribution differences in hybrid groupers. This study provides a new comprehensive understanding of the characterization of fish-related ARGs contamination in different mariculture systems and facilitates the assessment of potential risks of ARGs and pathogen taxa to human health.
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Affiliation(s)
- Mingqing Zhang
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Liping Hou
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Yating Zhu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Cuiping Zhang
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Wen Li
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xingxing Lai
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jinlin Yang
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Shuisheng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Hu Shu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
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Leroy-Freitas D, Machado EC, Torres-Franco AF, Dias MF, Leal CD, Araújo JC. Exploring the microbiome, antibiotic resistance genes, mobile genetic element, and potential resistant pathogens in municipal wastewater treatment plants in Brazil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156773. [PMID: 35724791 DOI: 10.1016/j.scitotenv.2022.156773] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/05/2022] [Accepted: 06/14/2022] [Indexed: 05/28/2023]
Abstract
Wastewater treatment plants (WWTPs) have been widely investigated in Europe, Asia and North America regarding the occurrence and fate of antibiotic resistance (AR) elements, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and antibiotic resistant bacteria and pathogens. However, monitoring data about AR elements in municipal WWTPs in Brazil are scarce. This study investigated the abundance of intI1, five ARGs (sul1, tetA, blaTEM, ermB and qnrB) and 16S rRNA in raw and treated wastewater of three WWTPs, using different sewage treatments named CAS (Conventional activated sludge), UASB/BTF (UASB followed by biological trickling filter) and MAS/UV (modified activated sludge with UV disinfection stage). Bacterial diversity and the presence of potentially pathogenic groups were also evaluated, and associations between genetic markers and the bacterial populations were presented. All WWTPs decreased the loads of genetic markers finally discharged to receiving water bodies and showed no evidence of being hotspots for antimicrobial resistance amplification in wastewater, since the abundances of intI1 and ARGs within the bacterial population were not increased in the treated effluents. UASB/BTF showed a similar performance to that of the CAS and MAS/UV, reinforcing the sanitary and environmental advantages of this biological treatment, widely applied for wastewater treatment in warm climate regions. Bacterial diversity and richness increased after treatments, and bacterial communities in wastewater samples differed due to catchment areas and treatment typologies. Potential pathogenic population underwent considerable decrease after the treatments; however, strong significant correlations with intI1 and ARGs revealed potential multidrug-resistant pathogenic bacteria (Aeromonas, Arcobacter, Enterobacter, Escherichia-Shigella, Stenotrophomonas and Streptococcus) in the treated effluents, although in reduced relative abundances. These are contributive results for understanding the fate of ARGs, MGEs and potential pathogenic bacteria after wastewater treatments, which might support actions to mitigate their release into Brazilian aquatic environments in the near future.
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Affiliation(s)
- D Leroy-Freitas
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte 31270-010, Brazil
| | - E C Machado
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte 31270-010, Brazil
| | - A F Torres-Franco
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte 31270-010, Brazil; Institute of Sustainable Processes, Valladolid University, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - M F Dias
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte 31270-010, Brazil
| | - C D Leal
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte 31270-010, Brazil
| | - J C Araújo
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte 31270-010, Brazil.
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Lin C, Huang FY, Zhou SYD, Li H, Zhang X, Su JQ. HiLi-chip: A high-throughput library construction chip for comprehensive profiling of environmental microbial communities. ENVIRONMENTAL RESEARCH 2022; 213:113650. [PMID: 35690091 DOI: 10.1016/j.envres.2022.113650] [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: 04/28/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Investigating the contribution and associations of environmental microbes to ecological health and human well-being is in great demand with the goal of One Health proposed. To achieve the goal, there is an urgent need for accurate approaches to obtaining a large amount of high-resolution molecular information from various microbes. In this study, we developed a high-throughput library construction chip (HiLi-Chip) for profiling environmental microbial communities and evaluated its performance. The HiLi-Chip showed high conformity with the conventional Pacbio method in terms of α-diversity, community composition of abundant bacteria (>83%), as well as rare taxa (>84%) and human pathogens detection (>67%), indicating its advantages of accuracy, high-throughput, cost-efficiency, and broad practicability. It is suggested that the optimal strategy of the HiLi-Chip was a 2.4 μL PCR mixture per sample (∼2.4 ng DNA) with a 216-sample × 24-replicate format. We have successfully applied the HiLi-Chip to the Jiulongjiang River and identified 51 potential human bacterial pathogens with a total relative abundance of 0.22%. Additionally, under limited nutrients and similar upstream environments, bacteria tended to impose competitive pressures, resulting in a more connected network at the downstream river confluence (RC). Whereas narrow niche breadth of bacteria and upstream environmental heterogeneity probably promoted niche complementary and environment selection leading to fewer links at RC in the midsection of the river. Core bacteria might represent the entire bacterial community and enhance network stability through synergistic interactions with other core bacteria. Collectively, our results demonstrate that the HiLi-Chip is a robust tool for rapid comprehensive profiling of microbial communities in environmental samples and has significant implications for a profound understanding of environmental microbial interactions.
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Affiliation(s)
- Chenshuo Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Fu-Yi Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China.
| | - Shu-Yi-Dan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Tianhe District, Guangzhou, 510650, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Xian Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
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Han B, Ma L, Yu Q, Yang J, Su W, Hilal MG, Li X, Zhang S, Li H. The source, fate and prospect of antibiotic resistance genes in soil: A review. Front Microbiol 2022; 13:976657. [PMID: 36212863 PMCID: PMC9539525 DOI: 10.3389/fmicb.2022.976657] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022] Open
Abstract
Antibiotic resistance genes (ARGs), environmental pollutants of emerging concern, have posed a potential threat to the public health. Soil is one of the huge reservoirs and propagation hotspot of ARGs. To alleviate the potential risk of ARGs, it is necessary to figure out the source and fate of ARGs in the soil. This paper mainly reviewed recent studies on the association of ARGs with the microbiome and the transmission mechanism of ARGs in soil. The compositions and abundance of ARGs can be changed by modulating microbiome, soil physicochemical properties, such as pH and moisture. The relationships of ARGs with antibiotics, heavy metals, polycyclic aromatic hydrocarbons and pesticides were discussed in this review. Among the various factors mentioned above, microbial community structure, mobile genetic elements, pH and heavy metals have a relatively more important impact on ARGs profiles. Moreover, human health could be impacted by soil ARGs through plants and animals. Understanding the dynamic changes of ARGs with influencing factors promotes us to develop strategies for mitigating the occurrence and dissemination of ARGs to reduce health risks.
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Affiliation(s)
- Binghua Han
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - Li Ma
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
| | - Jiawei Yang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - Wanghong Su
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - Mian Gul Hilal
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - Xiaoshan Li
- Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Faculty of Basic Medical Sciences, Chongqing Three Gorges Medical College, Wanzhou, China
| | - Shiheng Zhang
- Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Faculty of Basic Medical Sciences, Chongqing Three Gorges Medical College, Wanzhou, China
- *Correspondence: Shiheng Zhang, ; Huan Li,
| | - Huan Li
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
- *Correspondence: Shiheng Zhang, ; Huan Li,
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Wu H, Zhang Z, Wang J, Qin X, Chen J, Wu L, Lin S, Rensing C, Lin W. Bio-fertilizer Amendment Alleviates the Replanting Disease under Consecutive Monoculture Regimes by Reshaping Leaf and Root Microbiome. MICROBIAL ECOLOGY 2022; 84:452-464. [PMID: 34554283 DOI: 10.1007/s00248-021-01861-1] [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: 06/01/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Replanting disease is a growing problem in intensive agricultural systems. Application of bio-fertilizer containing beneficial microbes contributes to disease suppression and is a promising strategy to control replanting disease. However, the effect of both replanting disease and bio-fertilizer amendment on the assembly of crop microbiota in leaves and roots and their relationships to crop yield and quality remains elusive. In these experiments, roots and leaves of Radix pseudostellariae were collected from different consecutive monoculture and bio-fertilizer amended fields, and the associated microbiota were characterized by bacterial 16S rRNA gene sequencing and quantitative PCR. Consecutive monoculture altered the bacterial community structure and composition and significantly increased the abundance of potential pathogenic Ralstonia and Fusarium oxysporum in leaves and roots. Furthermore, bio-fertilizer application alleviated replanting disease by decreasing the pathogen load, increasing the potential beneficial genera Pseudomonas, Streptomyces, Paenibacillus, and Bradyrhizobium. The proportion of positive correlations in the co-occurrence network of bio-fertilizer application was the highest, implying that bio-fertilizer potentially enhanced ecological commensalism or mutualism of the bacterial community across the two compartments. Structural equation models indicated that bio-fertilizer had a positive and indirect effect on both yield and quality by shaping the leaf microbiota and the root microbiota. Our findings highlight the role of leaf and root microbiota on replanting disease, showing that bio-fertilizer contributes to alleviating replanting disease by improving microbe-microbe interactions.
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Affiliation(s)
- Hongmiao Wu
- Laboratory of Rhizosphere Ecology Processes and Management, College of Resource and Environment, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Zhen Zhang
- Laboratory of Rhizosphere Ecology Processes and Management, College of Resource and Environment, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
| | - Juanying Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Xianjin Qin
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Jun Chen
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Linkun Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Sheng Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
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Lu L, He Y, Peng C, Wen X, Ye Y, Ren D, Tang Y, Zhu D. Dispersal of antibiotic resistance genes in an agricultural influenced multi-branch river network. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154739. [PMID: 35331763 DOI: 10.1016/j.scitotenv.2022.154739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Rivers in agricultural regions serve as an important sink for livestock and poultry farm runoff, fertilizer runoff, and country living sewage, which could bring antibiotic resistance genes (ARGs) contaminations. However, the diversity and distribution of ARGs has not been well documented in the agricultural influenced river. Here, the diversity of ARGs, and their relationship with biochemical factors were determined in the surface water in an agricultural region of the Jialing River and its five rural branches. The 218 unique ARGs encoding resistance to eight major antibiotic classes have been detected using high-throughput quantitative PCR. The branches of the river had a remarkably higher abundance of ARGs than the mainstream. The aminoglycoside, beta_Lactamase, MLSB, and Multidrug resistance genes were significantly enriched in the branches compared to the mainstream. Compared with the mainstream, the ARGs profiles in the branches showed obvious higher spatial variability. Significant correlation between ARGs profiles and bacterial community structures were observed, and network analysis further showed that the ARGs were associated with their potential hosts, such as Ottowia and Novosphingobium. Redundancy discrimination analysis revealed that Cu content has a significant contribution to the increase of ARGs in the river. The microbial diversity index was negatively correlated with the abundance of the ARGs. These results provide evidence for the enrichment of ARGs in the agricultural influenced river and branches due to the joint influence of chemical and microbial variables.
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Affiliation(s)
- Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yan He
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Chao Peng
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Xingyue Wen
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yuqiu Ye
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Dong Ren
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yun Tang
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Dong Zhu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Yang LY, Zhou SYD, Lin CS, Huang XR, Neilson R, Yang XR. Effects of biofertilizer on soil microbial diversity and antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153170. [PMID: 35051473 DOI: 10.1016/j.scitotenv.2022.153170] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Spread of antibiotic resistance or the presence of antibiotic resistance genes (ARGs) in pathogens is a globally recognized threat to human health. Numerous studies have shown that application of organic fertilizers may increase the risk of ARGs, however, the risk of resistance genes associated with biofertilizers is largely unknown. To investigate whether biofertilizer application introduces ARGs to the soil, we used high-throughput quantitative polymerization chain reaction (HT-qPCR) to explore the effect of biofertilizer application over three years on soil ARGs in three orchards with different locations in China. Redundancy analysis showed specific and significant differences in the beta diversity of soil bacteria and fungi between treatments (fertilizer vs. no fertilizer). One-way ANOVA analysis revealed findings of the main driver of the significant difference in microbial community structure between fertilizer and control treatment was the change in soil properties following the application of biofertilizer. A total of 139 ARGs and 27 MGEs (mobile genetic elements), and 46 ARGs and 6 MGEs from 11 major taxa were detected in biofertilizer and soil samples, respectively. Only the samples from Guangxi had significant differences in the detected number of ARGs and MGEs between fertilization and control. Through structural equation modeling (SEM), we found that soil properties indirectly affected ARGs by shaping bacterial diversity, while bacterial abundance directly affected ARGs. Biofertilizer application did not significantly alter the relative abundance of ARGs in soil due to the complexity of the soil environment and competition between exogenous and native microorganisms. This study provided new insights into the spread of the antibiotic resistome of the soil through biofertilizer applications.
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Affiliation(s)
- Le-Yang Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Shu-Yi-Dan Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Chen-Shuo Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin-Rong Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; College of Life Sciences, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou 350002, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, UK
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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Wang T, Sun S, Xu Y, Waigi MG, Odinga ES, Vasilyeva GK, Gao Y, Hu X. Nitrogen Regulates the Distribution of Antibiotic Resistance Genes in the Soil-Vegetable System. Front Microbiol 2022; 13:848750. [PMID: 35359719 PMCID: PMC8964294 DOI: 10.3389/fmicb.2022.848750] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The increasing antibiotic resistance genes (ARGs) in fertilizer-amended soils can potentially enter food chains through their transfer in a soil-vegetable system, thus, posing threats to human health. As nitrogen is an essential nutrient in agricultural production, the effect of nitrogen (in the forms NH4 +-N and NO3 --N) on the distribution of ARGs (blaTEM-1, sul1, cmlA, str, and tetO) and a mobile genetic element (MGE; tnpA-4) in a soil-Chinese cabbage system was investigated. Not all the tested genes could transfer from soil to vegetable. For transferable ones (blaTEM-1, sul1, and tnpA-4), nitrogen application influenced their abundances in soil and vegetable but did not impact their distribution patterns (i.e., preference to either leaf or root tissues). For ARGs in soil, effects of nitrogen on their abundances varied over time, and the positive effect of NH4 +-N was more significant than that of NO3 --N. The ARG accumulation to vegetables was affected by nitrogen application, and the nitrogen form was no longer a key influencing factor. In most cases, ARGs were found to prefer being enriched in roots, and nitrogen application may slightly affect their migration from root to leaf. The calculated estimated human intake values indicated that both children and adults could intake 106-107 copies of ARGs per day from Chinese cabbage consumption, and nitrogen application affected ARG intake to varying degrees. These results provided a new understanding of ARG distribution in vegetables under the agronomic measures such as nitrogen application, which may offer knowledge for healthy vegetable cultivation in future.
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Affiliation(s)
- Tingting Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Silu Sun
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yanxing Xu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Emmanuel Stephen Odinga
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Galina K Vasilyeva
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Russia
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
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Yin Y, Zhu D, Yang G, Su J, Duan G. Diverse antibiotic resistance genes and potential pathogens inhabit in the phyllosphere of fresh vegetables. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152851. [PMID: 34990692 DOI: 10.1016/j.scitotenv.2021.152851] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Fresh vegetables are considered as a reservoir of pathogenic bacteria and antibiotic resistance genes (ARGs), which are the emerging environmental contaminants, posing increasing concerned risk to human health. However, the prevalence of pathogens in phyllosphere of fresh vegetables, as well as the association of ARGs with pathogenic bacteria, have not been well elaborated. In this study, we explored the structure of microbial communities and ARGs through high-throughput quantitative PCR and 16S rRNA gene Illumina sequencing, and characterized the microorganisms resisting to antibiotics by pure culture. From phyllosphere of six different kinds of vegetables, 205 ARGs were detected and genes for multidrug resistance was the most abundant. The predominant potential pathogens were classified to Pseudomonas, Klebsiella, and Acinetobacter genera, which carried various ARGs such as multidrug and beta-lactam resistance genes presumedly. Among six kinds of vegetables, Lactuca sativa var. asparagina carried the highest abundance of potential pathogens and ARGs, while Allium sativum L harbored the lowest abundance of pathogens and ARGs. In addition, various culturable bacteria resisting to colistin or meropenem could be isolated from all vegetables, remarkably, all the isolates resistant to both antibiotics are potential pathogens. Our study highlighted the risks of pathogens and ARGs from raw vegetables to consumers, characterized their structure patterns among different vegetables, and analyzed the potential mechanisms regulating phyllosphere pathogens and resistome of fresh vegetables, which would be helpful for reducing the microbial risk from vegetable ingestion.
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Affiliation(s)
- Yue Yin
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang Yang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jianqiang Su
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guilan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Vincent SA, Ebertz A, Spanu PD, Devlin PF. Salicylic Acid-Mediated Disturbance Increases Bacterial Diversity in the Phyllosphere but Is Overcome by a Dominant Core Community. Front Microbiol 2022; 13:809940. [PMID: 35283825 PMCID: PMC8908428 DOI: 10.3389/fmicb.2022.809940] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
Plant microbiomes and immune responses have coevolved through history, and this applies just as much to the phyllosphere microbiome and defense phytohormone signaling. When in homeostasis, the phyllosphere microbiome confers benefits to its host. However, the phyllosphere is also dynamic and subject to stochastic events that can modulate community assembly. Investigations into the impact of defense phytohormone signaling on the microbiome have so far been limited to culture-dependent studies; or focused on the rhizosphere. In this study, the impact of the foliar phytohormone salicylic acid (SA) on the structure and composition of the phyllosphere microbiome was investigated. 16S rRNA amplicons were sequenced from aerial tissues of two Arabidopsis mutants that exhibit elevated SA signaling through different mechanisms. SA signaling was shown to increase community diversity and to result in the colonization of rare, satellite taxa in the phyllosphere. However, a stable core community remained in high abundance. Therefore, we propose that SA signaling acts as a source of intermediate disturbance in the phyllosphere. Predictive metagenomics revealed that the SA-mediated microbiome was enriched for antibiotic biosynthesis and the degradation of a diverse range of xenobiotics. Core taxa were predicted to be more motile, biofilm-forming and were enriched for traits associated with microbe-microbe communication; offering potential mechanistic explanation of their success despite SA-mediated phyllospheric disturbance.
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Affiliation(s)
- Stacey A Vincent
- Department of Biological Sciences, Royal Holloway, University of London, Egham, United Kingdom
| | - Andreas Ebertz
- Department of Biological Sciences, Royal Holloway, University of London, Egham, United Kingdom
| | - Pietro D Spanu
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Paul F Devlin
- Department of Biological Sciences, Royal Holloway, University of London, Egham, United Kingdom
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40
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Zhang Y, Ma J, O'Connor P, Zhu YG. Microbial communities on biodegradable plastics under different fertilization practices in farmland soil microcosms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:152184. [PMID: 34890659 DOI: 10.1016/j.scitotenv.2021.152184] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
Plastic mulching is a common practice in agricultural systems and is often combined with fertilization. Biodegradable plastics (BPs) are becoming an alternative to non-biodegradable plastics (non-BPs) for soil mulching. However, the effects of fertilization on the microbial communities on BPs remain unclear. Here, we explored the responses of the plastisphere to different fertilization practices in soil-based microcosms containing three BPs: polylactic acid (PLA), poly (butylene succinate) (PBS), and poly (butylene-adipate-co-terephthalate) (PBAT), and one non-BP (low-density polyethylene, LDPE). The 16S and ITS rRNA gene-based Illumina sequencing method were used to identify the bacterial and fungal communities on the plastics and in the soils. Microbial community structure on BPs was significantly different from that in soils and on LDPE. The predicted functional profiles of bacteria on BPs, especially PBAT, were distinct from those in soils. The plastisphere communities on BPs were dominated by microbes adapted to access and utilize carbon sources compared with of the communities on LDPE. Application of manure increased the alpha diversity of bacterial communities on BPs but decreased it on LDPE. The structure of bacterial communities on BPs changed with the application of manure. Our research establishes the baseline dynamics of plastisphere communities on BPs in soils.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Ma
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Institute of Urban Environment, Chinese Academy of Sciences, Ningbo 315800, China.
| | - Patrick O'Connor
- Centre for Global Food and Resources, University of Adelaide, Adelaide 5005, Australia
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
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41
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Li H, Zheng X, Tan L, Shao Z, Cao H, Xu Y. The vertical migration of antibiotic-resistant genes and pathogens in soil and vegetables after the application of different fertilizers. ENVIRONMENTAL RESEARCH 2022; 203:111884. [PMID: 34400159 DOI: 10.1016/j.envres.2021.111884] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/04/2021] [Accepted: 08/10/2021] [Indexed: 05/28/2023]
Abstract
The prevalence of bacterial resistance caused by the application of animal manure has become an important environmental issue. Herein, the vertical migration of antibiotic resistance genes (ARGs) and pathogens in soil and vegetables after the application of different fertilizers was explored. The results showed that the application of composted manure considerably enhanced the abundance of most ARGs and pathogens, especially in surface soil and pakchoi roots. Moreover, the soil ARGs increased partially from log 1.93 to log 4.65 after the application of composted manure, and six pathogens were simultaneously detected. It was observed that the increase in soil depth decreased most ARGs and pathogens by log 1.04-2.24 and 53.98 %~85.54 %, respectively. This indicated that ARGs and pathogens still existed in the deep soil (80-100 cm). Moreover, total organic carbon had a significant influence on the pathogen distribution, whereas bacterial communities primarily drove the vertical migration of ARGs rather than environmental factors. Although most of the ARG-host associations observed in the surface soil were disappeared in deep soil as revealed by network analysis, some co-occurrence pattern still occurred in deep soil, suggesting that some ARGs might be carried to deep soil by their host bacteria. These results were novel in describing the vertical migration of ARGs in the environment after the application of different fertilizers, providing ideas for curbing their migration to crops.
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Affiliation(s)
- Houyu Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Xiangqun Zheng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Lu Tan
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Zhenlu Shao
- Shan Dong Agriculture University, Tai' An, 271018, China
| | - Haoyu Cao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yan Xu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
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42
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Wen X, Xu J, Xiang G, Cao Z, Yan Q, Mi J, Ma B, Zou Y, Zhang N, Liao X, Wang Y, Wu Y. Multiple driving factors contribute to the variations of typical antibiotic resistance genes in different parts of soil-lettuce system. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 225:112815. [PMID: 34562788 DOI: 10.1016/j.ecoenv.2021.112815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/03/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
The application of manure compost may cause the transmission of antibiotic resistance genes (ARGs) in agroecological environment, which poses a global threat to public health. However, the driving factors for the transmission of ARGs from animal manure to agroecological systems remains poorly understood. Here, we explored the spatiotemporal variation in ARG abundance and bacterial community composition as well as relative driving factors in a soil-lettuce system amended with swine manure compost. The results showed that ARGs abundance had different variation trends in soil, lettuce phylloplane and endophyere after the application of swine manure compost. The temporal variations of total ARGs abundance had no significant different in soil and lettuce phylloplane, while lettuce endosphere enriched half of ARGs to the highest level at harvest. There was a significant linear correlation between ARGs and integrase genes (IGs). In contrast to the ARGs variation trend, the alpha diversity of soil and phylloplane bacteria showed increasing trends over planting time, and endosphere bacteria remained stable. Correlation analysis showed no identical ARG-related genera in the three parts, but the shared Proteobacteria, Pseudomonas, Halomonas and Chelativorans, from manure compost dominated ARG profile in the soil-lettuce system. Moreover, redundancy analysis and structural equation modelling showed the variations of ARGs may have resulted from the combination of multiple driving factors in soil-lettuce system. ARGs in soil were more affected by the IGs, antibiotic and heavy metals, and bacterial community structure and IGs were the major influencing factors of ARG profiles in the lettuce. The study provided insight into the multiple driving factors contribute to the variations of typical ARGs in different parts of soil-lettuce system, which was conducive to the risk assessment of ARGs in agroecosystem and the development of effective prevention and control measures for ARGs spread in the environment.
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Affiliation(s)
- Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiaojiao Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Guangfeng Xiang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhen Cao
- WENS Foodstuff Group Co., Ltd., Yunfu, Xinxing 527400, China
| | - Qiufan Yan
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiandui Mi
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Na Zhang
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China.
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China.
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Fan H, Wu S, Dong W, Li X, Dong Y, Wang S, Zhu YG, Zhuang X. Characterization of tetracycline-resistant microbiome in soil-plant systems by combination of H 218O-based DNA-Stable isotope probing and metagenomics. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126440. [PMID: 34280721 DOI: 10.1016/j.jhazmat.2021.126440] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 05/12/2023]
Abstract
The emergence and spread of antibiotic resistance have been considered as a global health threat. However, effective methods to identify antibiotic-resistant bacteria (ARB) in complex microbial community are lacking, and the potential transmission pathways of ARB and antibiotic resistance genes (ARGs) in the soil-plant system remain scarce. Here in this study, tetracycline was chosen as the target antibiotic due to its globally wide usage and clinical significance. DNA-based stable isotope probing with H218O was applied to identify the tetracycline-resistant bacteria from soil-plant systems. Eighteen-year organic fertilization significantly changed the composition of the tetracycline-resistant microbiome in the soil-wheat system and resulted in a higher relative abundance of ARGs in the wheat endophyte. Rhizosphere harboring the most diverse ARGs and mobile genetic elements was identified as a hot spot for horizontal gene transfer and an important bridge between bulk soil and wheat endophyte. Micrococcaceae and Sphingomonadaceae carrying ARGs associated with abundant mobile genetic elements, were identified as the core bacterial taxa in long-term manure-amended and untreated soil-wheat systems, respectively. This method contributes to a more precise track of ARB in the environment, and our work depicts the high potential of ARG transfer in the rhizosphere mediated by the core species.
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Affiliation(s)
- Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxu Dong
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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44
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Na G, Zhang K, Gao H, Li R, Jin S, Zhao F, Zhang H, Li S. Occurrence and distribution characteristics of antibiotic resistance genes in sediments between urban and rural of the Liaohe River Basin, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:54002-54014. [PMID: 34043168 DOI: 10.1007/s11356-021-13560-y] [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: 12/17/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Antibiotic resistance genes (ARGs) are considered to be emerging pollutants related to human activities. The rapid development of global urbanization has expanded human activities, thereby exacerbating the global human health risks caused by antibiotic resistance genes. The effects of urban and rural environments are multifarious, which makes the source and distribution of ARGs in the environment diversification. Understanding the distribution and spread of ARGs is essential for studying the environmental behavior of ARGs. In this study, the occurrence 296 genes were detected by the high-throughput qPCR technology, and FC value was used to analyze the diversity of ARGs and mobile genetic elements (MGEs) in sediments between urban and rural areas of the Liaohe River Basin, China. The co-occurrence of MGEs and ARGs was analyzed using network to decipher core genes. A total of 187 ARGs and 10 MGEs were detected in all sediment samples. The average number of genes detected in urban sites is 89 higher than that in rural sites. The high abundance and various types of ARGs and MGEs detected in urban river sediments indicate that the occurrence of urban ARGs is more complex. MGEs were detected high levels and were significantly correlated with the abundance and diversity of ARGs in river sediments providing evidence that MGEs were related to the occurrence and distribution of ARGs and tnpA (tnpA-07, tnpA-01, and tnpA-03) gene were at the key position of co-occurrence of various types of ARGs.
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Affiliation(s)
- Guangshui Na
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China.
- National Marine Environmental Monitoring Center, Dalian, 116023, China.
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya, 572022, China.
| | - Keyu Zhang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China
- National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Hui Gao
- National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Ruijing Li
- National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Shuaichen Jin
- National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Fuqiang Zhao
- National Marine Environmental Monitoring Center, Dalian, 116023, China
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, 116023, China
| | - Haibo Zhang
- National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Shisheng Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China
- National Marine Environmental Monitoring Center, Dalian, 116023, China
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45
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Huang J, Mi J, Yan Q, Wen X, Zhou S, Wang Y, Ma B, Zou Y, Liao X, Wu Y. Animal manures application increases the abundances of antibiotic resistance genes in soil-lettuce system associated with shared bacterial distributions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 787:147667. [PMID: 34004530 DOI: 10.1016/j.scitotenv.2021.147667] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 06/12/2023]
Abstract
An increasing amount of animal manures is being used in agriculture, and the effect of animal manures application on the abundance of antibiotics resistance genes (ARGs) in soil-plant system has attracted widespread attention. However, the impacts of animal manures application on the various types of bacterial distribution that occur in soil-lettuce system are unclear. To address this topic, the effects of poultry manure, swine manure or chemical fertilizer application on ARG abundance and the distribution of shared bacteria were investigated in this study. In a lettuce pot experiment, 13 ARGs and 2 MGEs were quantified by qPCR, and bacterial communities in the soil, lettuce endosphere and lettuce phyllosphere were analysed by 16S rRNA sequence analysis. The results showed that the application of poultry or swine manure significantly increased ARG abundance in the soil, a result attributed mainly to increases in the abundances of tetG and tetC. The application of poultry manure, swine manure and chemical fertilizer significantly increased ARG abundance in the lettuce endosphere, and tetG abundance was significantly increased in the poultry and swine manure groups. However, animal manures application did not significantly increase ARG abundance in the lettuce phyllosphere. Flavobacteriaceae, Sphingomonadaceae and 11 other bacterial families were the shared bacteria in the soil, lettuce endosphere, and phyllosphere. The Streptomycetaceae and Methylobacteriaceae were significantly positively correlated with intI1 in both the soil and endosphere. Chemical fertilizer application increased both the proportions of Sphingomonadaceae and tetX abundance, which were positively correlated in the endosphere. Comamonadaceae and Flavobacteriaceae were not detected in the lettuce endosphere under swine manure application. Cu was related to Flavobacteriaceae in the lettuce endosphere. Overall, poultry and swine manure application significantly increased ARG abundance in the soil-lettuce system, which might be due to the shared bacterial distribution.
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Affiliation(s)
- Jielan Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Jiandui Mi
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Qiufan Yan
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Shizheng Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China.
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46
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Wei M, Lv D, Cao L, Zhou K, Jiang K. Adsorption behaviours and transfer simulation of levofloxacin in silty clay. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:46291-46302. [PMID: 33861425 DOI: 10.1007/s11356-021-13955-x] [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: 08/05/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Fluoroquinolone antibiotics in soil can cause serious antibiotic pollution. Adsorption is the main factor that influences their destination and transport of antibiotics. Therefore, research on the behaviour of antibiotics once they reach the soil environment is meaningful to design appropriate measures to reduce their potential risks. This research took levofloxacin (LVFX) as the research object and used a static adsorption experiment to study the adsorption behaviour of the vadose zone of silty clay on the North China Plain. The results showed that LVFX had high retention in silty clay, with an average adsorption ratio of more than 90%. Adsorption of LVFX on silty clay reached equilibrium in 24 h with an adsorption amount of 93.5 mg/kg at an initial LVFX concentration of 10 mg/L. Acidity, cations and soil organic matter could affect the adsorption of LVFX, with adsorption variation ratio of 3.3%, 3.4% and 0.6%, respectively. In addition, numerical simulation with Hydrus-1D was utilized, and the results show that LVFX may infiltrate into underground water through silty clay after 28 days and completely penetrate in 100 days.
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Affiliation(s)
- Mengxian Wei
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, 050000, Hebei Province, China
| | - Dunyu Lv
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences and Key Laboratory of Groundwater Science and Engineering, Ministry of Natural Resources, Shijiazhuang, 050000, Hebei Province, China.
| | - LianHai Cao
- Surveying and Geo-informatics, North China University of Water Resources and Electric Power, Zhengzhou, 450003, Henan Province, China
| | - Kai Zhou
- Subterranean Hydrology, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Kai Jiang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, 050000, Hebei Province, China
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47
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Guo Y, Qiu T, Gao M, Sun Y, Cheng S, Gao H, Wang X. Diversity and abundance of antibiotic resistance genes in rhizosphere soil and endophytes of leafy vegetables: Focusing on the effect of the vegetable species. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125595. [PMID: 34088171 DOI: 10.1016/j.jhazmat.2021.125595] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/04/2021] [Accepted: 03/03/2021] [Indexed: 05/27/2023]
Abstract
Antibiotic resistance genes (ARGs) in the endophytes of vegetables represent a potential route of human exposure to the soil resistome. However, the effect of vegetable species on the endophytic ARG profiles is unclear, hampering our understanding of how ARGs migrate into the soil-vegetable system and their potential health risks. Here, we planted four leafy vegetables (cilantro, endive, lettuce, and pak choi), which are commonly eaten raw, and analyzed the resistomes and microbiomes in three sample types (rhizosphere soil, root, and leaf endophytes). A total of 150 ARG subtypes were detected using high-throughput quantitative PCR. Vegetable species had a significant effect on ARG diversity and abundance, and pak choi accumulated more ARGs in its associated microbiome than the other three vegetables. The bacterial community was the primary factor shaping ARG profiles and was significantly correlated with ARG subtypes. We identified aadE, tet(34), and vanSB as shared ARGs among leaves of the four vegetables; the bacterial families correlated with tet(34) and vanSB were also shared across the vegetables and belonged to Proteobacteria. This study deepens our understanding of how endophytic ARG profiles vary among different vegetables and highlights the potential health risk associated with consuming these vegetables raw.
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Affiliation(s)
- Yajie Guo
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Tianlei Qiu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Min Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanmei Sun
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, Shaanxi 710069, China
| | - Shoutao Cheng
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Haoze Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xuming Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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48
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Xing L, Yang J, Jia Y, Hu X, Liu Y, Xu H, Yin H, Li J, Yi Z. Effects of ecological environment and host genotype on the phyllosphere bacterial communities of cigar tobacco ( Nicotiana tabacum L.). Ecol Evol 2021; 11:10892-10903. [PMID: 34429888 PMCID: PMC8366869 DOI: 10.1002/ece3.7861] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/05/2021] [Accepted: 06/10/2021] [Indexed: 12/03/2022] Open
Abstract
Microorganisms of plant phyllosphere play an important role in plant health and productivity and are influenced by abiotic and biotic factors. In this study, we investigated the phyllosphere bacterial communities of three cigar tobacco varieties cultivated in Guangcun (GC) and Wuzhishan (WZS), Hainan, China. Metagenomic DNA was extracted from tobacco leaf samples and sequenced by 16S rDNA amplicon sequencing. Our results showed that bacterial communities of cigar tobacco phyllosphere in GC exhibited remarkably higher alpha diversity than that in WZS. There was slight effect of tobacco genotype variations on the alpha diversity in both cultivation sites, and beta diversity and structure of bacterial community were not influenced significantly by the cultivation sites and tobacco varieties. Statistical analyses of species diversity unraveled that the dominant species in bacterial communities of cigar tobacco phyllosphere among all these samples were phylogenetically affiliated to Proteobacteria and Cyanobacteria. At the genus level, the most abundant microorganism was Limnobacter, followed by Brevundimonas, unidentified_Cyanobacteria, and Pseudomonas. Additionally, environmental conditions except for humidity were negatively correlated with the relative abundance of bacterial genera. Further analyses revealed that influence of site-specific factors on tobacco bacterial community was relatively higher than genotype-specific factors. In short, this study may contribute to the knowledge base of practical applications of bacterial inoculants for tobacco leaf production.
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Affiliation(s)
- Lei Xing
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Greatwall Cigar FactoryChina Tobacco Sichuan Industrial Co., LtdShifangChina
| | - Jianlei Yang
- School of Minerals Processing and BioengineeringCentral South UniversityChangshaChina
| | - Yuhong Jia
- Greatwall Cigar FactoryChina Tobacco Sichuan Industrial Co., LtdShifangChina
| | - Xi Hu
- Greatwall Cigar FactoryChina Tobacco Sichuan Industrial Co., LtdShifangChina
| | - Yi Liu
- Greatwall Cigar FactoryChina Tobacco Sichuan Industrial Co., LtdShifangChina
| | - Heng Xu
- Greatwall Cigar FactoryChina Tobacco Sichuan Industrial Co., LtdShifangChina
| | - Huaqun Yin
- School of Minerals Processing and BioengineeringCentral South UniversityChangshaChina
| | - Juan Li
- College of AgronomyHunan Agricultural UniversityChangshaChina
| | - Zhenxie Yi
- College of AgronomyHunan Agricultural UniversityChangshaChina
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49
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Ke M, Ye Y, Li Y, Zhou Z, Xu N, Feng L, Zhang J, Lu T, Cai Z, Qian H. Leaf metabolic influence of glyphosate and nanotubes on the Arabidopsis thaliana phyllosphere. J Environ Sci (China) 2021; 106:66-75. [PMID: 34210440 DOI: 10.1016/j.jes.2021.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/06/2021] [Accepted: 01/06/2021] [Indexed: 06/13/2023]
Abstract
Chemical exposure can indirectly affect leaf microbiota communities, but the mechanism driving this phenomenon remains largely unknown. Results revealed that the co-exposure of glyphosate and multi-carbon nanotubes (CNTs) caused a synergistic inhibitory effect on the growth and metabolism of Arabidopsis thaliana shoots. However, only a slight inhibitory effect was induced by nanotubes or glyphosate alone at the tested concentrations. Several intermediate metabolites of nitrogen metabolism and fatty acid synthesis pathways were upregulated under the combined treatment, which increased the amount of energy required to alleviate the disruption caused by the combined treatment. Additionally, compared with the two individual treatments, the glyphosate/nanotube combination treatment induced greater fluctuations in the phyllosphere bacterial community members with low abundance (relative abundance (RA) <1%) at both the family and genus levels, and among these bacteria some plant growth promotion and nutrient supplement related bacteria were markable increased. Strikingly, strong correlations between phyllosphere bacterial diversity and metabolites suggested a potential role of leaf metabolism, particularly nitrogen and carbohydrate metabolism, in restricting the range of leaf microbial taxa. These correlations between phyllosphere bacterial diversity and leaf metabolism will improve our understanding of plant-microbe interactions and the extent of their drivers of variation and the underlying causes of variability in bacterial community composition.
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Affiliation(s)
- Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yizhi Ye
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yan Li
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhigao Zhou
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Lan Feng
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Jinfeng Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhiqiang Cai
- Laboratory of Applied Microbiology and Biotechnology, School of Pharmaceutical Engineering & Life Science, Changzhou University, Changzhou 213164, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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50
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Kröber E, Wende S, Kanukollu S, Buchen-Tschiskale C, Besaury L, Keppler F, Vuilleumier S, Kolb S, Bringel F. 13 C-chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern. Environ Microbiol 2021; 23:4450-4465. [PMID: 34121306 DOI: 10.1111/1462-2920.15638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/20/2022]
Abstract
Chloromethane (CH3 Cl) is the most abundant halogenated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH3 Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH3 Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. We identified and characterized CH3 Cl-degrading bacteria associated with intact and living tree fern plants of the species Cyathea australis by stable isotope probing (SIP) with 13 C-labelled CH3 Cl combined with metagenomics. Metagenome-assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH3 Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH3 Cl degradation in the fern rhizosphere. The only known metabolic pathway for CH3 Cl degradation, via a methyltransferase system including the gene cmuA, was not detected in metagenomes or MAGs identified by SIP. Hence, a yet uncharacterized methylotrophic cmuA-independent pathway may drive CH3 Cl degradation in the investigated tree ferns.
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Affiliation(s)
- Eileen Kröber
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Sonja Wende
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Saranya Kanukollu
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Caroline Buchen-Tschiskale
- Isotope Biogeochemistry and Gas Fluxes, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Ludovic Besaury
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
| | - Frank Keppler
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
| | - Stéphane Vuilleumier
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
| | - Steffen Kolb
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Françoise Bringel
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
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