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Pan Y, Sun RZ, Wang Y, Chen GL, Fu YY, Yu HQ. Carbon source shaped microbial ecology, metabolism and performance in denitrification systems. WATER RESEARCH 2023; 243:120330. [PMID: 37482010 DOI: 10.1016/j.watres.2023.120330] [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: 06/04/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/25/2023]
Abstract
The limited information on microbial interactions and metabolic patterns in denitrification systems, especially those fed with different carbon sources, has hindered the establishment of ecological linkages between microscale connections and macroscopic reactor performance. In this work, denitrification performance, metabolic patterns, and ecological structure were investigated in parallel well-controlled bioreactors with four representative carbon sources, i.e., methanol, glycerol, acetate, and glucose. After long-term acclimation, significant differences were observed among the four bioreactors in terms of denitrification rates, organic utilization, and heterotrophic bacterial yields. Different carbon sources induced the succession of denitrifying microbiota toward different ecological structures and exhibited distinct metabolic patterns. Methanol-fed reactors showed distinctive microbial carbon utilization pathways and a more intricate microbial interaction network, leading to significant variations in organic utilization and metabolite production compared to other carbon sources. Three keystone taxa belonging to the Verrucomicrobiota phylum, SJA-15 order and the Kineosphaera genus appeared as network hubs in the methanol, glycerol, and acetate-fed systems, playing essential roles in their ecological functions. Several highly connected species were also identified within the glucose-fed system. The close relationship between microbial metabolites, ecological structures, and system performances suggests that this complex network relationship may greatly contribute to the efficient operation of bioreactors.
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Affiliation(s)
- Yuan Pan
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China; Anhui Province Key Laboratory of Industrial Wastewater and Environmental Treatment, Hefei 230026, China
| | - Rui-Zhe Sun
- School of Resources & Environmental Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yan Wang
- Anhui Province Key Laboratory of Industrial Wastewater and Environmental Treatment, Hefei 230026, China
| | - Guan-Lin Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Ying-Ying Fu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
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2
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Wang Z, Yang L, Zhou F, Li J, Wu X, Zhong X, Lv H, Yi S, Gao Q, Yang Z, Zhao P, Wu Y, Wu C, Zhang L, Wang H, Zhang L. Integrated comparative transcriptome and weighted gene co-expression network analysis provide valuable insights into the response mechanisms of crayfish (Procambarus clarkii) to copper stress. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130820. [PMID: 36860031 DOI: 10.1016/j.jhazmat.2023.130820] [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: 10/09/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
One of the significant limitations of aquaculture worldwide is the prevalence of divalent copper (Cu). Crayfish (Procambarus clarkii) are economically important freshwater species adapted to a variety of environmental stimuli, including heavy metal stresses; however, large-scale transcriptomic data of the hepatopancreas of crayfish in response to Cu stress are still scarce. Here, integrated comparative transcriptome and weighted gene co-expression network analyses were initially applied to investigate gene expression profiles of the hepatopancreas of crayfish subjected to Cu stress for different periods. As a result, 4662 significant differentially expressed genes (DEGs) were identified following Cu stress. Bioinformatics analyses revealed that the "focal adhesion" pathway was one of the most significantly upregulated response pathways following Cu stress, and seven DEGs mapped to this pathway were identified as hub genes. Furthermore, the seven hub genes were examined by quantitative PCR, and each was found to have a substantial increase in transcript abundance, suggesting a critical role of the "focal adhesion" pathway in the response of crayfish to Cu stress. Our transcriptomic data can be a good resource for the functional transcriptomics of crayfish, and these results may provide valuable insights into the molecular response mechanisms underlying crayfish to Cu stress.
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Affiliation(s)
- Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China.
| | - Lianlian Yang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Fan Zhou
- Zhejiang Fisheries Technical Extension Center, Hangzhou 310023, China
| | - Jiapeng Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xiaoyin Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xueting Zhong
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - He Lv
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Shaokui Yi
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Quanxin Gao
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Zi Yang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Pengfei Zhao
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Yi Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Choufei Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Liqin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Hua Wang
- Huzhou Key Laboratory of Medical and Environmental Application Technologies, College of Life Sciences, Huzhou University, Huzhou 313000, China.
| | - Lixia Zhang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang 453007, China.
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Qin G, Ai X, Xu J, Yang Y. Dual RNA-seq of spleens extracted from channel catfish infected with Aeromonas veronii reveals novel insights into host-pathogen interactions. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 252:114609. [PMID: 36739739 DOI: 10.1016/j.ecoenv.2023.114609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Interactions between host and pathogen are involving various dynamic changes in transcript expression and critical for understanding host immunity against infections and its associated pathogenesis. Herein, we established a model of channel catfish infected with Aeromonas veronii. The infected fish had prominent body surface bleeding, and the spleen showed hyperemia and swelling. Then, the spleen of channel catfish infected with A. veronii was analyzed by dual RNA sequencing (RNA-seq), and the transcriptome data were compared with uninfected channel catfish spleen or bacteria cultured in vitro. The transcript expression profile of pathogen-host interaction between A. veronii and channel catfish was successfully studied. During infection, the host was enriched for multiple immune-related signaling pathways, such as the Toll-like receptor signaling pathway, Cytokine-cytokine receptor interaction, and T cell receptor signaling pathway; and significantly upregulated for many innate immune-related genes, including IL-8. At the same time, we found that A. veronii mainly harmed the host spleen through hemolysin. Our current findings are of great significance in clarifying the pathogenesis of channel catfish induced by A. veronii and provide gene targets for developing preventive measures.
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Affiliation(s)
- Gaixiao Qin
- College of Animal Science and Technology, Henan university of animal husbandry and Economy, Zhengzhou 450046, China
| | - Xiaohui Ai
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Jin Xu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Yibin Yang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
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Scott-Fordsmand JJ, Amorim MJB. Using Machine Learning to make nanomaterials sustainable. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160303. [PMID: 36410486 DOI: 10.1016/j.scitotenv.2022.160303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/06/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Sustainable development is a key challenge for contemporary human societies; failure to achieve sustainability could threaten human survival. In this review article, we illustrate how Machine Learning (ML) could support more sustainable development, covering the basics of data gathering through each step of the Environmental Risk Assessment (ERA). The literature provides several examples showing how ML can be employed in most steps of a typical ERA.A key observation is that there are currently no clear guidance for using such autonomous technologies in ERAs or which standards/checks are required. Steering thus seems to be the most important task for supporting the use of ML in the ERA of nano- and smart-materials. Resources should be devoted to developing a strategy for implementing ML in ERA with a strong emphasis on data foundations, methodologies, and the related sensitivities/uncertainties. We should recognise historical errors and biases (e.g., in data) to avoid embedding them during ML programming.
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Affiliation(s)
| | - Mónica J B Amorim
- Department of Biology & CESAM, University of Aveiro, 3810-193 Aveiro, Portugal.
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González-Morelo KJ, Galán-Vásquez E, Melis F, Pérez-Rueda E, Garrido D. Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharides. Front Mol Biosci 2023; 10:1040721. [PMID: 36776740 PMCID: PMC9908966 DOI: 10.3389/fmolb.2023.1040721] [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: 09/09/2022] [Accepted: 01/12/2023] [Indexed: 01/27/2023] Open
Abstract
Biological systems respond to environmental perturbations and a large diversity of compounds through gene interactions, and these genetic factors comprise complex networks. Experimental information from transcriptomic studies has allowed the identification of gene networks that contribute to our understanding of microbial adaptations. In this study, we analyzed the gene co-expression networks of three Bifidobacterium species in response to different types of human milk oligosaccharides (HMO) using weighted gene co-expression analysis (WGCNA). RNA-seq data obtained from Geo Datasets were obtained for Bifidobacterium longum subsp. Infantis, Bifidobacterium bifidum and Bifidobacterium longum subsp. Longum. Between 10 and 20 co-expressing modules were obtained for each dataset. HMO-associated genes appeared in the modules with more genes for B. infantis and B. bifidum, in contrast with B. longum. Hub genes were identified in each module, and in general they participated in conserved essential processes. Certain modules were differentially enriched with LacI-like transcription factors, and others with certain metabolic pathways such as the biosynthesis of secondary metabolites. The three Bifidobacterium transcriptomes showed distinct regulation patterns for HMO utilization. HMO-associated genes in B. infantis co-expressed in two modules according to their participation in galactose or N-Acetylglucosamine utilization. Instead, B. bifidum showed a less structured co-expression of genes participating in HMO utilization. Finally, this category of genes in B. longum clustered in a small module, indicating a lack of co-expression with main cell processes and suggesting a recent acquisition. This study highlights distinct co-expression architectures in these bifidobacterial genomes during HMO consumption, and contributes to understanding gene regulation and co-expression in these species of the gut microbiome.
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Affiliation(s)
- Kevin J. González-Morelo
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigación en Matemáticas Aplicadas y en Sistemas. Universidad Nacional Autónoma de México, Ciudad Universitaria, México City, México
| | - Felipe Melis
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Mexico
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile,*Correspondence: Daniel Garrido,
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Chen P, Wang J, Lv J, Wang Q, Zhang C, Zhao W, Li S. Nitrogen removal by Rhodococcus sp. SY24 under linear alkylbenzene sulphonate stress: Carbon source metabolism activity, kinetics, and optimum culture conditions. BIORESOURCE TECHNOLOGY 2023; 368:128348. [PMID: 36400273 DOI: 10.1016/j.biortech.2022.128348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Artificial intervention combined with stress acclimation was used to screen a heterotrophic nitrifying-aerobic denitrifying (HN-AD) bacterial, strain Rhodococcus SY24, resistant to linear alkylbenzenesulfonic acid (LAS) stress. When LAS was<15 mg/L, strain SY24 performed better cell growth and carbon source metabolism activity. The maximum nitrification and denitrification rates of SY24 under LAS stress could reach 1.18 mg/L/h and 1.05 mg/L/h, respectively, which were 13.80 % and 8.81 % higher than those of the original strain CPZ24. Higher LAS tolerance was seen in the functional genes (amoA, nxrA, napA, narG, nirK, nirS, norB, and nosZ). Response surface modeling revealed that 2 mg/L LAS, sodium succinate as a carbon source, 190 rams, and carbon/nitrogen 11 were the ideal culture conditions for SY24 to nitrogen removal under the LAS environment. This study offered a new screening strategy for the functional species, and strain SY24 showed significant LAS tolerance and HN-AD potential.
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Affiliation(s)
- Peizhen Chen
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Jingli Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; Wuhan Economic and Technological Development Zone (Hanan District) Ecological Environment Monitoring Station, Wuhan 430090, China
| | - Jie Lv
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Qiang Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Chunxue Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Wenjie Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Shaopeng Li
- Tianjin Agricultural University, Tianjin 300392, China.
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Duan L, Li JL, Yin LZ, Luo XQ, Ahmad M, Fang BZ, Li SH, Deng QQ, Wang P, Li WJ. Habitat-dependent prokaryotic microbial community, potential keystone species, and network complexity in a subtropical estuary. ENVIRONMENTAL RESEARCH 2022; 212:113376. [PMID: 35561827 DOI: 10.1016/j.envres.2022.113376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/09/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Microbes (e.g., bacteria and archaea) are indispensable components for the key biological processes of estuarine ecosystems and three main habitats (sediment, particle, and water) are harboring diverse estuarine microbes. However, we still know little about how the microbial community structures, potential keystone species, and network properties change among these three habitats in estuarine ecosystems. In this study, we collected size-fractioned water and sediment samples from the Pearl River Estuary to reveal their microbial diversity, community structures, network properties, and potential keystone taxa. We found that the sediment microbial community was remarkably more diverse than particle-attached (PA) and free-living (FL) communities, whereas its ecological network was less complex in terms of node distance and connectivity. TOC was determined as the main driver of sediment community, while the PA and FL communities were predominantly shaped by NO2-, non-ionic ammonia (NH) and pH. Among the bulk water, there were no significant differences between PA and FL communities in diversity, community structure, and network complexity. However, the PA community was more susceptible to metal elements, suggesting their higher level of involvement in physiological metabolism. Potential keystone taxa among community networks were taxonomically divergent in three habitats. Specifically, Synechococcales (Cyanobacteria) and Actinomarinales (Actinobacteria) exclusively served as the module-hubs in FL network, while members from phylum Proteobacteria and Bacteroidetes were the module-hubs and connectors in PA network. Potential keystone taxa in sediment network were more diverse and covered 9 phyla, including the only archaeal lineage Bathyarchaeia (Crenarchaeota). Overall, our study provided more detailed information about estuarine microbial communities in three habitats, especially the potential keystone species, which provided new perspectives on evaluating further effects of anthropogenic disturbances on estuarine microbes and facilitated the environment monitoring based on microbial community.
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Affiliation(s)
- Li Duan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ling-Zi Yin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiao-Qing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Manzoor Ahmad
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Shan-Hui Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Qi-Qi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Hubei Key Laboratory of Marine Geological Resources, China University of Geosciences, Wuhan 430074, China; School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
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Bian J, Liao Y, Liu R, An X, Hu C, Liu H, Qu J. Synergy of cyano groups and cobalt single atoms in graphitic carbon nitride for enhanced bio-denitrification. WATER RESEARCH 2022; 218:118465. [PMID: 35461103 DOI: 10.1016/j.watres.2022.118465] [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: 02/02/2022] [Revised: 04/02/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Bio-denitrification plays a crucial role in the purification of nitrogen contaminated water, yet the low efficiency of the pure biological system often leads to the accumulation of harmful intermediates. Semi-biological catalysis provides an effective approach to improving the reaction efficiency through hybridizing artificial nanomaterials with natural organisms, yet the application of this strategy in bio-denitrification is limited. In this study, the effect of surface engineered carbon nitride on the denitrification capability of denitrifying bacteria was investigated. We found that cyano groups availed the biotic-abiotic interactions, while immobilized cobalt single atoms attenuated the local electrostatic repulsion. This synergistic effect endowed carbon nitride modified with cobalt atoms and cyano groups (Co/C3N4-C) with the unexpected acceleration of bio-denitrification reaction, without the accumulation of harmful intermediates. According to the metabolomics analysis, this improvement was attributed to the moderate metabolic adaptation caused by nanoelicitor, which induced dramatically boosted electron transfer and energy supply for extracellular polymeric substance (EPS) secretion. The elevation of intracellular iron level increased the activities of denitrification reductase, which was evidenced by metatranscriptomic analysis. Our results not only demonstrate the great potential of carbon nitride as an artificial elicitor for biological regulation, but also shed light on comprehending the complicated biotic-abiotic interactions for versatile application.
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Affiliation(s)
- Jiyong Bian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liao
- 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
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Xiaoqiang An
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Chengzhi Hu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiuhui Qu
- State Key Laboratory of Environmental Aquatic Chemistry, 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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9
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Yang X, Hashemi MM, Andini N, Li MM, Kuang S, Carroll KC, Wang TH, Yang S. RNA markers for ultra-rapid molecular antimicrobial susceptibility testing in fluoroquinolone-treated Klebsiella pneumoniae. J Antimicrob Chemother 2021; 75:1747-1755. [PMID: 32191305 DOI: 10.1093/jac/dkaa078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/06/2020] [Accepted: 02/09/2020] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Traditional antimicrobial susceptibility testing (AST) is growth dependent and time-consuming. With rising rates of drug-resistant infections, a novel diagnostic method is critically needed that can rapidly reveal a pathogen's antimicrobial susceptibility to guide appropriate treatment. Recently, RNA sequencing has been identified as a powerful diagnostic tool to explore transcriptional gene expression and improve AST. METHODS RNA sequencing was used to investigate the potential of RNA markers for rapid molecular AST using Klebsiella pneumoniae and ciprofloxacin as a model. Downstream bioinformatic analysis was applied for optimal marker selection. Further validation on 11 more isolates of K. pneumoniae was performed using quantitative real-time PCR. RESULTS From RNA sequencing, we identified RNA signatures that were induced or suppressed following exposure to ciprofloxacin. Significant shifts at the transcript level were observed as early as 10 min after antibiotic exposure. Lastly, we confirmed marker expression profiles with concordant MIC results from traditional culture-based AST and validated across 11 K. pneumoniae isolates. recA, coaA and metN transcripts harbour the most sensitive susceptibility information and were selected as our top markers. CONCLUSIONS Our results suggest that RNA signature is a promising approach to AST development, resulting in faster clinical diagnosis and treatment of infectious disease. This approach is potentially applicable in other models including other pathogens exposed to different classes of antibiotics.
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Affiliation(s)
- Xi Yang
- Department of Emergency Medicine, Stanford University, Stanford, CA, USA
| | - Marjan M Hashemi
- Department of Emergency Medicine, Stanford University, Stanford, CA, USA
| | - Nadya Andini
- Department of Emergency Medicine, Stanford University, Stanford, CA, USA
| | - Michelle M Li
- Department of Mathematical and Computational Science, Stanford University, Stanford, CA, USA
| | - Shuzhen Kuang
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Karen C Carroll
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University, Stanford, CA, USA
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Yang X, He Q, Guo F, Sun X, Zhang J, Chen Y. Impacts of carbon-based nanomaterials on nutrient removal in constructed wetlands: Microbial community structure, enzyme activities, and metabolism process. JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123270. [PMID: 32645543 DOI: 10.1016/j.jhazmat.2020.123270] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 06/08/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
The increasing use of raw carbon-based nanomaterials (CBNs) will inevitably affect wastewater treatment systems. Constructed wetlands (CWs) are ecological wastewater treatment facilities and can intercept the vast particles pollutant, including CBNs. However, the impacts of CBNs on the treatment performance of CWs have no available knowledge. Therefore, we systematically inspected the effects of single-walled and multi-walled carbon nanotubes (SWCNTs and MWCNTs) and fullerene nanoparticles (C60) on CW performance under 180-day exposure to 0, 10 and 1000 μg/L concentrations. The results showed that CBNs had marginally adverse impacts on chemical oxygen demand (COD) and total phosphorus (TP) removal, whereas nitrogen removal declined by 24.1 %-42.7 % following long-term exposure to CBNs. MWCNTs had the greatest inhibition effect on nitrogen removal, followed by SWCNTs and C60. The CBNs also induced reactive oxygen species (ROS) overproduction as the increasing concentration, which confirmed that CBNs have biotoxic effects in CWs. The variation of functional microbial community and the inhibition of enzyme activities were the dominant reasons for the decline in nitrogen removal efficiency. Furthermore, predictive functional profiling showed that CBNs affected functional gene abundance, and caused a decline in the enzymes abundance connected to nitrogen removal by the end of the 180-day exposure period.
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Affiliation(s)
- Xiangyu Yang
- Key Laboratory of the Three Gorges Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Campus B 83 Shabeijie, Shapingba, Chongqing, 400044, PR China; National Centre for International Research of Low-Carbon and Green Buildings, Chongqing University, Chongqing, 400044, PR China
| | - Qiang He
- Key Laboratory of the Three Gorges Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Campus B 83 Shabeijie, Shapingba, Chongqing, 400044, PR China; National Centre for International Research of Low-Carbon and Green Buildings, Chongqing University, Chongqing, 400044, PR China
| | - Fucheng Guo
- Key Laboratory of the Three Gorges Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Campus B 83 Shabeijie, Shapingba, Chongqing, 400044, PR China; National Centre for International Research of Low-Carbon and Green Buildings, Chongqing University, Chongqing, 400044, PR China
| | - Xiaohui Sun
- Key Laboratory of the Three Gorges Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Campus B 83 Shabeijie, Shapingba, Chongqing, 400044, PR China; National Centre for International Research of Low-Carbon and Green Buildings, Chongqing University, Chongqing, 400044, PR China
| | - Junmao Zhang
- Key Laboratory of the Three Gorges Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Campus B 83 Shabeijie, Shapingba, Chongqing, 400044, PR China; National Centre for International Research of Low-Carbon and Green Buildings, Chongqing University, Chongqing, 400044, PR China
| | - Yi Chen
- Key Laboratory of the Three Gorges Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Campus B 83 Shabeijie, Shapingba, Chongqing, 400044, PR China; National Centre for International Research of Low-Carbon and Green Buildings, Chongqing University, Chongqing, 400044, PR China.
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Systematic Identification of Key Functional Modules and Genes in Gastric Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8853348. [PMID: 33282955 PMCID: PMC7685902 DOI: 10.1155/2020/8853348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/14/2020] [Accepted: 10/28/2020] [Indexed: 11/24/2022]
Abstract
Gastric cancer (GC) is associated with high incidence and mortality rates worldwide. Differentially expressed gene (DEG) analysis and weighted gene coexpression network analysis (WGCNA) are important bioinformatic methods for screening core genes. In our study, DEG analysis and WGCNA were combined to screen the hub genes, and pathway enrichment analyses were performed on the DEGs. SBNO2 was identified as the hub gene based on the intersection between the DEGs and the purple module in WGCNA. The expression and prognostic value of SBNO2 were verified in UALCAN, GEPIA2, Human Cancer Metastasis Database, Kaplan–Meier plotter, and TIMER. We identified 1974 DEGs, and 28 modules were uncovered via WGCNA. The purple module was identified as the hub module in WGCNA. SBNO2 was identified as the hub gene, which was upregulated in tumour tissues. Moreover, patients with GC and higher SBNO2 expression had worse prognoses. In addition, SBNO2 was suggested to play an important role in immune cell infiltration. In summary, based on DEGs and key modules related to GC, we identified SBNO2 as a hub gene, thereby offering novel insights into the development and treatment of GC.
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Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach. Sci Rep 2020; 10:13717. [PMID: 32792590 PMCID: PMC7427096 DOI: 10.1038/s41598-020-70581-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that thrives in diverse environments and causes a variety of human infections. Pseudomonas aeruginosa AG1 (PaeAG1) is a high-risk sequence type 111 (ST-111) strain isolated from a Costa Rican hospital in 2010. PaeAG1 has both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases, and it is resistant to β-lactams (including carbapenems), aminoglycosides, and fluoroquinolones. Ciprofloxacin (CIP) is an antibiotic commonly used to treat P. aeruginosa infections, and it is known to produce DNA damage, triggering a complex molecular response. In order to evaluate the effects of a sub-inhibitory CIP concentration on PaeAG1, growth curves using increasing CIP concentrations were compared. We then measured gene expression using RNA-Seq at three time points (0, 2.5 and 5 h) after CIP exposure to identify the transcriptomic determinants of the response (i.e. hub genes, gene clusters and enriched pathways). Changes in expression were determined using differential expression analysis and network analysis using a top–down systems biology approach. A hybrid model using database-based and co-expression analysis approaches was implemented to predict gene–gene interactions. We observed a reduction of the growth curve rate as the sub-inhibitory CIP concentrations were increased. In the transcriptomic analysis, we detected that over time CIP treatment resulted in the differential expression of 518 genes, showing a complex impact at the molecular level. The transcriptomic determinants were 14 hub genes, multiple gene clusters at different levels (associated to hub genes or as co-expression modules) and 15 enriched pathways. Down-regulation of genes implicated in several metabolism pathways, virulence elements and ribosomal activity was observed. In contrast, amino acid catabolism, RpoS factor, proteases, and phenazines genes were up-regulated. Remarkably, > 80 resident-phage genes were up-regulated after CIP treatment, which was validated at phenomic level using a phage plaque assay. Thus, reduction of the growth curve rate and increasing phage induction was evidenced as the CIP concentrations were increased. In summary, transcriptomic and network analyses, as well as the growth curves and phage plaque assays provide evidence that PaeAG1 presents a complex, concentration-dependent response to sub-inhibitory CIP exposure, showing pleiotropic effects at the systems level. Manipulation of these determinants, such as phage genes, could be used to gain more insights about the regulation of responses in PaeAG1 as well as the identification of possible therapeutic targets. To our knowledge, this is the first report of the transcriptomic analysis of CIP response in a ST-111 high-risk P. aeruginosa strain, in particular using a top-down systems biology approach.
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Chen D, Zuo X, Li J, Wang X, Liu J. Carbon migration and metagenomic characteristics during anaerobic digestion of rice straw. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:130. [PMID: 32699553 PMCID: PMC7372879 DOI: 10.1186/s13068-020-01770-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/11/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Considerable interest has been expressed in the development of anaerobic digestion (AD) of straw to solve the environmental problems caused by the dumping and burning of straw and to generate clean energy. However, the poor biodegradability of straw and the low efficiency of energy generation achieved during its AD are problematic. Studying the parameter changes involved in the process of AD is helpful for clarifying its micro-mechanisms and providing a theoretical basis for improving its efficiency. Currently, most research into process parameters has focused on gas production, methane content, pH, and volatile fatty acid (VFA) content; limited research has focused on carbon migration and functional gene changes during the AD of straw. RESULTS Carbon migration and changes in metagenomic characteristics during the AD of rice straw (RS) were investigated. Accumulated biogas production was 388.43 mL/g VS. Carbon in RS was consumed, and the amount of carbon decreased from 76.28 to 36.83 g (conversion rate 51.72%). The degree of hydrolysis rapidly increased during the first 5 days, and a large amount of carbon accumulated in the liquid phase before migrating into the gas phase. By the end of AD, the amount of carbon in the liquid and gas phases was 2.67 and 36.78 g, respectively. According to our metagenomic analysis, at the module level, the abundance of M00357, M00567, M00356, and M00563 (the modules related to the generation of methane) during AD were 51.23-65.43%, 13.96-26.88%, 16.44-22.98%, and 0.83-2.40%, respectively. Methyl-CoM, 5-methyl-5,6,7,8-tetrahydromethanopterin, and Acetyl-CoA were important intermediates. CONCLUSIONS Carbon was enriched in the liquid phase for the first 5 days and then gradually consumed, and most of the carbon was transferred to the gas phase by the end of AD. In this study, AD proceeded mainly via aceticlastic methanogenesis, which was indicated to be a dominant pathway in methane metabolism. Batch AD could be divided into three stages, including initiation (days 1-5), adaptation (days 6-20), and stabilization (days 21-50), according to biogas production performance, carbon migration, and metagenomic characteristics during AD.
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Affiliation(s)
- Dadi Chen
- Department of Environmental Science and Engineering, College of Chemical Engineering, Beijing University of Chemical Technology, 15 BeiSanhuan East Road, ChaoYang District, Beijing, 100029 People’s Republic of China
- Beijing Municipal Research Institute of Environmental Protection, Beijing, 100037 People’s Republic of China
| | - Xiaoyu Zuo
- Department of Environmental Science and Engineering, College of Chemical Engineering, Beijing University of Chemical Technology, 15 BeiSanhuan East Road, ChaoYang District, Beijing, 100029 People’s Republic of China
| | - Juan Li
- Department of Environmental Science and Engineering, College of Chemical Engineering, Beijing University of Chemical Technology, 15 BeiSanhuan East Road, ChaoYang District, Beijing, 100029 People’s Republic of China
- Beijing Municipal Ecological and Environmental Monitoring Center, 14 Chegongzhuang West Road, Haidian District, Beijing, 100048 People’s Republic of China
| | - Xitong Wang
- Department of Environmental Science and Engineering, College of Chemical Engineering, Beijing University of Chemical Technology, 15 BeiSanhuan East Road, ChaoYang District, Beijing, 100029 People’s Republic of China
| | - Jie Liu
- Department of Environmental Science and Engineering, College of Chemical Engineering, Beijing University of Chemical Technology, 15 BeiSanhuan East Road, ChaoYang District, Beijing, 100029 People’s Republic of China
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Awadallah-F A, Al-Muhtaseb S. Carbon Nanoparticles-Decorated Carbon Nanotubes. Sci Rep 2020; 10:4878. [PMID: 32184418 PMCID: PMC7078261 DOI: 10.1038/s41598-020-61726-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/03/2020] [Indexed: 12/18/2022] Open
Abstract
Multi walled carbon nanotubes (MWCNTs) were decorated by activated carbon nanoparticles of resorcinol-formaldehyde aerogels. Carbon nanospheres and MWCNTs were mixed by equal mass ratios for different durations. The products were characterized by Raman spectroscopy, thermal gravimetric analysis, nanoscanning electron microscopy, transmission electron microscopy and x-ray diffraction. The results indicated that a significant decoration with carbon nanoparticles occurred onto the MWCNTs.
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Affiliation(s)
- Ahmed Awadallah-F
- Department of Chemical Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Shaheen Al-Muhtaseb
- Department of Chemical Engineering, Qatar University, P.O. Box 2713, Doha, Qatar.
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15
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Genetic regulatory networks for salt-alkali stress in Gossypium hirsutum with differing morphological characteristics. BMC Genomics 2020; 21:15. [PMID: 31906862 PMCID: PMC6945603 DOI: 10.1186/s12864-019-6375-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/08/2019] [Indexed: 12/13/2022] Open
Abstract
Background Cotton grows in altering environments that are often unfavorable or stressful for its growth and development. Consequently, the plant must cope with abiotic stresses such as soil salinity, drought, and excessive temperatures. Alkali-salt stress response remains a cumbersome biological process and is regulated via a multifaceted transcriptional regulatory network in cotton. Results To discover the molecular mechanisms of alkali-salt stress response in cotton, a comprehensive transcriptome analysis was carried out after alkali-salt stress treatment in three accessions of Gossypium hirsutum with contrasting phenotype. Expression level analysis proved that alkali-salt stress response presented significant stage-specific and tissue-specific. GO enrichment analysis typically suggested that signal transduction process involved in salt-alkali stress response at SS3 and SS12 stages in leaf; carbohydrate metabolic process and oxidation-reduction process involved in SS48 stages in leaf; the oxidation-reduction process involved at all three phases in the root. The Co-expression analysis suggested a potential GhSOS3/GhCBL10-SOS2 network was involved in salt-alkali stress response. Furthermore, Salt-alkali sensitivity was increased in GhSOS3 and GhCBL10 Virus-induced Gene Silencing (VIGS) plants. Conclusion The findings may facilitate to elucidate the underlying mechanisms of alkali-salt stress response and provide an available resource to scrutinize the role of candidate genes and signaling pathway governing alkali-salt stress response.
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Luo J, Zhang Q, Wu L, Feng Q, Fang F, Xue Z, Li C, Cao J. Promoting the anaerobic production of short-chain fatty acids from food wastes driven by the reuse of linear alkylbenzene sulphonates-enriched laundry wastewater. BIORESOURCE TECHNOLOGY 2019; 282:301-309. [PMID: 30875598 DOI: 10.1016/j.biortech.2019.03.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
An efficient attempt to improve the anaerobic fermentation of food wastes (FW) via the reuse of linear alkylbenzene sulphonates (LAS)-enriched laundry wastewater was reported. The production of short-chain fatty acids (SCFAs) from FW was enhanced by approximate 6-folds with high proportions of butyric and valeric acids at appropriate LAS level. Mechanism investigations demonstrated that the solubilization of macromolecule organics in FW was effectively improved by surface tension reduction. The hydrolysis and acidification processes during FW fermentation were accelerated and enhanced with the stimulation of microbial activities (higher activities of hydrolases and ATP concentrations). Also, the abundances of anaerobic microorganisms responsible for SCFAs production were enriched. Metatranscriptomic analysis indicated that the encoding genes involved in the metabolism of fermentation substrates for SCFAs production were highly expressed in LAS-added reactors. It was the simultaneous increase of bioavailable substrates and metabolic activities that contribute to the efficient SCFAs production in LAS-added reactors.
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Affiliation(s)
- Jingyang Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China.
| | - Qin Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China; Wanjiang University of Technology, Ma'anshan 243031, China
| | - Lijuan Wu
- Jiangsu Provincial Academy of Environmental Science, Nanjing 210098, China
| | - Qian Feng
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Fang Fang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Zhaoxia Xue
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Chao Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Jiashun Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
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Anh Le TT, Thuptimdang P, McEvoy J, Khan E. Phage shock protein and gene responses of Escherichia coli exposed to carbon nanotubes. CHEMOSPHERE 2019; 224:461-469. [PMID: 30831497 DOI: 10.1016/j.chemosphere.2019.02.159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
Two-dimensional electrophoretic, western blotting, and quantitative polymerase chain reaction analyses of Escherichia coli cells exposed to pristine single walled carbon nanotubes (SWCNTs), and hydroxyl and carboxylic functionalized SWCNTs (SWCNT-OHs and SWCNT-COOHs) were conducted. SWCNT concentration and length were experimental variables. Exposing E. coli cells to SWCNTs led to changes in protein and gene expressions. Several proteins altered their regulations at a low SWCNT concentration (10 μg/ml) and were shut down at a high SWCNT concentration (100 μg/ml). The expressions of the phage shock protein (psp) operon including pspA, pspB, and pspC genes responded to the membrane stressors, SWCNTs, were also examined. While pspA and pspC expressions were influenced by the length, concentration, and functional groups of SWCNTs, pspB expression was not induced by SWCNTs. The alterations in phage shock protein and gene expressions indicated that SWCNTs caused cell membrane perturbation.
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Affiliation(s)
- Tu Thi Anh Le
- Environmental and Conservation Sciences Program, North Dakota State University, Fargo, ND 58108, USA; Biology Department, Dalat University, Dalat, Lamdong, Viet Nam.
| | - Pumis Thuptimdang
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand; Environmental Science Research Center (ESRC), Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - John McEvoy
- Microbiological Sciences Department, North Dakota State University, Fargo, ND 58108, USA.
| | - Eakalak Khan
- Civil and Environmental Engineering and Construction Department, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA.
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18
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Maksimova YG. Microorganisms and Carbon Nanotubes: Interaction and Applications (Review). APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819010101] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Luo J, Zhang Q, Wu L, Cao J, Feng Q, Fang F, Chen Y. Inhibition of 1, 4-dioxane on the denitrification process by altering the viability and metabolic activity of Paracoccus denitrificans. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:27274-27282. [PMID: 30032369 DOI: 10.1007/s11356-018-2642-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/24/2018] [Indexed: 06/08/2023]
Abstract
1,4-Dioxane is an emerging pollutant, which widely exists in natural environments and poses potential risks to the living organisms. However, its effect on the denitrification process is still unknown. In this study, the effects of 1,4-dioxane on the denitrification process were therefore investigated by using Paracoccus denitrificans as the model denitrifier. The obtained results showed that the exposure of 1,4-dioxane exhibited remarkable lag or inhibition on the denitrification process, especially with high dose. In the control without 1,4-dioxane exposure, Paracoccus denitrificans showed high denitrification efficiency (98.5%). However, the efficiency decreased to 78.5, 63.9, and 9.3% with 0.50, 0.75, and 1.0% (v/v) 1,4-dioxane dose, respectively. The dose-induced inhibition of denitrification by 1,4-dioxane could be partially attributed to the negative effects on proliferation and viability of functional microorganisms by conjugating and disrupting the cell membranes. Furthermore, 1,4-dioxane caused biotoxicity to the intracellular activities of denitrifiers via disturbing carbon source utilization and interfering the key enzymes responsible for glycolysis. The decrease of microbial viability and activity inevitably resulted in the decline of key enzymes (NAR, NIR, NOR, and N2OR) closely related with denitrification process, which could be the direct reason for the decrease of denitrification performance.
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Affiliation(s)
- Jingyang Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Qin Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Lijuan Wu
- Jiangsu Provincial Academy of Environmental Science, Nanjing, 210098, China
| | - Jiashun Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, China.
- College of Environment, Hohai University, Nanjing, 210098, China.
| | - Qian Feng
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Fang Fang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Yinguang Chen
- State key laboratory of pollution control and Resources reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
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