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Wu L, Lin H, Zhang L, Kiet TQ, Liu P, Song J, Duan Y, Hu C, Yang H, Duan W, Yang X. Construction of high-quality genomes and gene catalogue for culturable microbes of sugarcane (Saccharum spp.). Sci Data 2024; 11:534. [PMID: 38789459 PMCID: PMC11126615 DOI: 10.1038/s41597-024-03379-w] [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: 11/22/2023] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Microbes living inside or around sugarcane (Saccharum spp.) are crucial for their resistance to abiotic and biotic stress, growth, and development. Sequences of microbial genomes and genes are helpful to understand the function of these microbes. However, there is currently a lack of such knowledge in sugarcane. Here, we combined Nanopore and Illumina sequencing technologies to successfully construct the first high-quality metagenome-assembled genomes (MAGs) and gene catalogues of sugarcane culturable microbes (GCSCMs), which contained 175 species-level genome bins (SGBs), and 7,771,501 non-redundant genes. The SGBs included 79 novel culturable bacteria genomes, and 3 bacterial genomes with nitrogen-fixing gene clusters. Four single scaffold near-complete circular MAGs (cMAGs) with 0% contamination were obtained from Nanopore sequencing data. In conclusion, we have filled a research gap in the genomes and gene catalogues of culturable microbes of sugarcane, providing a vital data resource for further understanding the genetic basis and functions of these microbes. In addition, our methodology and results can provide guidance and reference for other plant microbial genome and gene catalogue studies.
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Affiliation(s)
- Liang Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Haidong Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Lijun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming, 650221, China
| | - Ta Quang Kiet
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Peng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Jinkang Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Yong Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Chunyu Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Hao Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Weixing Duan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences / Sugarcane Research Center, Chinese Academy of Agricultural Sciences / Guangxi Key Laboratory of Sugarcane Genetic Improvement / Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Nanning, Guangxi, 530007, China.
| | - Xiping Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
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Fang X, Zhang M, Zheng P, Wang H, Wang K, Lv J, Shi F. Biochar-bacteria-plant combined potential for remediation of oil-contaminated soil. Front Microbiol 2024; 15:1343366. [PMID: 38835489 PMCID: PMC11148334 DOI: 10.3389/fmicb.2024.1343366] [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: 11/24/2023] [Accepted: 04/26/2024] [Indexed: 06/06/2024] Open
Abstract
Oil pollution is a common type of soil organic pollution that is harmful to the ecosystem. Bioremediation, particularly microbe-assisted phytoremediation of oil-contaminated soil, has become a research hotspot in recent years. In order to explore more appropriate bioremediation strategies for soil oil contamination and the mechanism of remediation, we compared the remediation effects of three plants when applied in combination with a microbial agent and biochar. The combined remediation approach of Tagetes erecta, microbial agent, and biochar exhibited the best plant growth and the highest total petroleum hydrocarbons degradation efficiency (76.60%). In addition, all of the remediation methods provided varying degrees of restoration of carbon and nitrogen contents of soils. High-throughput sequencing found that microbial community diversity and richness were enhanced in most restored soils. Some soil microorganisms associated with oil degradation and plant growth promotion such as Cavicella, C1_B045, Sphingomonas, MND1, Bacillus and Ramlibacter were identified in this study, among which Bacillus was the major component in the microbial agent. Bacillus was positively correlated with all soil remediation indicators tested and was substantially enriched in the rhizosphere of T. erecta. Functional gene prediction of the soil bacterial community based on the KEGG database revealed that pathways of carbohydrate metabolism and amino acid metabolism were up-regulated during remediation of oil-contaminated soils. This study provides a potential method for efficient remediation of oil-contaminated soils and thoroughly examines the biochar-bacteria-plant combined remediation mechanisms of oil-contaminated soil, as well as the combined effects from the perspective of soil bacterial communities.
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Affiliation(s)
- Xin Fang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Mei Zhang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Pufan Zheng
- Key Laboratory of Storage and Preservation of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Postharvest Physiology and Storage and Preservation of Agricultural Products, Institute of Agricultural Products Preservation and Processing Technology, Tianjin Academy of Agricultural Sciences (National Research Center of Agricultural Products Preservation Engineering and Technology (Tianjin)), Tianjin, China
| | - Haomin Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Kefan Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Juan Lv
- School of Environmental Science and Engineering, Tiangong University, Tianjin, China
| | - Fuchen Shi
- College of Life Sciences, Nankai University, Tianjin, China
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Su Y, Zhu M, Zhang H, Chen H, Wang J, Zhao C, Liu Q, Gu Y. Application of bacterial agent YH for remediation of pyrene-heavy metal co-pollution system: Efficiency, mechanism, and microbial response. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119841. [PMID: 38109828 DOI: 10.1016/j.jenvman.2023.119841] [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: 09/14/2023] [Revised: 11/22/2023] [Accepted: 12/03/2023] [Indexed: 12/20/2023]
Abstract
The combination of organic and heavy metal pollutants can be effectively and sustainably remediated using bioremediation, which is acknowledged as an environmentally friendly and economical approach. In this study, bacterial agent YH was used as the research object to explore its potential and mechanism for bioremediation of pyrene-heavy metal co-contaminated system. Under the optimal conditions (pH 7.0, temperature 35°C), it was observed that pyrene (PYR), Pb(II), and Cu(II) were effectively eliminated in liquid medium, with removal rates of 43.46%, 97.73% and 81.60%, respectively. The microscopic characterization (SEM/TEM-EDS, XPS, XRD and FTIR) results showed that Pb(II) and Cu(II) were eliminated by extracellular adsorption and intracellular accumulation of YH. Furthermore, the presence of resistance gene clusters (cop, pco, cus and pbr) plays an important role in the detoxification of Pb(II) and Cu(II) by strains YH. The degradation rate of PYR reached 72.51% in composite contaminated soil, which was 4.33 times that of the control group, suggesting that YH promoted the dissipation of pyrene. Simultaneously, the content of Cu, Pb and Cr in the form of F4 (residual state) increased by 25.17%, 6.34% and 36.88%, respectively, indicating a decrease in the bioavailability of heavy metals. Furthermore, YH reorganized the microbial community structure and enriched the abundance of hydrocarbon degradation pathways and enzyme-related functions. This study would provide an effective microbial agent and new insights for the remediation of soil and water contaminated with organic pollutants and heavy metals.
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Affiliation(s)
- Yuhua Su
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Mingjun Zhu
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Hang Zhang
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Hongxu Chen
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jiguo Wang
- Toroivd Technology Company Limited, Shanghai, 200439, China
| | - Chaocheng Zhao
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, China
| | - Qiyou Liu
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, China.
| | - Yingying Gu
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China; State Key Laboratory of Petroleum Pollution Control, Qingdao, 266580, China
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Yan M, Xu C, Li C, Feng Y, Duan J, Zhao K, Wu D, Li G, Yang S, Han X, Xie Y, Huang Y, Yu X, Wu J, Zou L. Effects of environmental disinfection on microbial population and resistance genes: A case study of the microecology within a panda enclosure. ENVIRONMENTAL RESEARCH 2023; 235:116662. [PMID: 37453509 DOI: 10.1016/j.envres.2023.116662] [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: 05/16/2023] [Revised: 07/02/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Widespread use of disinfectants raises concerns over their involvement in altering microbial communities and promoting antimicrobial resistance. This study explores the influence of disinfection protocols on microbial populations and resistance genes within an isolated enclosure environment and in the gut of giant pandas (GPs) held within. Samples of panda feces, air conditioning ducts, soil and bamboo were collected before and after disinfection. High-throughput sequencing characterized the microbial flora of GP gut and environmental microbes inside the artificial habitat. Microbial cultures showed that Escherichia coli (34.6%), Enterococcus (15.4%) and other pathogenic bacteria deposited in feces and the enclosure. Isolates exhibit a consistent resistance to disinfectant, with the greatest resistance shown to cyanuric acid, and the lowest to glutaraldehyde-dodecyl dimethyl ammonium bromide (GD-DDAB) and dodecyl dimethyl ammonium bromide (DDAB). The total number of the culturable bacteria in soil and bamboo were significantly diminished after disinfection but increased in the gut. After disinfection, the richness (Chao1 index) of environment samples increased significantly (P < 0.05), while the richness in gut decreased significantly (P < 0.05). Ten genera showed significant change in feces after disinfection. Metagenome sequencing showed that 126 types of virulence genes were present in feces before disinfection and 37 in soil. After disinfection, 110 virulence genes localized in feces and 53 in soil. Eleven virulence genes including ECP and T2SS increased in feces. A total of 182 antibiotic resistance genes (ARGs) subtypes, potentially conferring resistance to 20 classes of drugs, were detected in the soils and feces, with most belonging to efflux pump protein pathways. After disinfection, the number of resistance genes increased both in gut and soil, which suggests disinfection protocols increase the number of resistance pathways. Our study shows that the use of disinfectants helps to shape the microbial community of GPs and their habitat, and increases populations of resistant strain bacteria.
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Affiliation(s)
- Min Yan
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park, Shanghai, 201399, China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Yongqi Feng
- Shanghai Wild Animal Park, Shanghai, 201399, China
| | - Juntang Duan
- Shanghai Wild Animal Park, Shanghai, 201399, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Daifu Wu
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Guo Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Shengzhi Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Xinfeng Han
- College of Veterinary Science, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yue Xie
- College of Veterinary Science, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Xiumei Yu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jiawei Wu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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5
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Zheng K, Liu Z, Liu C, Liu J, Zhuang J. Enhancing remediation potential of heavy metal contaminated soils through synergistic application of microbial inoculants and legumes. Front Microbiol 2023; 14:1272591. [PMID: 37840744 PMCID: PMC10571051 DOI: 10.3389/fmicb.2023.1272591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/07/2023] [Indexed: 10/17/2023] Open
Abstract
Soil microorganisms play a crucial role in remediating contaminated soils in modern ecosystems. However, the potential of combining microorganisms with legumes to enhance the remediation of heavy metal-contaminated soils remains unexplored. To investigate this, we isolated and purified a highly efficient cadmium and lead-tolerant strain. Through soil-cultivated pot experiments with two leguminous plants (Robinia pseudoacacia L. and Sophora xanthantha), we studied the effects of applying this microbial agent on plant nutrient uptake of soil nutrients, heavy metal accumulation, and the dynamics of heavy metal content. Additionally, we examined the response characteristics of inter-root microbial and bacterial communities. The results demonstrated that microorganisms screened from heavy metal-contaminated soil environments exhibited strong survival and adaptability in heavy metal solutions. The use of the Serratia marcescens WZ14 strain-phytoremediation significantly increased the soil's ammonium nitrogen (AN) and organic carbon (OC) contents compared to monoculture. In addition, the lead (Pb) and cadmium (Cd) contents of the soil significantly decreased after combined remediation than those of the soil before potting. However, the remediation effects on Pb- and Cd-contaminated soils differed between the two legumes following the Serratia marcescens WZ14 inoculation. The combined restoration altered the composition of the plant inter-rhizosphere bacterial community, with the increase in the relative abundance of both Proteobacteria and Firmicutes. Overall, the combined remediation using the tolerant strain WZ14 with legumes proved advantageous. It effectively reduced the heavy metal content of the soil, minimized the risk of heavy metal migration, and enhanced heavy metal uptake, accumulation, and translocation in the legumes of S. xanthantha and R. pseudoacacia. Additionally, it improved the adaptability and resistance of both legumes, leading to an overall improvement in the soil's environmental quality. These studies can offer primary data and technical support for remediating and treating Cd and Pb in soils, as well as rehabilitating mining sites.
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Affiliation(s)
| | | | | | | | - Jiayao Zhuang
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing, China
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Liu Y, Zhong X, Luo Z, Meng X, Li R, Zhong W, Yang L, Wang H, Wei D. The identification of a robust leucine dehydrogenase from a directed soil metagenome for efficient synthesis of L-2-aminobutyric acid. Biotechnol J 2023; 18:e2200590. [PMID: 37149736 DOI: 10.1002/biot.202200590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/29/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
L-2-aminobutyric acid (L-2-ABA) is a chiral precursor for the synthesis of anti-epileptic drug levetiracetam and anti-tuberculosis drug ethambutol. Asymmetric synthesis of L-2-ABA by leucine dehydrogenases has been widely developed. However, the limitations of natural enzymes, such as poor stability, low catalytic efficiency, and inhibition of high-concentration substrates, limit large-scale applications. Herein, by directed screening of a metagenomic library from unnatural amino acid-enriched environments, a robust leucine dehydrogenase, TvLeuDH, was identified, which exhibited high substrate tolerance and excellent enzymatic activity towards 2-oxobutyric acid. In addition, TvLeuDH has strong affinity for NADH. Subsequently, a three-enzyme co-expression system containing L-threonine deaminase, TvLeuDH, and glucose dehydrogenase was established. By optimizing reaction conditions, 1.5 M L-threonine could be converted to L-2-ABA with a 99% molar conversion rate and a space-time yield of 51.5 g·L-1 ·h-1 . In this process, no external coenzyme was added. The robustness of TvLeuDH allowed the reaction to be performed without the addition of extra salt as the buffer, demonstrating the simplest reaction system currently reported. These unique properties for the efficient and environmentally friendly production of chiral amino acids make TvLeuDH a particularly promising candidate for industrial applications, which reveals the great potential of directed metagenomics for industrial biotechnology.
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Affiliation(s)
- Yan Liu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xuezhao Zhong
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Zi Luo
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xiangqi Meng
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Rui Li
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Wa Zhong
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Lin Yang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
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Zhu F, Yan Y, Xue XM, Yu RL, Ye J. Identification and characterization of a phosphinothricin N-acetyltransferase from Enterobacter LSJC7. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 193:105464. [PMID: 37247996 DOI: 10.1016/j.pestbp.2023.105464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 05/31/2023]
Abstract
Phosphinothricin (PPT) is a widely used and non-selective herbicide. PPT-resistance genes, especially PPT N-acetyltransferase genes, have been used in the development of transgenic PPT-resistant crops. However, there are only a limited number of available PPT-resistance genes for use in plant biotechnology. In this study, we found that Enterobacter LSJC7 is highly resistant to PPT and can acetylate PPT to N-acetyl phosphinothricin (Ac-PPT). Furthermore, a novel PPT N-acetyltransferase gene, named LsarsN, was identified from LSJC7. When LsarsN was expressed in E. coli AW3110, it confered resistance to PPT. Ac-PPT was detected in both the culture medium and cells of AW3110 expressing the LsarsN-pET22b plasmid. The purified LsArsN protein also showed strong N-acetylation ability in vitro, and its enzymatic kinetic curve was fitted with the Michaelis-Mentan equation. Compared with wild-type LsArsN, both R72A and R74A mutants showed significantly lower PPT N-acetylation ability. In summary, our results systematically characterized LsArsN with strong ability for PPT N-acetylation, which lays the groundwork for future research into the use of this novel gene, LsarsN, to create PPT-resistant crops.
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Affiliation(s)
- Feng Zhu
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yu Yan
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Xi-Mei Xue
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Rui-Lian Yu
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China.
| | - Jun Ye
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China.
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Zhang H, Liu X, Wang Y, Duan L, Liu X, Zhang X, Dong L. Deep relationships between bacterial community and polycyclic aromatic hydrocarbons in soil profiles near typical coking plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:64486-64498. [PMID: 37071357 DOI: 10.1007/s11356-023-26903-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/05/2023] [Indexed: 05/11/2023]
Abstract
Bacterial communities play an important role in maintaining the normal functioning of ecosystems; therefore, it is important to understand the effects of polycyclic aromatic hydrocarbons (PAHs) on the bacterial community. In addition, understanding the metabolic potential of bacterial communities for PAHs is important for the remediation of PAH-contaminated soils. However, the deep relationship between PAHs and bacterial community in coking plants is not clear. In this study, we determined the bacterial community and the concentration of PAHs in three soil profiles contaminated by coke plants in Xiaoyi Coking Park, Shanxi, China, using 16S rRNA and gas chromatography coupled with mass spectrometry, respectively. The results show that 2 ~ 3 rings PAHs are the main PAHs and Acidobacteria (23.76%) was the dominant bacterial community in three soil profiles. Statistical analysis showed that there were significant differences in the composition of bacterial communities at different depths and different sites. Redundancy analysis (RDA) and variance partitioning analysis (VPA) illustrate the influence of environmental factors (including PAHs, soil organic matter (SOM), and pH) on the vertical distribution of soil bacterial community, and PAHs were the main factors affecting the bacterial community in this study. The co-occurrence networks further indicated correlations between bacterial community and PAHs and found that Nap has the greatest effect on bacterial community compared with other PAHs. In addition, some operational taxonomic units (OTUs, OTU2, and OTU37) have the potential to degrade PAHs. PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used for further study on the potential of microbial PAHs degradation from a genetic perspective, which showed that different PAH metabolism genes were present in the genomes of bacterial communities in the three soil profiles, and a total of 12 PAH degradation-related genes were isolated, mainly dioxygenase and dehydrogenase genes.
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Affiliation(s)
- Handan Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
- Research and Development Center for Watershed Environmental Eco-Engineering (Zhuhai), Beijing Normal University, Zhuhai, 519087, People's Republic of China
| | - Xinhui Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China.
- Research and Development Center for Watershed Environmental Eco-Engineering (Zhuhai), Beijing Normal University, Zhuhai, 519087, People's Republic of China.
| | - Yujing Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Linshuai Duan
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xiqin Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xin Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
- Research and Development Center for Watershed Environmental Eco-Engineering (Zhuhai), Beijing Normal University, Zhuhai, 519087, People's Republic of China
| | - Lu Dong
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
- Research and Development Center for Watershed Environmental Eco-Engineering (Zhuhai), Beijing Normal University, Zhuhai, 519087, People's Republic of China
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9
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Li J, Yu S, Liu Q, Wang D, Yang L, Wang J, Zuo R. Screening of hazardous groundwater pollutants responsible for microbial ecological consequences by integrated nontargeted analysis and high-throughput sequencing technologies. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130516. [PMID: 36463738 DOI: 10.1016/j.jhazmat.2022.130516] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/08/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Organic contaminants, especially hydrophobic organic contaminants (HOCs), pose potential ecological threats even at environmental concentrations. Characterization of HOC profiles and identification of key environmental stressors are vital but still challenging in groundwater quality management. In this study, a strategy for identifying the key environmental stressors among HOCs in groundwater based on integrated chemical monitoring technologies and microbial ecology analysis methods was proposed and applied to typical groundwater samples. Specifically, the characteristics of HOCs were systematically analyzed based on nontargeted and targeted approaches, and microbial community assembly and specific biomarker analysis were combined to determine the major ecological processes and key environmental stressors. The results showed that a total of 234 HOCs were detected in groundwater collected from Tongzhou, Beijing; among them, phthalate esters (PAEs) were screened out as key environmental stressors, considering that they made relatively higher microbial ecology contributions. Furthermore, their influences on the structure and function of the groundwater microbial community were evaluated by adopting high-throughput sequencing and bioinformatics analysis technologies. These findings confirmed PAEs as vital determinants driving microbial assembly, shifting community structure, and regulating community function in groundwater; in addition, the findings validated the feasibility and suitability of the proposed strategy.
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Affiliation(s)
- Jian Li
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China.
| | - Shihang Yu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Quanzhen Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Donghong Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Lei Yang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Jinsheng Wang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Rui Zuo
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
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10
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Zhao Y, Zhang L, Tang X, Ren S, Zhang Y. Anthropogenic disturbance promotes the diversification of antibiotic resistance genes and virulence factors in the gut of plateau pikas (Ochotona curzoniae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1027941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The prevalence and transmission of antibiotic resistance genes (ARGs) and virulence factors (VFs) pose a great threat to public health. The importance of pollution in determining the occurrence of ARGs and VFs in wildlife is poorly understood. Using a metagenomic approach, this study investigates the composition and functional pathways of bacteria, ARGs, and VFs in the gut microbiome of Plateau pikas in regions of medical pollution (MPR), heavy tourist traffic (HTR), and no contamination (NCR). We found that the abundance of probiotic genera (Clostridium, Eubacterium, Faecalibacterium, and Roseburia) were significantly lower in the HTR. The metabolic pathways of replication and repair in the endocrine and nervous systems were significantly enriched in the MPR, whereas endocrine and metabolic diseases were significantly enriched in the NCR. The Shannon and Gini–Simpson α-diversity indices of ARGs were highest in the HTR, and there were significant differences in β-diversity among the three regions. The resistance of ARGs to glycopeptide antibiotics increased significantly in the MPR, whereas the ARGs for aminocoumarins increased significantly in the HTR. The diversity of mobile genetic elements (MGEs) was significantly higher in the MPR than in other regions. We observed a strong positive correlation between ARGs and pathogenic bacteria, and the network structure was the most complex in the MPR. There were significant differences in the β-diversity of VFs among the three regions. Medical pollution led to significant enrichment of fibronectin-binding protein and PhoP, whereas tourism-related pollution (in the HTR) led to significant enrichment of LPS and LplA1. Our study indicates that environmental pollution can affect the structure and function of gut microbes and disseminate ARGs and VFs via horizontal transmission, thereby posing a threat to the health of wild animals.
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Su H, Wu C, Han P, Liu Z, Liang M, Zhang Z, Wang Z, Guo G, He X, Pang J, Wang C, Weng S, He J. The microbiome and its association with antibiotic resistance genes in the hadal biosphere at the Yap Trench. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129543. [PMID: 35870206 DOI: 10.1016/j.jhazmat.2022.129543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The hadal biosphere, the deepest part of the ocean, is known as the least-explored aquatic environment and hosts taxonomically diverse microbial communities. However, the microbiome and its association with antibiotic resistance genes (ARGs) in the hadal ecosystem remain unknown. Here, we profiled the microbiome diversity and ARG occurrence in seawater and sediments of the Yap Trench (YT) using metagenomic sequencing. Within the prokaryote (bacteria and archaea) lineages, the main components of bacteria were Gammaproteobacteria (77.76 %), Firmicutes (8.36 %), and Alphaproteobacteria (2.25 %), whereas the major components of archaea were Nitrososphaeria (6.51 %), Nanoarchaeia (0.42 %), and Thermoplasmata (0.25 %), respectively. Taxonomy of viral contigs showed that the classified viral communities in YT seawater and sediments were dominated by Podoviridae (45.96 %), Siphoviridae (29.41 %), and Myoviridae (24.63 %). A large majority of viral contigs remained uncharacterized and exhibited endemicity. A total of 48 ARGs encoding resistance to 12 antibiotic classes were identified and their hosts were bacteria and viruses. Novel ARG subtypes mexFYTV-1, mexFYTV-2, mexFYTV-3, vanRYTV-1, vanSYTV-1 (carried by unclassified viruses), and bacAYTB-1 (carried by phylum Firmicutes) were detected in seawater samples. Overall, our findings imply that the hadal environment of the YT is a repository of viral and ARG diversity.
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Affiliation(s)
- Hualong Su
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Chengcheng Wu
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Peiyun Han
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zixuan Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Mincong Liang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Zheng Zhang
- Baidu International Technology (Shenzhen), Shenzhen 518062, China
| | - Zhike Wang
- Hainan Guodun Information Development, Haikou 570206, China
| | - Guangyu Guo
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Xinyi He
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianhu Pang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Cheng Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Shaoping Weng
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianguo He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China; State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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12
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Sharma P, Singh SP. Identification and profiling of microbial community from industrial sludge. Arch Microbiol 2022; 204:234. [PMID: 35362813 DOI: 10.1007/s00203-022-02831-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/05/2022] [Accepted: 03/06/2022] [Indexed: 02/03/2023]
Abstract
The purpose of this study is to identify microbial communities in pulp and paper industry sludge and their metagenomic profiling on the basis of; phylum, class, order, family, genus and species level. Results revealed that the dominant phyla in 16S rRNA Illumina Miseq analysis inside sludge were Anaerolinea, Pseudomonas, Clostridia, Bacteriodia, Gammaproteobacteria, Spirochetia, Deltaproteobacteria, Spirochaetaceae, Prolixibacteraceae and some unknown microbial strains are also dominant. Metagenomics is a molecular biology-based technology that uses bioinformatics to evaluate huge gene sequences extracted from environmental samples to assess the composition and function of microbiota. The results of metabarcoding of the V3-V4 16S rRNA regions acquired from paired-end Illumina MiSeq sequencing were used to analyze bacterial communities and structure. The present work demonstrates the potential approach to sludge treatment in the open environment via the naturally adapted microorganism, which could be an essential addition to the disposal site. In summary, these investigations indicate that the indigenous microbial community is an acceptable bioresource for remediation or detoxification following secondary treatment. This research aims at understanding the structure of microbial communities and their diversity (%) in highly contaminated sludge to perform in situ bioremediation.
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Affiliation(s)
- Pooja Sharma
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar (A Central) University, Lucknow, 226 025, Uttar Pradesh, India.
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University, Kanpur, 208 001, India.
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Liu J, Liu Y, Dong W, Li J, Yu S, Wang J, Zuo R. Shifts in microbial community structure and function in polycyclic aromatic hydrocarbon contaminated soils at petrochemical landfill sites revealed by metagenomics. CHEMOSPHERE 2022; 293:133509. [PMID: 34995620 DOI: 10.1016/j.chemosphere.2021.133509] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/26/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Investigations of the microbial community structures, potential functions and polycyclic aromatic hydrocarbon (PAH) degradation-related genes in PAH-polluted soils are useful for risk assessments, microbial monitoring, and the potential bioremediation of soils polluted by PAHs. In this study, five soil sampling sites were selected at a petrochemical landfill in Beijing, China, to analyze the contamination characteristics of PAHs and their impact on microorganisms. The concentrations of 16 PAHs were detected by gas chromatography-mass spectrometry. The total concentrations of the PAHs ranged from ND to 3166.52 μg/kg, while phenanthrene, pyrene, fluoranthene and benzo [ghi]perylene were the main components in the soil samples. According to the specific PAH ratios, the PAHs mostly originated from petrochemical wastes in the landfill. The levels of the total toxic benzo [a]pyrene equivalent (1.63-107.73 μg/kg) suggested that PAHs might result in adverse effects on soil ecosystems. The metagenomic analysis showed that the most abundant phyla in the soils were Proteobacteria and Actinobacteria, and Solirubrobacter was the most important genus. At the genus level, Bradyrhizobium, Mycobacterium and Anaeromyxobacter significantly increased under PAH stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, the most abundant category of functions that are involved in adapting to contaminant pressures was identified. Ten PAH degradation-related genes were significantly influenced by PAH pressure and showed correlations with PAH concentrations. All of the results suggested that the PAHs from the petrochemical landfill could be harmful to soil environments and impact the soil microbial community structures, while microorganisms would change their physiological functions to resist pollutant stress.
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Affiliation(s)
- Jiayou Liu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yun Liu
- South China Institute of Environmental Sciences, Ministry of Environmental Protection of the People's Republic of China, State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, Guangzhou, 510655, China
| | - Weihong Dong
- Key Laboratory of Groundwater Resources and Environments, Ministry of Education, Jilin University, Changchun, Jilin, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, Jilin, 130021, China
| | - Jian Li
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Shihang Yu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jinsheng Wang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Rui Zuo
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
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Liu J, Song M, Wei X, Zhang H, Bai Z, Zhuang X. Responses of Phyllosphere Microbiome to Ozone Stress: Abundance, Community Compositions and Functions. Microorganisms 2022; 10:microorganisms10040680. [PMID: 35456732 PMCID: PMC9024792 DOI: 10.3390/microorganisms10040680] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Ozone is a typical hazardous pollutant in Earth’s lower atmosphere, but the phyllosphere and its microbiome are promising for air pollution remediation. Despite research to explore the efficiency and mechanism of ozone phylloremediation, the response and role of the phyllosphere microbiome remains untouched. In this study, we exposed Euonymus japonicus to different ozone levels and revealed microbial successions and roles of the phyllosphere microbiome during the exposure. The low-level exposure (156 ± 20 ppb) induced limited response compared to other environmental factors. Fungi failed to sustain the community richness and diversity, despite the stable ITS concentration, while bacteria witnessed an abundance loss. We subsequently elevated the exposure level to 5000~10,000 ppb, which considerably deteriorated the bacterial and fungal diversity. Our results identified extremely tolerant species, including bacterial genera (Curtobacterium, Marmoricola, and Microbacterium) and fungal genera (Cladosporium and Alternaria). Compositional differences suggested that most core fungal taxa were related to plant diseases and biocontrol, and ozone exposure might intensify such antagonism, thus possibly influencing plant health and ozone remediation. This assumption was further evidenced in the functional predictions via a pathogen predominance. This study shed light on microbial responses to ozone exposure in the phyllosphere and enlightened the augmentation of ozone phylloremediation through the microbial role.
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Affiliation(s)
- Jiayu Liu
- Beijing Key Laboratory of Water Resources and Environment Engineering, School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China; (J.L.); (H.Z.)
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (M.S.); (X.W.)
| | - Manjiao Song
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (M.S.); (X.W.)
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyuan Wei
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (M.S.); (X.W.)
| | - Huanzhen Zhang
- Beijing Key Laboratory of Water Resources and Environment Engineering, School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China; (J.L.); (H.Z.)
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (M.S.); (X.W.)
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- Xiongan Institute of Innovation, Xiongan New Area 071000, China
- Correspondence: (Z.B.); (X.Z.); Tel.: +86-10-6284-9156 (Z.B.); +86-10-6284-9193 (X.Z.)
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (M.S.); (X.W.)
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (Z.B.); (X.Z.); Tel.: +86-10-6284-9156 (Z.B.); +86-10-6284-9193 (X.Z.)
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15
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Chen ZJ, Liu J, Zhang N, Yang H. Identification, characterization and expression of rice (Oryza sativa) acetyltransferase genes exposed to realistic environmental contamination of mesotrione and fomesafen. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 233:113349. [PMID: 35219957 DOI: 10.1016/j.ecoenv.2022.113349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
The plant acetyltransferases (ACEs) belong to a super family of proteins that contribute to secondary metabolisms and involve various abiotic and biotic stress responses. However, how rice ACEs respond to toxic agrochemicals is largely unknown. This study demonstrates that 86 and 83 genes coding ACEs in the transcriptome profiling were expressed under mesotrione (MTR) and fomesafen (FSA) exposure, respectively. Of these, 18 and 8 ACE differentially expressed genes (DEGs) were identified in MTR- and FSA-exposed rice transcriptome datasets. Some of the ACE genes were validated by quantitative RT-PCR analysis. Analysis of biochemical properties of ACEs revealed that many genes have various cis-elements and structural domain which may cope with a variety of biotic and abiotic stress responses and detoxification of xenobiotics. Moreover, the ACE activities in rice were induced under MTR and FSA exposure and reached out to the highest value at the 0.1 mg L-1. The ACE activities in the MTR and FSA treated roots were 2.6 and 3.5 fold over the control and those in shoots with MTR and FSA were 4.0 and 26.1 fold over the control, respectively. These results indicate that the ACE-coding genes can respond to the MTR and FSA stress by increasing their transcriptional level, along with the enhanced specific ACE protein activities in rice tissues.
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Affiliation(s)
- Zhao Jie Chen
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Jintong Liu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Nan Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Yang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China.
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16
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Chen ZJ, Qiao YX, Zhang N, Liu J, Yang H. Insight into metabolism pathways of pesticide fomesafen in rice: Reducing cropping and environmental risks. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 283:117128. [PMID: 33862343 DOI: 10.1016/j.envpol.2021.117128] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/20/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Fomesafen (FSA) is widely used in soybean fields for weed control. However, the persisting characteristics of FSA in the agricultural soil or water may become a hidden danger causing environmental pollution and phytotoxicity to succession crops. In this study, the growth and physiological responses of rice to FSA were investigated. It was found that the growth of rice seedlings was obviously inhibited by FSA exposure especially at over 0.1 mg L-1. To gain an insight into the molecular mechanisms for the potential ecotoxicology, four libraries of rice roots and shoots exposed to FSA were created and subjected to the global RNA-sequencing (RNA-Seq) combined with HRLC-Q-TOF-MS/MS analytical technologies to comprehensively characterize the biochemical processes and catalytic reactions involved in FSA metabolism in rice. Compared with those without FSA, 499 and 450 up-regulated genes in roots and shoots with FSA were detected. Many of them were closely correlated with the tolerance to environmental stress, detoxification of xenobiotics and molecular metabolism process including cytochrome P450, glutathione S-transferases and acetyltransferase. A total of eight metabolites and fourteen conjugates in the reactive pathways of hydrolysis, substitution, reduction, methylation, glycosylation, acetylation, and malonylation were characterized by HRLC-Q-TOF-MS/MS. The relationship between the metabolized derivatives of FSA and enhanced expression the corresponding enzymatic regulators was established. This study will help understand the mechanisms and pathways of FSA metabolism and inspire the further research on FSA degradation in the paddy crops and environmental or health risks.
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Affiliation(s)
- Zhao Jie Chen
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing, 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Xin Qiao
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing, 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jintong Liu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing, 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong Yang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing, 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China.
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17
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Liu X, Guo W, Cui S, Tang X, Zhao J, Zhang H, Mao B, Chen W. A Comprehensive Assessment of the Safety of Blautia producta DSM 2950. Microorganisms 2021; 9:microorganisms9050908. [PMID: 33922843 PMCID: PMC8146736 DOI: 10.3390/microorganisms9050908] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/17/2021] [Accepted: 04/18/2021] [Indexed: 12/19/2022] Open
Abstract
In recent years, Blautia has attracted attention for its role in ameliorating host diseases. In particular, Blautia producta DSM 2950 has been considered a potential probiotic due to its ability to mitigate inflammation in poly(I:C) induced HT-29 cells. Thus, to promote the development of indigenous intestinal microorganisms with potential probiotic function, we conducted a comprehensive experimental analysis of DSM 2950 to determine its safety. This comprised a study of its potential virulence genes, antibiotic resistance genes, genomic islands, antibiotic resistance, and hemolytic activity and a 14-day test of its acute oral toxicity in mice. The results indicated no toxin-related virulence genes in the DSM 2950 genome. Most of the genomic islands in DSM 2950 were related to metabolism, rather than virulence expression. DSM 2950 was sensitive to most of the tested antibiotics but was tolerant of treatment with kanamycin, neomycin, clindamycin, or ciprofloxacin, probably because it possessed the corresponding antibiotic resistance genes. Oral acute toxicity tests indicated that the consumption of DSM 2950 does not cause toxic side effects in mice. Overall, the safety profile of DSM 2950 confirmed that it could be a candidate probiotic for use in food and pharmaceutical preparations.
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Affiliation(s)
- Xuemei Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Weiling Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shumao Cui
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Correspondence: (S.C.); (B.M.); Tel.: +86-510-8591-2155 (B.M.)
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Bingyong Mao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Correspondence: (S.C.); (B.M.); Tel.: +86-510-8591-2155 (B.M.)
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (X.L.); (W.G.); (X.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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18
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Commichaux S, Shah N, Ghurye J, Stoppel A, Goodheart JA, Luque GG, Cummings MP, Pop M. A critical assessment of gene catalogs for metagenomic analysis. Bioinformatics 2021; 37:2848-2857. [PMID: 33792639 PMCID: PMC8479683 DOI: 10.1093/bioinformatics/btab216] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/02/2021] [Accepted: 03/31/2021] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although gene catalogs are commonly used, they have not been critically evaluated for their effectiveness as a basis for metagenomic analyses. RESULTS As a case study, we investigate one such catalog, the Integrated Gene Catalog (IGC), however, our observations apply broadly to most gene catalogs constructed to date. We focus on both the approach used to construct this catalog and on its effectiveness when used as a reference for microbiome studies. Our results highlight important limitations of the approach used to construct the IGC and call into question the broad usefulness of gene catalogs more generally. We also recommend best practices for the construction and use of gene catalogs in microbiome studies and highlight opportunities for future research. AVAILABILITY AND IMPLEMENTATION All supporting scripts for our analyses can be found on GitHub: https://github.com/SethCommichaux/IGC.git. The supporting data can be downloaded from: https://obj.umiacs.umd.edu/igc-analysis/IGC_analysis_data.tar.gz. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Seth Commichaux
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA,Biological Science Graduate Program, University of Maryland, College Park, MD, 20742, USA,Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, 20708, USA
| | - Nidhi Shah
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA,Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Jay Ghurye
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA,Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Alexander Stoppel
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Jessica A Goodheart
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Guillermo G Luque
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Michael P Cummings
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA,Department of Computer Science, University of Maryland, College Park, MD, 20742, USA,To whom correspondence should be addressed.
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Li J, Xu Y, Song Q, Yang J, Xie L, Yu S, Zheng L. Polycyclic aromatic hydrocarbon and n-alkane pollution characteristics and structural and functional perturbations to the microbial community: a case-study of historically petroleum-contaminated soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:10589-10602. [PMID: 33098556 DOI: 10.1007/s11356-020-11301-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/18/2020] [Indexed: 05/25/2023]
Abstract
Characterization of the typical petroleum pollutants, polycyclic aromatic hydrocarbons (PAHs) and n-alkanes, and indigenous microbial community structure and function in historically contaminated soil at petrol stations is critical. Five soil samples were collected from a petrol station in Beijing, China. The concentrations of 16 PAHs and 31 n-alkanes were measured by gas chromatography-mass spectrometry. The total concentrations of PAHs and n-alkanes ranged from 973 ± 55 to 2667 ± 183 μg/kg and 6.40 ± 0.38 to 8.65 ± 0.59 mg/kg (dry weight), respectively, which increased with depth. According to the observed molecular indices, PAHs and n-alkanes originated mostly from petroleum-related sources. The levels of ΣPAHs and the total toxic benzo[a]pyrene equivalent (ranging from 6.41 to 72.54 μg/kg) might exert adverse biological effects. Shotgun metagenomic sequencing was employed to investigate the indigenous microbial community structure and function. The results revealed that Proteobacteria and Actinobacteria were the most abundant phyla, and Nocardioides and Microbacterium were the important genera. Based on COG and KEGG annotations, the highly abundant functional classes were identified, and these functions were involved in allowing microorganisms to adapt to the pressure from contaminants. Five petroleum hydrocarbon degradation-related genes were annotated, revealing the distribution of degrading microorganisms. This work facilitates the understanding of the composition, source, and potential ecological impacts of residual PAHs and n-alkanes in historically contaminated soil.
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Affiliation(s)
- Jian Li
- State Key Laboratory of Petroleum Pollution Control, Beijing, 102206, China
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Ying Xu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Quanwei Song
- State Key Laboratory of Petroleum Pollution Control, Beijing, 102206, China
| | - Jie Yang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lin Xie
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Shihang Yu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lei Zheng
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China.
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Kumar Awasthi M, Ravindran B, Sarsaiya S, Chen H, Wainaina S, Singh E, Liu T, Kumar S, Pandey A, Singh L, Zhang Z. Metagenomics for taxonomy profiling: tools and approaches. Bioengineered 2020; 11:356-374. [PMID: 32149573 PMCID: PMC7161568 DOI: 10.1080/21655979.2020.1736238] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/25/2022] Open
Abstract
The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.
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Affiliation(s)
- Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - B. Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University Youngtong-Gu, Suwon, South Korea
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hongyu Chen
- Institute of Biology, Freie Universität Berlin Altensteinstr, Berlin, Germany
| | - Steven Wainaina
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - Ekta Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Sunil Kumar
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Lal Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
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