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Olaya‐Abril A, Biełło K, Rodríguez‐Caballero G, Cabello P, Sáez LP, Moreno‐Vivián C, Luque‐Almagro VM, Roldán MD. Bacterial tolerance and detoxification of cyanide, arsenic and heavy metals: Holistic approaches applied to bioremediation of industrial complex wastes. Microb Biotechnol 2024; 17:e14399. [PMID: 38206076 PMCID: PMC10832572 DOI: 10.1111/1751-7915.14399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Cyanide is a highly toxic compound that is found in wastewaters generated from different industrial activities, such as mining or jewellery. These residues usually contain high concentrations of other toxic pollutants like arsenic and heavy metals that may form different complexes with cyanide. To develop bioremediation strategies, it is necessary to know the metabolic processes involved in the tolerance and detoxification of these pollutants, but most of the current studies are focused on the characterization of the microbial responses to each one of these environmental hazards individually, and the effect of co-contaminated wastes on microbial metabolism has been hardly addressed. This work summarizes the main strategies developed by bacteria to alleviate the effects of cyanide, arsenic and heavy metals, analysing interactions among these toxic chemicals. Additionally, it is discussed the role of systems biology and synthetic biology as tools for the development of bioremediation strategies of complex industrial wastes and co-contaminated sites, emphasizing the importance and progress derived from meta-omic studies.
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Affiliation(s)
- Alfonso Olaya‐Abril
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Karolina Biełło
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Gema Rodríguez‐Caballero
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Lara P. Sáez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Conrado Moreno‐Vivián
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Víctor Manuel Luque‐Almagro
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
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Maurya S, Arya CK, Parmar N, Sathyanarayanan N, Joshi CG, Ramanathan G. Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF. Arch Microbiol 2023; 206:6. [PMID: 38015256 DOI: 10.1007/s00203-023-03729-z] [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: 03/31/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.
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Affiliation(s)
- Shiwangi Maurya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Chetan Kumar Arya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Nidhi Parmar
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Nitish Sathyanarayanan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, 560065, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Gurunath Ramanathan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
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Zhang K, Zeng Q, Jiang R, Shi S, Yang J, Long L, Tian X. Three Novel Marine Species of Paracoccus, P. aerodenitrificans sp. nov., P. sediminicola sp. nov. and P. albus sp. nov., and the Characterization of Their Capability to Perform Heterotrophic Nitrification and Aerobic Denitrification. Microorganisms 2023; 11:1532. [PMID: 37375034 DOI: 10.3390/microorganisms11061532] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Heterotrophic nitrification-aerobic denitrification (HN-AD) is an efficient nitrogen removal process and the genus Paracoccus is one important group of the HN-AD bacteria. During an investigation of the microbial diversity in marine ranching of the Pearl River Estuary (PR China), three bacterial strains, designated SCSIO 75817T, SCSIO 76264T and SCSIO 80058T, were isolated from sediments. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the three strains belonged to the genus Paracoccus and their closest neighbors were P. isoporae DSM 22220T (97.6-98.0%), P. aurantiacus CGMCC 1.13898T (97.3-97.6%) and P. xiamenensis MCCC 1A16381T (97.1-97.4%), respectively. The analysis results of 16S rRNA gene similarity, ANI, AAI and dDDH showed that the pairwise similarities between these three strains and their closest neighbors were 97.4-98.5%, 76.9-81.0%, 75.5-79.6% and 20.3-23.3%, respectively. Polyphasic taxonomic data of the phylogenetic, phenotypic and chemotaxonomic analyses indicate that these strains represent three novel species in the genus Paracoccus, for which the names Paracoccus aerodenitrificans sp. nov., Paracoccus sediminicola sp. nov. and Paracoccus albus sp. nov. are proposed, respectively. The study also demonstrated the heterotrophic nitrification-aerobic denitrification (HN-AD) ability of the novel species P. aerodenitrificans SCSIO 75817T. When it was aerobically cultivated at 28 °C using NH4+-N, NO3--N and NO2--N as the sole nitrogen sources, the nitrogen removal efficiencies were 73.4, 55.27 and 49.2%, respectively, and the maximum removal rates were 3.05, 1.82 and 1.63 mg/L/h, respectively. The results suggest that it has promising potential for wastewater treatment.
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Affiliation(s)
- Kun Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, SCSIO, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Zeng
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, SCSIO, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rouyun Jiang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, SCSIO, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songbiao Shi
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, SCSIO, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, SCSIO, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, SCSIO, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Xinpeng Tian
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, SCSIO, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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Ray A, Spiro S. DksA, ppGpp, and RegAB Regulate Nitrate Respiration in Paracoccus denitrificans. J Bacteriol 2023; 205:e0002723. [PMID: 36920204 PMCID: PMC10127633 DOI: 10.1128/jb.00027-23] [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: 01/19/2023] [Accepted: 02/17/2023] [Indexed: 03/16/2023] Open
Abstract
The periplasmic (NAP) and membrane-associated (Nar) nitrate reductases of Paracoccus denitrificans are responsible for nitrate reduction under aerobic and anaerobic conditions, respectively. Expression of NAP is elevated in cells grown on a relatively reduced carbon and energy source (such as butyrate); it is believed that NAP contributes to redox homeostasis by coupling nitrate reduction to the disposal of excess reducing equivalents. Here, we show that deletion of either dksA1 (one of two dksA homologs in the P. denitrificans genome) or relA/spoT (encoding a bifunctional ppGpp synthetase and hydrolase) eliminates the butyrate-dependent increase in nap promoter and NAP enzyme activity. We conclude that ppGpp likely signals growth on a reduced substrate and, together with DksA1, mediates increased expression of the genes encoding NAP. Support for this model comes from the observation that nap promoter activity is increased in cultures exposed to a protein synthesis inhibitor that is known to trigger ppGpp synthesis in other organisms. We also show that, under anaerobic growth conditions, the redox-sensing RegAB two-component pair acts as a negative regulator of NAP expression and as a positive regulator of expression of the membrane-associated nitrate reductase Nar. The dksA1 and relA/spoT genes are conditionally synthetically lethal; the double mutant has a null phenotype for growth on butyrate and other reduced substrates while growing normally on succinate and citrate. We also show that the second dksA homolog (dksA2) and relA/spoT have roles in regulation of expression of the flavohemoglobin Hmp and in biofilm formation. IMPORTANCE Paracoccus denitrificans is a metabolically versatile Gram-negative bacterium that is used as a model for studies of respiratory metabolism. The organism can utilize nitrate as an electron acceptor for anaerobic respiration, reducing it to dinitrogen via nitrite, nitric oxide, and nitrous oxide. This pathway (known as denitrification) is important as a route for loss of fixed nitrogen from soil and as a source of the greenhouse gas nitrous oxide. Thus, it is important to understand those environmental and genetic factors that govern flux through the denitrification pathway. Here, we identify four proteins and a small molecule (ppGpp) which function as previously unknown regulators of expression of enzymes that reduce nitrate and oxidize nitric oxide.
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Affiliation(s)
- Ashvini Ray
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Stephen Spiro
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
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Biełło KA, Cabello P, Rodríguez-Caballero G, Sáez LP, Luque-Almagro VM, Roldán MD, Olaya-Abril A, Moreno-Vivián C. Proteomic Analysis of Arsenic Resistance during Cyanide Assimilation by Pseudomonas pseudoalcaligenes CECT 5344. Int J Mol Sci 2023; 24:ijms24087232. [PMID: 37108394 PMCID: PMC10138600 DOI: 10.3390/ijms24087232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Wastewater from mining and other industries usually contains arsenic and cyanide, two highly toxic pollutants, thereby creating the need to develop bioremediation strategies. Here, molecular mechanisms triggered by the simultaneous presence of cyanide and arsenite were analyzed by quantitative proteomics, complemented with qRT-PCR analysis and determination of analytes in the cyanide-assimilating bacterium Pseudomonas pseudoalcaligenes CECT 5344. Several proteins encoded by two ars gene clusters and other Ars-related proteins were up-regulated by arsenite, even during cyanide assimilation. Although some proteins encoded by the cio gene cluster responsible for cyanide-insensitive respiration decreased in the presence of arsenite, the nitrilase NitC required for cyanide assimilation was unaffected, thus allowing bacterial growth with cyanide and arsenic. Two complementary As-resistance mechanisms were developed in this bacterium, the extrusion of As(III) and its extracellular sequestration in biofilm, whose synthesis increased in the presence of arsenite, and the formation of organoarsenicals such as arseno-phosphoglycerate and methyl-As. Tetrahydrofolate metabolism was also stimulated by arsenite. In addition, the ArsH2 protein increased in the presence of arsenite or cyanide, suggesting its role in the protection from oxidative stress caused by both toxics. These results could be useful for the development of bioremediation strategies for industrial wastes co-contaminated with cyanide and arsenic.
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Affiliation(s)
- Karolina A Biełło
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Gema Rodríguez-Caballero
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Lara P Sáez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Víctor M Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
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Kong Z, Wang H, Yan G, Yan Q, Kim JR. Limited dissolved oxygen facilitated nitrogen removal at biocathode during the hydrogenotrophic denitrification process using bioelectrochemical system. BIORESOURCE TECHNOLOGY 2023; 372:128662. [PMID: 36693505 DOI: 10.1016/j.biortech.2023.128662] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Effects of limited dissolved oxygen (DO) on hydrogenotrophic denitrification at biocathode was investigated using bioelectrochemical system. It was found that total nitrogen removal increased by 5.9%, as DO reached about 0.24 mg/L with the cathodic chamber unplugged (group R_Exposure). With the presence of limited DO, not only the nitrogen metabolic pathway was influenced, but the composition of microbial communities of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were enriched accordingly. After metagenomic analysis, enriched genes in R_Exposure were found to be associated with nearly each of nitrogen removal steps as denitrification, nitrification, DNRA, nitrate assimilation and even nitrogen fixation. Moreover, genes encoding both Complexes III and IV constituted the electron transfer chain were significantly enriched, indicating that more electrons would be orientated to the reduction of NO2--N, NO-N and oxygen. Therefore, enhanced nitrogen removal could be attained through the co-respiration of nitrate and oxygen by means of NH4+-N oxidation.
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Affiliation(s)
- Ziang Kong
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Han Wang
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Guoliang Yan
- College of Food Science and Nutritional Engineering, China Agricultural University, 17 East Tsinghua Rd, Beijing 100083, China
| | - Qun Yan
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou 215011, China.
| | - Jung Rae Kim
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea
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Biełło KA, Lucena C, López-Tenllado FJ, Hidalgo-Carrillo J, Rodríguez-Caballero G, Cabello P, Sáez LP, Luque-Almagro V, Roldán MD, Moreno-Vivián C, Olaya-Abril A. Holistic view of biological nitrogen fixation and phosphorus mobilization in Azotobacter chroococcum NCIMB 8003. Front Microbiol 2023; 14:1129721. [PMID: 36846808 PMCID: PMC9945222 DOI: 10.3389/fmicb.2023.1129721] [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: 12/22/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Nitrogen (N) and phosphorus (P) deficiencies are two of the most agronomic problems that cause significant decrease in crop yield and quality. N and P chemical fertilizers are widely used in current agriculture, causing environmental problems and increasing production costs. Therefore, the development of alternative strategies to reduce the use of chemical fertilizers while maintaining N and P inputs are being investigated. Although dinitrogen is an abundant gas in the atmosphere, it requires biological nitrogen fixation (BNF) to be transformed into ammonium, a nitrogen source assimilable by living organisms. This process is bioenergetically expensive and, therefore, highly regulated. Factors like availability of other essential elements, as phosphorus, strongly influence BNF. However, the molecular mechanisms of these interactions are unclear. In this work, a physiological characterization of BNF and phosphorus mobilization (PM) from an insoluble form (Ca3(PO4)2) in Azotobacter chroococcum NCIMB 8003 was carried out. These processes were analyzed by quantitative proteomics in order to detect their molecular requirements and interactions. BNF led to a metabolic change beyond the proteins strictly necessary to carry out the process, including the metabolism related to other elements, like phosphorus. Also, changes in cell mobility, heme group synthesis and oxidative stress responses were observed. This study also revealed two phosphatases that seem to have the main role in PM, an exopolyphosphatase and a non-specific alkaline phosphatase PhoX. When both BNF and PM processes take place simultaneously, the synthesis of nitrogenous bases and L-methionine were also affected. Thus, although the interdependence is still unknown, possible biotechnological applications of these processes should take into account the indicated factors.
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Affiliation(s)
- Karolina A. Biełło
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Carlos Lucena
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Francisco J. López-Tenllado
- Departamento de Química Orgánica, Instituto Universitario de Investigación en Química Fina y Nanoquímica (IUNAN), Universidad de Córdoba, Córdoba, Spain
| | - Jesús Hidalgo-Carrillo
- Departamento de Química Orgánica, Instituto Universitario de Investigación en Química Fina y Nanoquímica (IUNAN), Universidad de Córdoba, Córdoba, Spain
| | - Gema Rodríguez-Caballero
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Lara P. Sáez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Víctor Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain,*Correspondence: Alfonso Olaya-Abril,
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Preparation for Denitrification and Phenotypic Diversification at the Cusp of Anoxia: a Purpose for N 2O Reductase Vis-à-Vis Multiple Roles of O 2. Appl Environ Microbiol 2022; 88:e0105322. [PMID: 36250705 PMCID: PMC9642011 DOI: 10.1128/aem.01053-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adaptation to anoxia by synthesizing a denitrification proteome costs metabolic energy, and the anaerobic respiration conserves less energy per electron than aerobic respiration. This implies a selective advantage of the stringent O2 repression of denitrification gene transcription, which is found in most denitrifying bacteria. In some bacteria, the metabolic burden of adaptation can be minimized further by phenotypic diversification, colloquially termed "bet-hedging," where all cells synthesize the N2O reductase (NosZ) but only a minority synthesize nitrite reductase (NirS), as demonstrated for the model strain Paracoccus denitrificans. We hypothesized that the cells lacking NirS would be entrapped in anoxia but with the possibility of escape if supplied with O2 or N2O. To test this, cells were exposed to gradual O2 depletion or sudden anoxia and subsequent spikes of O2 and N2O. The synthesis of NirS in single cells was monitored by using an mCherry-nirS fusion replacing the native nirS, and their growth was detected as dilution of green, fluorescent fluorescein isothiocyanate (FITC) stain. We demonstrate anoxic entrapment due to e--acceptor deprivation and show that O2 spiking leads to bet-hedging, while N2O spiking promotes NirS synthesis and growth in all cells carrying NosZ. The cells rescued by the N2O spike had much lower respiration rates than those rescued by the O2 spike, however, which could indicate that the well-known autocatalytic synthesis of NirS via NO production requires O2. Our results bring into relief a fitness advantage of pairing restrictive nirS expression with universal NosZ synthesis in energy-limited systems. IMPORTANCE Denitrifying bacteria have evolved elaborate regulatory networks securing their respiratory metabolism in environments with fluctuating oxygen concentrations. Here, we provide new insight regarding their bet-hedging in response to hypoxia, which minimizes their N2O emissions because all cells express NosZ, reducing N2O to N2, while a minority express NirS + Nor, reducing NO2- to N2O. We hypothesized that the cells without Nir were entrapped in anoxia, without energy to synthesize Nir, and that they could be rescued by short spikes of O2 or N2O. We confirm such entrapment and the rescue of all cells by an N2O spike but only a fraction by an O2 spike. The results shed light on the role of O2 repression in bet-hedging and generated a novel hypothesis regarding the autocatalytic nirS expression via NO production. Insight into the regulation of denitrification, including bet-hedging, holds a clue to understanding, and ultimately curbing, the escalating emissions of N2O, which contribute to anthropogenic climate forcing.
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The NtrYX Two-Component System of Paracoccus denitrificans Is Required for the Maintenance of Cellular Iron Homeostasis and for a Complete Denitrification under Iron-Limited Conditions. Int J Mol Sci 2022; 23:ijms23169172. [PMID: 36012437 PMCID: PMC9409073 DOI: 10.3390/ijms23169172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 02/08/2023] Open
Abstract
Denitrification consists of the sequential reduction of nitrate to nitrite, nitric oxide, nitrous oxide, and dinitrogen. Nitrous oxide escapes to the atmosphere, depending on copper availability and other environmental factors. Iron is also a key element because many proteins involved in denitrification contain iron-sulfur or heme centers. The NtrYX two-component regulatory system mediates the responses in a variety of metabolic processes, including denitrification. A quantitative proteomic analysis of a Paracoccus denitrificans NtrY mutant grown under denitrifying conditions revealed the induction of different TonB-dependent siderophore transporters and proteins related to iron homeostasis. This mutant showed lower intracellular iron content than the wild-type strain, and a reduced growth under denitrifying conditions in iron-limited media. Under iron-rich conditions, it releases higher concentrations of siderophores and displayes lower nitrous oxide reductase (NosZ) activity than the wild-type, thus leading to nitrous oxide emission. Bioinformatic and qRT-PCR analyses revealed that NtrYX is a global transcriptional regulatory system that responds to iron starvation and, in turn, controls expression of the iron-responsive regulators fur, rirA, and iscR, the denitrification regulators fnrP and narR, the nitric oxide-responsive regulator nnrS, and a wide set of genes, including the cd1-nitrite reductase NirS, nitrate/nitrite transporters and energy electron transport proteins.
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Kim JY, Cho KS. Inoculation effect of Pseudomonas sp. TF716 on N 2O emissions during rhizoremediation of diesel-contaminated soil. Sci Rep 2022; 12:13018. [PMID: 35906374 PMCID: PMC9338077 DOI: 10.1038/s41598-022-17356-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022] Open
Abstract
The demand for rhizoremediation technology that can minimize greenhouse gas emissions while effectively removing pollutants in order to mitigate climate change has increased. The inoculation effect of N2O-reducing Pseudomonas sp. TF716 on N2O emissions and on remediation performance during the rhizoremediation of diesel-contaminated soil planted with tall fescue (Festuca arundinacea) or maize (Zea mays) was investigated. Pseudomonas sp. TF716 was isolated from the rhizosphere soil of tall fescue. The maximum N2O reduction rate of TF716 was 18.9 mmol N2O g dry cells−1 h−1, which is superior to the rates for previously reported Pseudomonas spp. When Pseudomonas sp. TF716 was added to diesel-contaminated soil planted with tall fescue, the soil N2O-reduction potential was 2.88 times higher than that of soil with no inoculation during the initial period (0–19 d), and 1.08–1.13 times higher thereafter. However, there was no enhancement in the N2O-reduction potential for the soil planted with maize following inoculation with strain TF716. In addition, TF716 inoculation did not significantly affect diesel degradation during rhizoremediation, suggesting that the activity of those microorganisms involved in diesel degradation was unaffected by TF716 treatment. Analysis of the dynamics of the bacterial genera associated with N2O reduction showed that Pseudomonas had the highest relative abundance during the rhizoremediation of diesel-contaminated soil planted with tall fescue and treated with strain TF716. Overall, these results suggest that N2O emissions during the rhizoremediation of diesel-contaminated soil using tall fescue can be reduced with the addition of Pseudomonas sp. TF716.
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Affiliation(s)
- Ji-Yoon Kim
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Kyung-Suk Cho
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea.
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11
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Zhang X, Yu T, Liu C, Fan X, Wu Y, Wang M, Zhao C, Chen Y. Cysteine reduced the inhibition of CO 2 on heterotrophic denitrification: Restoring redox balance, facilitating iron acquisition and carbon metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154173. [PMID: 35240182 DOI: 10.1016/j.scitotenv.2022.154173] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/13/2022] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
The direct effect of CO2 on denitrification has attracted great attention currently. Our previous studies have confirmed that CO2 inhibited heterotrophic denitrification and caused high nitrite accumulation and nitrous oxide emission. Cysteine is a widely reported bio-accelerator; however, its effect on denitrification under CO2 exposure remains unknown. In this paper, the effect of cysteine on heterotrophic denitrification and its mechanisms under CO2 exposure were explored with the model denitrifier, Paracoccus denitrificans. We observed that total nitrogen removal increased from 17.9% to 90.4% as cysteine concentration increased from 0 to 50 μM, probably due to restoration of cell growth and viability. Further study showed that cysteine reduced the inhibition of CO2 on denitrification due to multiple positive influences: (1) regulating glutathione metabolism to eliminate intracellular reactive nitrogen species (RNS), while reducing extracellular polymeric substances (EPS) levels and altering its composition, ultimately restoring cell membrane integrity (2) facilitating the transport and metabolism of carbon sources to increase NADH production, and (3) increasing intracellular iron and up-regulating the expression of key iron transporters genes (AfuA, AfuB, ExbB and TonB) to restore the transport and consumption of electron. This study suggests that cysteine can be added to recover heterotrophic denitrification performance after inhibition by elevated CO2.
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Affiliation(s)
- Xuemeng Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Tong Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Chao Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xinyun Fan
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yang Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Meng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Chunxia Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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12
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Morawska LP, Hernandez-Valdes JA, Kuipers OP. Diversity of bet-hedging strategies in microbial communities-Recent cases and insights. WIREs Mech Dis 2022; 14:e1544. [PMID: 35266649 PMCID: PMC9286555 DOI: 10.1002/wsbm.1544] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 12/12/2022]
Abstract
Microbial communities are continuously exposed to unpredictable changes in their environment. To thrive in such dynamic habitats, microorganisms have developed the ability to readily switch phenotypes, resulting in a number of differently adapted subpopulations expressing various traits. In evolutionary biology, a particular case of phenotypic heterogeneity that evolved in an unpredictably changing environment has been defined as bet‐hedging. Bet‐hedging is a risk‐spreading strategy where isogenic populations stochastically (randomly) diversify their phenotypes, often resulting in maladapted individuals that suffer lower reproductive success. This fitness trade‐off in a specific environment may have a selective advantage upon the sudden environmental shift. Thus, a bet‐hedging strategy allows populations to persist in very dynamic habitats, but with a particular fitness cost. In recent years, numerous examples of phenotypic heterogeneity in different microorganisms have been observed, some suggesting bet‐hedging. Here, we highlight the latest reports concerning bet‐hedging phenomena in various microorganisms to show how versatile this strategy is within the microbial realms. This article is categorized under:Infectious Diseases > Molecular and Cellular Physiology
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Affiliation(s)
- Luiza P Morawska
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
| | - Jhonatan A Hernandez-Valdes
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
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13
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Pérez MD, Olaya-Abril A, Cabello P, Sáez LP, Roldán MD, Moreno-Vivián C, Luque-Almagro VM. Alternative Pathway for 3-Cyanoalanine Assimilation in Pseudomonas pseudoalcaligenes CECT5344 under Noncyanotrophic Conditions. Microbiol Spectr 2021; 9:e0077721. [PMID: 34730416 PMCID: PMC8567248 DOI: 10.1128/spectrum.00777-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/27/2021] [Indexed: 11/20/2022] Open
Abstract
3-Cyanoalanine and cyanohydrins are intermediate nitriles produced in cyanide degradation pathways in plants and bacteria. 3-Cyanoalanine is generated from cyanide by the 3-cyanoalanine synthase, an enzyme mainly characterized in cyanogenic plants. NIT4-type nitrilases use 3-cyanoalanine as a substrate, forming ammonium and aspartate. In some organisms, this enzyme also generates asparagine through an additional nitrile hydratase activity. The alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 assimilates cyanide through an intermediate cyanohydrin, which is further converted into ammonium by the nitrilase NitC. This bacterium also contains three additional nitrilases, including Nit4. In this work, a proteomic analysis of P. pseudoalcaligenes CECT5344 cells grown with 3-cyanoalanine as the sole nitrogen source has revealed the overproduction of different proteins involved in nitrogen metabolism, including the nitrilase NitC. In contrast, the nitrilase Nit4 was not induced by 3-cyanoalanine, and it was only overproduced in cells grown with a cyanide-containing jewelry-manufacturing residue. Phenotypes of single and double mutant strains defective in nit4 or/and nitC revealed the implication of the nitrilase NitC in the assimilation of 3-cyanoalanine and suggest that the 3-cyanoalanine assimilation pathway in P. pseudoalcaligenes CECT5344 depends on the presence or absence of cyanide. When cyanide is present, 3-cyanoalanine is assimilated via Nit4, but in the absence of cyanide, a novel pathway for 3-cyanoalanine assimilation, in which the nitrilase NitC uses the nitrile generated after deamination of the α-amino group from 3-cyanoalanine, is proposed. IMPORTANCE Nitriles are organic cyanides with important industrial applications, but they are also found in nature. 3-Cyanoalanine is synthesized by plants and some bacteria to detoxify cyanide from endogenous or exogenous sources, but this nitrile may be also involved in other processes such as stress tolerance, nitrogen and sulfur metabolism, and signaling. The cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344 grows with 3-cyanoalanine as the sole nitrogen source, but it does not use this nitrile as an intermediate in the cyanide assimilation pathway. In this work, a quantitative proteomic analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to study, for the first time, the response to 3-cyanoalanine at the proteomic level. Proteomic data, together with phenotypes of different nitrilase-defective mutants of P. pseudoalcaligenes CECT5344, provide evidence that in the absence of cyanide, the nitrilase Nit4 is not involved in 3-cyanoalanine assimilation, and instead, the nitrilase NitC participates in a novel alternative 3-cyanoalanine assimilation pathway.
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Affiliation(s)
- María D. Pérez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Lara P. Sáez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - M. Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Víctor M. Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
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14
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Gago JF, Viver T, Urdiain M, Pastor S, Kämpfer P, Robledo PA, Ferreira E, Rosselló-Móra R. Comparative genome analysis of the genus Hydrotalea and proposal of the novel species Hydrotalea lipotrueae sp. nov., isolated from a groundwater aquifer in the south of Mallorca Island, Spain. Syst Appl Microbiol 2021; 44:126277. [PMID: 34788687 DOI: 10.1016/j.syapm.2021.126277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/07/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022]
Abstract
From a collection of > 140 strains isolated from groundwater with thermal anomalies for the purpose of obtaining good candidates with applications in the cosmetic industry, two strains were selected because of their taxonomic novelty. Among the isolates, strains TMF_100T and TFM_099 stood out for their potential biotechnological relevance, and a comparative analysis of 16S rRNA gene sequences indicated that these strains represented a new species of the genus Hydrotalea. In addition, from the public genomic databases, metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) could be retrieved that affiliated with this genus. These MAGs and SAGs had been obtained from different environmental samples, such as acid mine drainage or marine sediments. In addition to the description of the new species, the ecological relevance of the members of this genus was demonstrated by means of denitrification, CRISPR-Cas system diversity and heavy metal resistance, as well as their wide geographical distribution and environmental versatility. Supported by the taxonomic study, together with physiological and morphological differences and ecological features, we concluded that strain TMF_100T represented a novel species within the genus Hydrotalea, for which we propose the name Hydrotalea lipotrueae sp. nov.
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Affiliation(s)
- Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; The Deep Blue Sea Enterprise S.L., Barcelona, Spain.
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | | | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig Universität Giessen, Giessen, Germany
| | - Pedro A Robledo
- Delegation of Geological and Mining Institute of Spain (IGME-CSIC) in Balearic Islands, Palma de Mallorca, Spain
| | | | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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15
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Olaya-Abril A, Hidalgo-Carrillo J, Luque-Almagro VM, Fuentes-Almagro C, Urbano FJ, Moreno-Vivián C, Richardson DJ, Roldán MD. Effect of pH on the denitrification proteome of the soil bacterium Paracoccus denitrificans PD1222. Sci Rep 2021; 11:17276. [PMID: 34446760 PMCID: PMC8390676 DOI: 10.1038/s41598-021-96559-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/23/2021] [Indexed: 11/25/2022] Open
Abstract
Denitrification is a respiratory process by which nitrate is reduced to dinitrogen. Incomplete denitrification results in the emission of the greenhouse gas nitrous oxide and this is potentiated in acidic soils, which display reduced denitrification rates and high N2O/N2 ratios compared to alkaline soils. In this work, impact of pH on the proteome of the soil denitrifying bacterium Paracoccus denitrificans PD1222 was analysed with nitrate as sole energy and nitrogen source under anaerobic conditions at pH ranging from 6.5 to 7.5. Quantitative proteomic analysis revealed that the highest difference in protein representation was observed when the proteome at pH 6.5 was compared to the reference proteome at pH 7.2. However, this difference in the extracellular pH was not enough to produce modification of intracellular pH, which was maintained at 6.5 ± 0.1. The biosynthetic pathways of several cofactors relevant for denitrification and nitrogen assimilation like cobalamin, riboflavin, molybdopterin and nicotinamide were negatively affected at pH 6.5. In addition, peptide representation of reductases involved in nitrate assimilation and denitrification were reduced at pH 6.5. Data highlight the strong negative impact of pH on NosZ synthesis and intracellular copper content, thus impairing active NosZ assembly and, in turn, leading to elevated nitrous oxide emissions.
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Affiliation(s)
- Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Jesús Hidalgo-Carrillo
- Departamento de Química Orgánica, Universidad de Córdoba, Edificio Marie Curie, Campus de Rabanales, 14071, Córdoba, Spain
| | - Víctor M Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Carlos Fuentes-Almagro
- Servicio Central de Apoyo a la Investigación (SCAI), Unidad de Proteómica, Universidad de Córdoba, Campus de Rabanales, 14071, Córdoba, Spain
| | - Francisco J Urbano
- Departamento de Química Orgánica, Universidad de Córdoba, Edificio Marie Curie, Campus de Rabanales, 14071, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain.
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16
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Eltarahony M, Ibrahim A, El-shall H, Ibrahim E, Althobaiti F, Fayad E. Antibacterial, Antifungal and Antibiofilm Activities of Silver Nanoparticles Supported by Crude Bioactive Metabolites of Bionanofactories Isolated from Lake Mariout. Molecules 2021; 26:3027. [PMID: 34069487 PMCID: PMC8161313 DOI: 10.3390/molecules26103027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/24/2022] Open
Abstract
Lake Mariout is one of the polluted coastal marine ecosystems in Egypt which is considered to be a reservoir of serious effluents from different anthropogenic activities. Such selective pressure enforces indigenous microbial populations to acquire new advantageous themes. Thus, in this study, two Streptomyces strains were screened, from Lake Mariout's sediment for bioreduction of 5 mM AgNO3. Both strains were identified molecularly; their biochemical and physiological characterization revealed their ability to secrete bioactive metabolites with antagonistic activity. The cultural and incubation conditions influencing AgNPs productivity were evaluated. Subsequently, the physicochemical properties of the biofabricated AgNPs were pursued. UV-Vis spectroscopy detected surface plasmon resonance at range 458-422 nm. XRD indicated crystalline, pure, face-centered cubic AgNPs; EDX demonstrated strong silver signal at 3.5 keV. Besides, FT-IR and TGA analysis unveiled self-stabilization and functionalization of AgNPs by bioorganic molecules. However, electron microscopy micrographs depicted numerous uniform spherical AgNPs (1.17-13.3 nm). Potent bactericidal and fungicide activity were recorded by zone of inhibition assay at 50 μg/mL. Further, the antibiofilm activity was exerted in a dose-dependent manner. Moreover, the conjugation of AgNPs with the crude bioactive metabolites of both bionanofactories ameliorated the antimicrobial potency, reflecting a synergistic efficiency versus examined pathogens (free-living and biofilm).
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Affiliation(s)
- Marwa Eltarahony
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Alexandria, Egypt; (H.E.-s.); (E.I.)
| | - Amany Ibrahim
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Hadeel El-shall
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Alexandria, Egypt; (H.E.-s.); (E.I.)
| | - Eman Ibrahim
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Alexandria, Egypt; (H.E.-s.); (E.I.)
| | - Fayez Althobaiti
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (F.A.); (E.F.)
| | - Eman Fayad
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (F.A.); (E.F.)
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17
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Gross Ammonification and Nitrification Rates in Soil Amended with Natural and NH4-Enriched Chabazite Zeolite and Nitrification Inhibitor DMPP. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11062605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Using zeolite-rich tuffs for improving soil properties and crop N-use efficiency is becoming popular. However, the mechanistic understanding of their influence on soil N-processes is still poor. This paper aims to shed new light on how natural and NH4+-enriched chabazite zeolites alter short-term N-ammonification and nitrification rates with and without the use of nitrification inhibitor (DMPP). We employed the 15N pool dilution technique to determine short-term gross rates of ammonification and nitrification in a silty-clay soil amended with two typologies of chabazite-rich tuff: (1) at natural state and (2) enriched with NH4+-N from an animal slurry. Archaeal and bacterial amoA, nirS and nosZ genes, N2O-N and CO2-C emissions were also evaluated. The results showed modest short-term effects of chabazite at natural state only on nitrate production rates, which was slightly delayed compared to the unamended soil. On the other hand, the addition of NH4+-enriched chabazite stimulated NH4+-N production, N2O-N emissions, but reduced NO3−-N production and abundance of nirS-nosZ genes. DMPP efficiency in reducing nitrification rates was dependent on N addition but not affected by the two typologies of zeolites tested. The outcomes of this study indicated the good compatibility of both natural and NH4+-enriched chabazite zeolite with DMPP. In particular, the application of NH4+-enriched zeolites with DMPP is recommended to mitigate short-term N losses.
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18
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Puri A, Bajaj A, Lal S, Singh Y, Lal R. Phylogenomic Framework for Taxonomic Delineation of Paracoccus spp. and Exploration of Core-Pan Genome. Indian J Microbiol 2021; 61:180-194. [PMID: 33927459 DOI: 10.1007/s12088-021-00929-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 02/24/2021] [Indexed: 11/26/2022] Open
Abstract
The taxonomic classification of metabolically versatile Paracoccus spp. has been so far performed using polyphasic approach. The topology of single gene phylogenies, however, has highlighted ambiguous species assignments. In the present study, genome based multi-gene phylogenies and overall genome related index were used for species threshold assessment. Comprehensive phylogenomic analysis of Paracoccus genomes (n = 103) showed concordant clustering of strains across multi-gene marker set phylogenies (nMC = 0.08-0.14); as compared to 16S rDNA phylogeny (nMC = 0.37-0.42) suggesting robustness of multi gene phylogenies in drawing phylogenetic inferences. Functional gene content distribution across the genus showed that only 1.7% gene content constitutes the core genome highlighting the significance of extensive genomic variability in the evolution of Paracoccus spp. Further, genome metrics were used to validate characterized strains, identifying classification anomalies (n = 13), and based on this, genome derived taxonomic amendments were notified in present study. Conclusively, validated metric tools can be employed on whole genome sequences, including draft assemblies, for the assessment and assignment of uncharacterized strains and species level ascription of newly isolated Paracoccus strains in future.
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Affiliation(s)
- Akshita Puri
- Department of Zoology, University of Delhi, Delhi, India
- Present Address: P.G.T.D, Zoology, R.T.M Nagpur University, Nagpur, 440033 India
| | - Abhay Bajaj
- Department of Zoology, University of Delhi, Delhi, India
- Present Address: EBGD, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020 India
| | - Sukanya Lal
- Present Address: Ramjas College, University of Delhi, Delhi, India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India
- Present Address: The Energy and Resources Institute Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003 India
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Pascual MB, Sánchez-Monedero MÁ, Cayuela ML, Li S, Haderlein SB, Ruser R, Kappler A. Biochar as electron donor for reduction of N2O by Paracoccus denitrificans. FEMS Microbiol Ecol 2020; 96:fiaa133. [PMID: 32602887 PMCID: PMC7360485 DOI: 10.1093/femsec/fiaa133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/29/2020] [Indexed: 11/13/2022] Open
Abstract
Biochar (BC) has been shown to influence microbial denitrification and mitigate soil N2O emissions. However, it is unclear if BC is able to directly stimulate the microbial reduction of N2O to N2. We hypothesized that the ability of BC to lower N2O emissions could be related not only to its ability to store electrons, but to donate them to bacteria that enzymatically reduce N2O. Therefore, we carried out anoxic incubations with Paracoccus denitrificans, known amounts of N2O, and nine contrasting BCs, in the absence of any other electron donor or acceptor. We found a strong and direct correlation between the extent and rates of N2O reduction with BC's EDC/EEC (electron donating capacity/electron exchange capacity). Apart from the redox capacity, other BC properties were found to regulate the BC's ability to increase N2O reduction by P. denitrificans. For this specific BC series, we found that a high H/C and ash content, low surface area and poor lignin feedstocks favored N2O reduction. This provides valuable information for producing tailored BCs with the potential to assist and promote the reduction of N2O in the pursuit of reducing this greenhouse gas emissions.
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Affiliation(s)
- Mª Blanca Pascual
- Department of Soil and Water Conservation and Waste Management, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo 30100 Murcia, Spain
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Sigwartstrasse 10, 72074 Tübingen, Germany
| | - Miguel Ángel Sánchez-Monedero
- Department of Soil and Water Conservation and Waste Management, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo 30100 Murcia, Spain
| | - María L Cayuela
- Department of Soil and Water Conservation and Waste Management, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo 30100 Murcia, Spain
| | - Shun Li
- Environmental Mineralogy and Chemistry, Center for Applied Geosciences, University of Tübingen, Sigwartstrasse 10, 72074 Tübingen, Germany
| | - Stefan B Haderlein
- Environmental Mineralogy and Chemistry, Center for Applied Geosciences, University of Tübingen, Sigwartstrasse 10, 72074 Tübingen, Germany
| | - Reiner Ruser
- Institute of Crop Science, Department of Fertilization and Soil Matter Dynamics, University of Hohenheim, Fruwirthstraβe 20, 70599 Stuttgart, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Sigwartstrasse 10, 72074 Tübingen, Germany
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20
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Liu Y, Pei T, Zhu H. Paracoccus bengalensis is a later heterotypic synonym of Paracoccus versutu. Int J Syst Evol Microbiol 2020; 70:2049-2052. [PMID: 32038007 DOI: 10.1099/ijsem.0.004014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The present study aimed to examine the taxonomic relationship between two species, Paracoccus bengalensis Ghosh et al. 2006 and Paracoccus versutus (Harrison 1983) Katayama et al. 1996. Comparison of 16S rRNA gene sequences revealed that P. bengalensis JJJT was highly similar (99.9 %) to P. versutus A2T. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Paracoccus. Whole genomic comparison between the two strains showed a digital DNA-DNA hybridization estimate of 82. 0 % and an average nucleotide identity value of 98.2 %, clearly indicating that the two strains were members of the same species. Moreover, the type strains of both species shared similar physiological and biochemical properties and fatty acids profiles. Based on genotypic and phenotypic evidence, we conclude that Paracoccus bengalensis Ghosh et al. 2006 is a later heterotypic synonym of Paracoccus versutus (Harrison 1983) Katayama et al. 1996 according to the priority of publication and validation of the name.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Tao Pei
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
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21
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Olaya-Abril A, Pérez MD, Cabello P, Martignetti D, Sáez LP, Luque-Almagro VM, Moreno-Vivián C, Roldán MD. Role of the Dihydrodipicolinate Synthase DapA1 on Iron Homeostasis During Cyanide Assimilation by the Alkaliphilic Bacterium Pseudomonas pseudoalcaligenes CECT5344. Front Microbiol 2020; 11:28. [PMID: 32038602 PMCID: PMC6989483 DOI: 10.3389/fmicb.2020.00028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/08/2020] [Indexed: 11/13/2022] Open
Abstract
Cyanide is a toxic compound widely used in mining and jewelry industries, as well as in the synthesis of many different chemicals. Cyanide toxicity derives from its high affinity for metals, which causes inhibition of relevant metalloenzymes. However, some cyanide-degrading microorganisms like the alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 may detoxify hazardous industrial wastewaters that contain elevated cyanide and metal concentrations. Considering that iron availability is strongly reduced in the presence of cyanide, mechanisms for iron homeostasis should be required for cyanide biodegradation. Previous omic studies revealed that in the presence of a cyanide-containing jewelry residue the strain CECT5344 overproduced the dihydrodipicolinate synthase DapA1, a protein involved in lysine metabolism that also participates in the synthesis of dipicolinates, which are excellent metal chelators. In this work, a dapA1 - mutant of P. pseudoalcaligenes CECT5344 has been generated and characterized. This mutant showed reduced growth and cyanide consumption in media with the cyanide-containing wastewater. Intracellular levels of metals like iron, copper and zinc were increased in the dapA1 - mutant, especially in cells grown with the jewelry residue. In addition, a differential quantitative proteomic analysis by LC-MS/MS was carried out between the wild-type and the dapA1 - mutant strains in media with jewelry residue. The mutation in the dapA1 gene altered the expression of several proteins related to urea cycle and metabolism of arginine and other amino acids. Additionally, the dapA1 - mutant showed increased levels of the global nitrogen regulator PII and the glutamine synthetase. This proteomic study has also highlighted that the DapA1 protein is relevant for cyanide resistance, oxidative stress and iron homeostasis response, which is mediated by the ferric uptake regulator Fur. DapA1 is required to produce dipicolinates that could act as iron chelators, conferring protection against oxidative stress and allowing the regeneration of Fe-S centers to reactivate cyanide-damaged metalloproteins.
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Affiliation(s)
- Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
| | - María Dolores Pérez
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Diego Martignetti
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
| | - Lara Paloma Sáez
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
| | | | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
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22
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Functional interactions between nitrite reductase and nitric oxide reductase from Paracoccus denitrificans. Sci Rep 2019; 9:17234. [PMID: 31754148 PMCID: PMC6872814 DOI: 10.1038/s41598-019-53553-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/29/2019] [Indexed: 12/25/2022] Open
Abstract
Denitrification is a microbial pathway that constitutes an important part of the nitrogen cycle on earth. Denitrifying organisms use nitrate as a terminal electron acceptor and reduce it stepwise to nitrogen gas, a process that produces the toxic nitric oxide (NO) molecule as an intermediate. In this work, we have investigated the possible functional interaction between the enzyme that produces NO; the cd1 nitrite reductase (cd1NiR) and the enzyme that reduces NO; the c-type nitric oxide reductase (cNOR), from the model soil bacterium P. denitrificans. Such an interaction was observed previously between purified components from P. aeruginosa and could help channeling the NO (directly from the site of formation to the side of reduction), in order to protect the cell from this toxic intermediate. We find that electron donation to cNOR is inhibited in the presence of cd1NiR, presumably because cd1NiR binds cNOR at the same location as the electron donor. We further find that the presence of cNOR influences the dimerization of cd1NiR. Overall, although we find no evidence for a high-affinity, constant interaction between the two enzymes, our data supports transient interactions between cd1NiR and cNOR that influence enzymatic properties of cNOR and oligomerization properties of cd1NiR. We speculate that this could be of particular importance in vivo during metabolic switches between aerobic and denitrifying conditions.
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Hou L, Li J, Zheng Z, Sun Q, Liu Y, Zhang K. Cultivating river sediments into efficient denitrifying sludge for treating municipal wastewater. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190304. [PMID: 31598285 PMCID: PMC6774965 DOI: 10.1098/rsos.190304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
The river sediment contains a lot of pollutants in many cases, and needs to be treated appropriately for the restoration of water environments. In this study, a novel method was developed to convert river sediment into denitrifying sludge in a sequencing batch reactor (SBR). The river sediment was added into the reactor daily and the hydraulic retention time (HRT) of the reactor was gradually reduced from 8 to 4 h. The reactor achieved in the N O 3 - N removal efficiency of 85% with the N O 3 - N removal rate of 0.27 kg N m-3 d-1. Response surface analysis represents that nitrate removal was affected mainly by HRT, followed by sediment addition. The denitrifying sludge achieved the highest activity with the following conditions: N O 3 - N 50 mg l-1, HRT 6 h and adding 6 ml river sediments to 1 l wastewater of reactor per day. As a result, the cultivated denitrifying sludge could remove 80% N O 3 - N for real municipal wastewater, and the high-throughput sequence analysis indicated that major denitrifying bacteria genera and the relative abundance in the cultivated denitrifying sludge were Diaphorobacter (33.82%) and Paracoccus (24.49%). The river sediments cultivating method in this report can not only obtain denitrifying sludge, but also make use of sediment resources, which has great application potential.
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Affiliation(s)
| | - Jun Li
- Author for correspondence: Jun Li e-mail:
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24
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Korth B, Harnisch F. Spotlight on the Energy Harvest of Electroactive Microorganisms: The Impact of the Applied Anode Potential. Front Microbiol 2019; 10:1352. [PMID: 31293531 PMCID: PMC6606774 DOI: 10.3389/fmicb.2019.01352] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/31/2019] [Indexed: 11/13/2022] Open
Abstract
Electroactive microorganisms (EAM) harvest energy by reducing insoluble terminal electron acceptors (TEA) including electrodes via extracellular electron transfer (EET). Therefore, compared to microorganisms respiring soluble TEA, an adapted approach is required for thermodynamic analyses. In EAM, the thermodynamic frame (i.e., maximum available energy) is restricted as only a share of the energy difference between electron donor and TEA is exploited via the electron-transport chain to generate proton-motive force being subsequently utilized for ATP synthesis. However, according to a common misconception, the anode potential is suggested to co-determine the thermodynamic frame of EAM. By comparing the model organism Geobacter spp. and microorganisms respiring soluble TEA, we reason that a considerable part of the electron-transport chain of EAM performing direct EET does not contribute to the build-up of proton-motive force and thus, the anode potential does not co-determine the thermodynamic frame. Furthermore, using a modeling platform demonstrates that the influence of anode potential on energy harvest is solely a kinetic effect. When facing low anode potentials, NADH is accumulating due to a slow direct EET rate leading to a restricted exploitation of the thermodynamic frame. For anode potentials ≥ 0.2 V (vs. SHE), EET kinetics, NAD+/NADH ratio as well as exploitation of the thermodynamic frame are maximized, and a further potential increase does not result in higher energy harvest. Considering the limited influence of the anode potential on energy harvest of EAM is a prerequisite to improve thermodynamic analyses, microbial resource mining, and to transfer microbial electrochemical technologies (MET) into practice.
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Affiliation(s)
- Benjamin Korth
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Falk Harnisch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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25
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Thakur IS, Medhi K. Nitrification and denitrification processes for mitigation of nitrous oxide from waste water treatment plants for biovalorization: Challenges and opportunities. BIORESOURCE TECHNOLOGY 2019; 282:502-513. [PMID: 30898409 DOI: 10.1016/j.biortech.2019.03.069] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas. Even though its emissions is much lesser than CO2 but its global warming potential (GWP) is 298 times more than CO2. N2O emissions from wastewater treatment plants was caused due to incomplete nitrification or incomplete denitrification catalyzed by ammonia-oxidizing bacteria and heterotrophic denitrifiers. Low dissolved oxygen, high nitrite accumulation, change in optimal pH or temperature, fluctuation in C/N ratio, short solid retention time and non-availability of Cu ions were responsible for higher N2O leakage. Regulation of enzyme metabolic pathways involved in N2O production and reduction has also been reviewed. Sequential bioreactors, bioscrubbers, membrane biofilters usage have helped microbial nitrification-denitrification processes in succumbing N2O production in wastewater treatment plants. Reduction of N2O negativity has been studied through its valorization for the formation of value added products such as biopolymers has led to biorefinery approaches as an upcoming mitigation strategy.
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Affiliation(s)
- Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Kristina Medhi
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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26
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Otwell AE, López García de Lomana A, Gibbons SM, Orellana MV, Baliga NS. Systems biology approaches towards predictive microbial ecology. Environ Microbiol 2018; 20:4197-4209. [DOI: 10.1111/1462-2920.14378] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 01/17/2023]
Affiliation(s)
| | | | - Sean M. Gibbons
- Institute for Systems Biology Seattle WA USA
- eScience Institute, University of Washington Seattle WA USA
- Molecular and Cellular Biology Program University of Washington Seattle WA USA
| | - Mónica V. Orellana
- Institute for Systems Biology Seattle WA USA
- Polar Science Center Applied Physics Lab, University of Washington Seattle WA
| | - Nitin S. Baliga
- Institute for Systems Biology Seattle WA USA
- Molecular and Cellular Biology Program University of Washington Seattle WA USA
- Departments of Biology and Microbiology University of Washington Seattle WA USA
- Lawrence Berkeley National Lab Berkeley CA USA
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