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Thakur P, Gauba P. Expression Analysis of Nitrogen Metabolism Genes in Lelliottia amnigena PTJIIT1005, Comparison with Escherichia coli K12 and Validation of Nitrogen Metabolism Genes. Biochem Genet 2024:10.1007/s10528-024-10677-w. [PMID: 38341394 DOI: 10.1007/s10528-024-10677-w] [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: 02/08/2023] [Accepted: 01/02/2024] [Indexed: 02/12/2024]
Abstract
Escherichia coli K12 and Lelliottia amnigena PTJIIT1005 bacteria were isolated from the polluted Yamuna River (Delhi, India) site, which can remediate nitrate from groundwater media under anaerobic conditions. BV-BRC (Bacterial and Viral Bioinformatics Resource Center) information system, RAST, and PGAP servers were used to annotate the nitrogen metabolism genes from the genome sequence of these microbes. Here we compared the strains L. amnigena PTJIIT1005 with E. coli K12 in the context of nitrogen metabolism genes. Sequence alignment, similarity percentage, and phylogenetic analysis were done to find similarities between the genes. Common nitrogen genes of these strains, like respiratory nitrate reductase, nitrite reductase, nitric oxide reductase, glutamine synthetase, and hydroxylamine reductase, have found good sequence similarity (83-94%) with each other. The PATRIC tool identified N-operons, and the nitrate reductase gene clusters were also determined as per literature survey. Protein-protein interaction network was constructed using STRING 12.0 database and Cytoscape v 3.10.0 software plug-in Network analyzer. On the basis of network topological parameters NarG, NarZ, NarY, NarH, NarI, NarV, NirB, NirD, NapA, and NapB are the key genes in network of E. coli K12 strain. Nar, NirB, NirD, NasA, NasB, NasC, NasD, NasE, and GlnA are the key genes in network of L. amnigena PTJIIT1005. Among these, NarG and NirB are the superhub genes because of having highest Betweenness centrality (BC) and node degree. The functional enrichment analysis was determined using PANTHER GENE ONTOLOGY and DAVID software exhibited their role in nitrogen metabolism pathway and nitrate assimilation. Further, SWISS-MODEL was used to predict the 3D protein structure of these enzymes, and after, these structures were validated by Ramachandran plot using the PROCHECK tool. The Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) method was used to determine the N-genes expression level in both strains. This study showed that E. coli K12 and L. amnigena PTJIIT1005 have common nitrogen metabolism genes involved in the same functional role, like the denitrification pathway. Additionally, operon arrangement study and PPI network revealed that E. coli K12 has only a denitrification pathway, while L. amnigena PTJIIT1005 has both an assimilation and denitrification pathway. PCR successfully amplified selected N-metabolizing genes, and the expression level of N-genes was high in strain L. amnigena PTJIIT1005. Our previous experimental study exhibited a better nitrate remediation rate in L. amnigena PTJIIT1005 over E. coli K12. This study confirmed the presence of assimilation and denitrification process through amplified N-metabolizing genes and showed high expression of N-genes in L. amnigena PTJIIT1005, which favor the evidence of better nitrate remediation in L. amnigena PTJIIT1005 over E. coli K12.
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Affiliation(s)
- Preeti Thakur
- Department of Biotechnology, Jaypee Institute of Information & Technology, Noida, 201307, India
| | - Pammi Gauba
- Head of Department, Jaypee Institute of Information & Technology, Noida, Uttar Pradesh, 201307, India.
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Wang K, Pan R, Fei H, Tong Q, Han F. Changes in soil prokaryotic communities and nitrogen cycling functions along a groundwater table drawdown gradient in desert wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156868. [PMID: 35752234 DOI: 10.1016/j.scitotenv.2022.156868] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Desert wetlands are evolving into deserts by groundwater table (GWT) drawdown. However, the changes in microbial communities and functions during the GWT drawdown are unclear, which hinders the predictive power of biogeochemical processes across the desertification. Here, 16S rRNA gene sequencing, PICRUSt2 and qPCR were used to investigate soil prokaryotic diversity, composition and nitrogen cycling gene abundance at four vegetation types [flooded swamp (FS), drained swamp (DS), desert grassland (DG), and bare sandy land (BS)] along a GWT decline gradient in the Mu Us Desert, northern China. Results showed that prokaryotic Shannon and Chao1 indexes were significantly reduced at BS than those at FS (p < 0.05). Whereas no significant difference was observed between FS, DS and DG (p > 0.05). Distinct shifts in community composition were found along the GWT decline gradient. The dominant taxa gradually changed from obligate anaerobes and eutrophic microbes to facultative anaerobes, and finally to aerobic, oligotrophic and drought-tolerant microbes. Soil moisture was the most important factor in regulating the communities. In addition, GWT drawdown inhibited the relative abundance of genes involved in nitrogen fixation, assimilatory nitrite reduction, and nitrate oxidation, but enhanced the relative abundance of genes related to denitrification, assimilated nitrate reduction, ammonia oxidation and ammonification. Thus, GWT drawdown inhibits nitrogen input potential and exacerbates nitrogen loss potential. These results help in understanding the succession characteristics of desert wetland desertification.
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Affiliation(s)
- Kun Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Ruopeng Pan
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Hongyan Fei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Qian Tong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Fengpeng Han
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China; Research Center on Soil & Water Conservation, Institute of Soil and Water Conservation, Chinese Academy of Sciences Ministry of Water Resources, Yangling, Shaanxi Province 712100, PR China.
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Zhao Y, Chen Z, Wang Q, Zhang C, Ji M. A new insight to explore toxic Cd(II) affecting denitrification: Reaction kinetic, electron behavior and microbial community. CHEMOSPHERE 2022; 305:135419. [PMID: 35752314 DOI: 10.1016/j.chemosphere.2022.135419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 05/24/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Denitrification process is a crucial step in nitrogen removal and is more vulnerable to external shocks due to the fact that anoxic process is always located before aerobic process in conventional sewage treatment. This study aims to elaborate the nitrogen conversion characteristics by investigating denitrification kinetics, electron behavior and microbial community under Cd(II) shock. Reaction kinetics showed that 10 mg/L of Cd(II) accelerated nitrate reduction rate by 52.29% but 80 mg/L of Cd(II) severely decelerated it by 95.41% with the accumulation of nitrite. High concentration of COD (C/N = 10.4) in the system caused by Cd(II) disrupting the integrity of cell membrane (lactate dehydrogenase increased by 328.7%) was proved to induce occurrence of Dissimilatory Nitrate Reduction to Ammonia (DNRA). The electron transport system activity (ETSA), electron consumption and electron distribution were combined to reveal the electron behavior regulated by Cd(II). The electron ratio of nitrate reductase to nitrite reductase increased from 1.48 (control) to 3.91 and 3.52 (40 and 80 mg/L of Cd(II)) indicated the electrons allocating tendency and further explained the nitrite accumulation. High concentration of Cd(II) also decreased ETSA by weakening the physiological activities of flavin adenine dinucleotide, flavin mononucleotide and cytochrome c or hindered the microbes to secrete these electron carriers. Furthermore, Cd(II) inhibited dominant bacteria genera containing napA gene (Azospirillum and Thauera) and nirS gene (unclassified_c_Betaproteobacteria). Enterobacteriaceae family was found to dominate the DNRA process.
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Affiliation(s)
- Yingxin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China.
| | - Zhihui Chen
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China
| | - Qian Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China
| | - Chenggong Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China
| | - Min Ji
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China
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Liébana R, Modin O, Persson F, Szabó E, Hermansson M, Wilén BM. Combined Deterministic and Stochastic Processes Control Microbial Succession in Replicate Granular Biofilm Reactors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:4912-4921. [PMID: 30969774 DOI: 10.1021/acs.est.8b06669] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Granular sludge is an efficient and compact biofilm process for wastewater treatment. However, the ecological factors involved in microbial community assembly during the granular biofilm formation are poorly understood, and little is known about the reproducibility of the process. Here, three replicate bioreactors were used to investigate microbial succession during the formation of granular biofilms. We identified three successional phases. During the initial phase, the successional turnover was high and α-diversity decreased as a result of the selection of taxa adapted to grow on acetate and form aggregates. Despite these dynamic changes, the microbial communities in the replicate reactors were similar. The second successional phase occurred when the settling time was rapidly decreased to selectively retain granules in the reactors. The influence of stochasticity on succession increased and new niches were created as granules emerged, resulting in temporarily increased α-diversity. The third successional phase occurred when the settling time was kept stable and granules dominated the biomass. Turnover was low, and selection resulted in the same abundant taxa in the reactors, but drift, which mostly affected low-abundant community members, caused the community in one reactor to diverge from the other two. Even so, performance was stable and similar between reactors.
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Affiliation(s)
- Raquel Liébana
- Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Oskar Modin
- Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Enikö Szabó
- Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Malte Hermansson
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE405 30 Gothenburg , Sweden
| | - Britt-Marie Wilén
- Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
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Li D, Zhang S, Li S, Zeng H, Zhang J. The nitrogen removal of autotrophic and heterotrophic bacteria in aerobic granular reactors with different feast/famine ratio. BIORESOURCE TECHNOLOGY 2019; 272:370-378. [PMID: 30384212 DOI: 10.1016/j.biortech.2018.10.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/17/2018] [Accepted: 10/19/2018] [Indexed: 05/21/2023]
Abstract
Aerobic granular sludge was cultivated in three column reactors, which had been operated for 120 days under different feast/famine ratio (1:7, 1:11, 1:15). The composition of total bacteria was analyzed by testing oxygen uptake rates of mixed liquor samples taken from the reactors and calculating according to activated sludge model. The results revealed that long famine phase favored the growth of heterotrophic bacteria. The heterotrophic bacteria accounts for 49.80, 53.37, 91.39% of total bacteria respectively in R1, R2 and R3. The heterotrophic nitrification was also observed in all the reactors, which accounts for 58.62, 58.33, 61.54% of total nitrification respectively in R1, R2 and R3. A novel nitrogen-removal pathway involving simultaneous nitrification-denitrification by heterotrophic nitrification bacteria was proposed. The results revealed that microbial system consisted of heterotrophic ammonia oxidizing bacteria showed stronger capacity of simultaneous nitrification-denitrification.
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Affiliation(s)
- Dong Li
- Key Laboratory of Water Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100123, China.
| | - Shirui Zhang
- Key Laboratory of Water Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100123, China
| | - Shuai Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Huiping Zeng
- Key Laboratory of Water Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100123, China
| | - Jie Zhang
- Key Laboratory of Water Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100123, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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张 新. Dominant Factors of Dissimilatory Nitrate Reduction to Ammonia (DNRA) in Activated Sludge System: A Comment. ACTA ACUST UNITED AC 2018. [DOI: 10.12677/aep.2018.82012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Sander EM, Virdis B, Freguia S. Dissimilatory nitrate reduction to ammonium as an electron sink during cathodic denitrification. RSC Adv 2015. [DOI: 10.1039/c5ra19241b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nitrate reduction to ammonium is shown as a competitive pathway during cathodic denitrification at low potential, and is dependent on biofilm age and electron uptake capacity.
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Affiliation(s)
- Elisa M. Sander
- Advanced Water Management Centre
- The University of Queensland, Level 4
- Brisbane
- Australia
| | - Bernardino Virdis
- Advanced Water Management Centre
- The University of Queensland, Level 4
- Brisbane
- Australia
- Centre for Microbial Electrochemical Systems
| | - Stefano Freguia
- Advanced Water Management Centre
- The University of Queensland, Level 4
- Brisbane
- Australia
- Centre for Microbial Electrochemical Systems
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