1
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Bataeva Y, Delegan Y, Bogun A, Shishkina L, Grigoryan L. Whole Genome Analysis and Assessment of the Metabolic Potential of Streptomyces carpaticus SCPM-O-B-9993, a Promising Phytostimulant and Antiviral Agent. BIOLOGY 2024; 13:388. [PMID: 38927268 PMCID: PMC11200584 DOI: 10.3390/biology13060388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024]
Abstract
This work aimed to study the genome organization and the metabolic potential of Streptomyces carpaticus strain SCPM-O-B-9993, a promising plant-protecting and plant-stimulating strain isolated from brown semi-desert soils with very high salinity. The strain genome contains a linear chromosome 5,968,715 bp long and has no plasmids. The genome contains 5331 coding sequences among which 2139 (40.1%) are functionally annotated. Biosynthetic gene clusters (BGCs) of secondary metabolites exhibiting antimicrobial properties (ohmyungsamycin, pellasoren, naringenin, and ansamycin) were identified in the genome. The most efficient period of SCPM-O-B-9993 strain cultivation was 72 h: during this period, the culture went from the exponential to the stationary growth phase as well as exhibited excellent phytostimulatory properties and antiviral activity against the cucumber mosaic virus in tomatoes under laboratory conditions. The Streptomyces carpaticus SCPM-OB-9993 strain is a biotechnologically promising producer of secondary metabolites exhibiting antiviral and phytostimulatory properties.
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Affiliation(s)
- Yulia Bataeva
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia;
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Russia; (Y.D.); (A.B.)
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Russia; (Y.D.); (A.B.)
| | - Lidiya Shishkina
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia;
| | - Lilit Grigoryan
- Department of Biology, Tatishchev Astrakhan State University, 414056 Astrakhan, Russia;
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2
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Ruan Z, Xu M, Xing Y, Jiang Q, Yang B, Jiang J, Xu X. Interspecies Metabolic Interactions in a Synergistic Consortium Drive Efficient Degradation of the Herbicide Bromoxynil Octanoate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11613-11622. [PMID: 36089742 DOI: 10.1021/acs.jafc.2c03057] [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] [Indexed: 06/15/2023]
Abstract
Microbial communities play vital roles in biogeochemical cycles, allowing biodegradation of a wide range of pollutants. Although many studies have shown the importance of interspecies interactions on activities of communities, fully elucidating the complex interactions in microbial communities is still challenging. Here, we isolated a consortium containing two bacterial strains (Acinetobacter sp. AG3 and Bacillus sp. R45), which could mineralize bromoxynil octanoate (BO) with higher efficiency than either strain individually. The BO degradation pathway by the synergistic consortium was elucidated, and interspecies interactions in the consortium were explored using genome-scale metabolic models (GSMMs). Modeling showed that growth and degradation enhancements were driven by metabolic interactions, such as syntrophic exchanges of small metabolites in the consortium. Besides, nutritional enhancers were predicted to improve BO degradation, which were tested experimentally. Overall, our results will enhance our understanding of microbial mineralization of BO by consortia and promote the application of microbial communities for bioremediation.
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Affiliation(s)
- Zhepu Ruan
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Mengjun Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Youwen Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Qi Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Bingang Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
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Vaishnav A, Kumar R, Singh HB, Sarma BK. Extending the benefits of PGPR to bioremediation of nitrile pollution in crop lands for enhancing crop productivity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154170. [PMID: 35227717 DOI: 10.1016/j.scitotenv.2022.154170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/06/2022] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Incessant release of nitrile group of compounds such as cyanides into agricultural land through industrial effluents and excessive use of nitrile pesticides has resulted in increased nitrile pollution. Release of nitrile compounds (NCs) as plant root exudates is also contributing to the problem. The released NCs interact with soil elements and persists for a long time. Persistent higher concentration of NCs in soil cause toxicity to beneficial microflora and affect crop productivity. The NCs can cause more problems to human health if they reach groundwater and enter the food chain. Nitrile degradation by soil bacteria can be a solution to the problem if thoroughly exploited. However, the impact of such bacteria in plant and soil environments is still not properly explored. Plant growth-promoting rhizobacteria (PGPR) with nitrilase activity has recently gained attention as potential solution to address the problem. This paper reviews the core issue of nitrile pollution in soil and the prospects of application of nitrile degrading bacteria for soil remediation, soil health improvement and plant growth promotion in nitrile-polluted soils. The possible mechanisms of PGPR that can be exploited to degrade NCs, converting them into plant useful compounds and synthesis of the phytohormone IAA from degraded NCs are also discussed at length.
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Affiliation(s)
- Anukool Vaishnav
- Department of Biotechnology, GLA University, Mathura 281406, India; Agroecology and Environment, Agroscope (Reckenholz), Zürich 8046, Switzerland
| | - Roshan Kumar
- National Centre for Biological Sciences (TIFR-NCBS), Bengaluru 560065, India
| | | | - Birinchi Kumar Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221110, India.
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Sun S, Zhou J, Jiang J, Dai Y, Sheng M. Nitrile Hydratases: From Industrial Application to Acetamiprid and Thiacloprid Degradation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10440-10449. [PMID: 34469128 DOI: 10.1021/acs.jafc.1c03496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The widespread application of neonicotinoid insecticides (NEOs) in agriculture causes a series of environmental and ecological problems. Microbial remediation is a popular approach to relieve these negative impacts, but the associated molecular mechanisms are rarely explored. Nitrile hydratase (NHase), an enzyme commonly used in industry for amide production, was discovered to be responsible for the degradation of acetamiprid (ACE) and thiacloprid (THI) by microbes. Since then, research into NHases in NEO degradation has attracted increasing attention. In this review, microbial degradation of ACE and THI is briefly described. We then focus on NHase evolution, gene composition, maturation mechanisms, expression, and biochemical properties with regard to application of NHases in NEO degradation for bioremediation.
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Affiliation(s)
- Shilei Sun
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jiangsheng Zhou
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Yijun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Miaomiao Sheng
- College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou 310053, People's Republic of China
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Knossow N, Siebner H, Bernstein A. Isotope Fractionation (δ 13C, δ 15N) in the Microbial Degradation of Bromoxynil by Aerobic and Anaerobic Soil Enrichment Cultures. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:1546-1554. [PMID: 31986047 DOI: 10.1021/acs.jafc.9b07653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bromoxynil is an increasingly applied nitrile herbicide. Under aerobic conditions, hydration, nitrilation, or hydroxylation of the nitrile group commonly occurs, whereas under anaerobic conditions reductive dehalogenation is common. This work studied the isotope effects associated with these processes by soil cultures. The aerobic soil enrichment culture presented a significant increase in Stenotrophomonas, Pseudomonas, Chryseobacterium, Achromobacter, Azospirillum, and Arcticibacter, and degradation products indicated that nitrile hydratase was the dominant degradation route. The anaerobic culture was dominated by Proteobacteria and Firmicutes phyla with a significant increase in Dethiosulfatibacter, and degradation products indicated reductive debromination as a major degradation route. Distinct dual-isotope trends (δ13C, δ15N) were determined for the two routes: a strong inverse nitrogen isotope effect (εN = 10.56 ± 0.36‰) and an insignificant carbon isotope effect (εC = 0.37 ± 0.36‰) for the aerobic process versus a negligible effect for both elements in the anaerobic process. These trends differ from formerly reported trends for the photodegradation of bromoxynil and enable one to distinguish between the processes in the field.
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Affiliation(s)
- Nadav Knossow
- Zuckerberg Institute for Water Research, Department of Environmental Hydrology and Microbiology , Ben-Gurion University of the Negev , Sede Boqer Campus , Sede Boqer 8499000 , Israel
| | - Hagar Siebner
- Zuckerberg Institute for Water Research, Department of Environmental Hydrology and Microbiology , Ben-Gurion University of the Negev , Sede Boqer Campus , Sede Boqer 8499000 , Israel
| | - Anat Bernstein
- Zuckerberg Institute for Water Research, Department of Environmental Hydrology and Microbiology , Ben-Gurion University of the Negev , Sede Boqer Campus , Sede Boqer 8499000 , Israel
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6
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Mashweu AR, Chhiba-Govindjee VP, Bode ML, Brady D. Substrate Profiling of the Cobalt Nitrile Hydratase from Rhodococcus rhodochrous ATCC BAA 870. Molecules 2020; 25:molecules25010238. [PMID: 31935987 PMCID: PMC6983157 DOI: 10.3390/molecules25010238] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/22/2019] [Accepted: 12/26/2019] [Indexed: 02/04/2023] Open
Abstract
The aromatic substrate profile of the cobalt nitrile hydratase from Rhodococcus rhodochrous ATCC BAA 870 was evaluated against a wide range of nitrile containing compounds (>60). To determine the substrate limits of this enzyme, compounds ranging in size from small (90 Da) to large (325 Da) were evaluated. Larger compounds included those with a bi-aryl axis, prepared by the Suzuki coupling reaction, Morita-Baylis-Hillman adducts, heteroatom-linked diarylpyridines prepared by Buchwald-Hartwig cross-coupling reactions and imidazo[1,2-a]pyridines prepared by the Groebke-Blackburn-Bienaymé multicomponent reaction. The enzyme active site was moderately accommodating, accepting almost all of the small aromatic nitriles, the diarylpyridines and most of the bi-aryl compounds and Morita-Baylis-Hillman products but not the Groebke-Blackburn-Bienaymé products. Nitrile conversion was influenced by steric hindrance around the cyano group, the presence of electron donating groups (e.g., methoxy) on the aromatic ring, and the overall size of the compound.
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Affiliation(s)
- Adelaide R. Mashweu
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa; (A.R.M.); (V.P.C.-G.)
| | - Varsha P. Chhiba-Govindjee
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa; (A.R.M.); (V.P.C.-G.)
- CSIR Chemical Production Cluster, PO Box 395, Pretoria 0001, South Africa
| | - Moira L. Bode
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa; (A.R.M.); (V.P.C.-G.)
- Correspondence: (M.L.B.); (D.B.); Tel.: +27-117176745 (D.B.)
| | - Dean Brady
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa; (A.R.M.); (V.P.C.-G.)
- Correspondence: (M.L.B.); (D.B.); Tel.: +27-117176745 (D.B.)
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7
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Anteneh YS, Franco CMM. Whole Cell Actinobacteria as Biocatalysts. Front Microbiol 2019; 10:77. [PMID: 30833932 PMCID: PMC6387938 DOI: 10.3389/fmicb.2019.00077] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/15/2019] [Indexed: 12/25/2022] Open
Abstract
Production of fuels, therapeutic drugs, chemicals, and biomaterials using sustainable biological processes have received renewed attention due to increasing environmental concerns. Despite having high industrial output, most of the current chemical processes are associated with environmentally undesirable by-products which escalate the cost of downstream processing. Compared to chemical processes, whole cell biocatalysts offer several advantages including high selectivity, catalytic efficiency, milder operational conditions and low impact on the environment, making this approach the current choice for synthesis and manufacturing of different industrial products. In this review, we present the application of whole cell actinobacteria for the synthesis of biologically active compounds, biofuel production and conversion of harmful compounds to less toxic by-products. Actinobacteria alone are responsible for the production of nearly half of the documented biologically active metabolites and many enzymes; with the involvement of various species of whole cell actinobacteria such as Rhodococcus, Streptomyces, Nocardia and Corynebacterium for the production of useful industrial commodities.
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Affiliation(s)
- Yitayal Shiferaw Anteneh
- College of Medicine and Public Health, Medical Biotechnology, Flinders University, Bedford Park, SA, Australia
- Department of Medical Microbiology, College of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
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8
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Yu H, Jiao S, Wang M, Liang Y, Tang L. Biodegradation of Nitriles by Rhodococcus. BIOLOGY OF RHODOCOCCUS 2019. [DOI: 10.1007/978-3-030-11461-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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9
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Achermann S, Falås P, Joss A, Mansfeldt CB, Men Y, Vogler B, Fenner K. Trends in Micropollutant Biotransformation along a Solids Retention Time Gradient. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:11601-11611. [PMID: 30208701 DOI: 10.1021/acs.est.8b02763] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
For many polar organic micropollutants, biotransformation by activated sludge microorganisms is a major removal process during wastewater treatment. However, our current understanding of how wastewater treatment operations influence microbial communities and their micropollutant biotransformation potential is limited, leaving major parts of observed variability in biotransformation rates across treatment facilities unexplained. Here, we present biotransformation rate constants for 42 micropollutants belonging to different chemical classes along a gradient of solids retention time (SRT). The geometric mean of biomass-normalized first-order rate constants shows a clear increase between 3 and 15 d SRT by 160% and 87%, respectively, in two experiments. However, individual micropollutants show a variety of trends. Rate constants of oxidative biotransformation reactions mostly increased with SRT. Yet, nitrifying activity could be excluded as primary driver. For substances undergoing other than oxidative reactions, i.e., mostly substitution-type reactions, more diverse dependencies on SRT were observed. Most remarkably, characteristic trends were observed for groups of substances undergoing similar types of initial transformation reaction, suggesting that shared enzymes or enzyme systems that are conjointly regulated catalyze biotransformation reactions within such groups. These findings open up opportunities for correlating rate constants with measures of enzyme abundance such as genes or gene products, which in turn should help to identify enzymes associated with the respective biotransformation reactions.
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Affiliation(s)
- Stefan Achermann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf , Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich , 8092 Zürich , Switzerland
| | - Per Falås
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf , Switzerland
- Department of Chemical Engineering , Lund University , 221 00 Lund , Sweden
| | - Adriano Joss
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf , Switzerland
| | - Cresten B Mansfeldt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf , Switzerland
| | - Yujie Men
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf , Switzerland
- Department of Civil and Environmental Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Bernadette Vogler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf , Switzerland
| | - Kathrin Fenner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf , Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich , 8092 Zürich , Switzerland
- Department of Chemistry , University of Zürich , 8057 Zürich , Switzerland
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10
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Oliveira KO, Silva AR, da Silva BF, Milagre HM, Milagre CD. Insights into the microbial degradation pathways of the ioxynil octanoate herbicide. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Efficient biodegradation of dihalogenated benzonitrile herbicides by recombinant Escherichia coli harboring nitrile hydratase-amidase pathway. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.05.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Groundwater contamination with 2,6-dichlorobenzamide (BAM) and perspectives for its microbial removal. Appl Microbiol Biotechnol 2017; 101:5235-5245. [PMID: 28616645 DOI: 10.1007/s00253-017-8362-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/23/2017] [Accepted: 05/25/2017] [Indexed: 01/26/2023]
Abstract
The pesticide metabolite 2,6-dichlorobenzamide (BAM) is very persistent in both soil and groundwater and has become one of the most frequently detected groundwater micropollutants. BAM is not removed by the physico-chemical treatment techniques currently used in drinking water treatment plants (DWTP); therefore, if concentrations exceed the legal threshold limit, it represents a sizeable problem for the stability and quality of drinking water production, especially in places that depend on groundwater for drinking water. Bioremediation is suggested as a valuable strategy for removing BAM from groundwater by deploying dedicated BAM-degrading bacteria in DWTP sand filters. Only a few bacterial strains with the capability to degrade BAM have been isolated, and of these, only three isolates belonging to the Aminobacter genus are able to mineralise BAM. Considerable effort has been made to elucidate degradation pathways, kinetics and degrader genes, and research has recently been presented on the application of strain Aminobacter sp. MSH1 for the purification of BAM-contaminated water. The aim of the present review was to provide insight into the issue of BAM contamination and to report on the current status and knowledge with regard to the application of microorganisms for purification of BAM-contaminated water resources. This paper discusses the prospects and challenges for bioaugmentation of DWTP sand filters with specific BAM-degrading bacteria and identifies relevant perspectives for future research.
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Guo FM, Wu JP, Yang LR, Xu G. Soluble and functional expression of a recombinant enantioselective amidase from Klebsiella oxytoca KCTC 1686 in Escherichia coli and its biochemical characterization. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Fang S, An X, Liu H, Cheng Y, Hou N, Feng L, Huang X, Li C. Enzymatic degradation of aliphatic nitriles by Rhodococcus rhodochrous BX2, a versatile nitrile-degrading bacterium. BIORESOURCE TECHNOLOGY 2015; 185:28-34. [PMID: 25746475 DOI: 10.1016/j.biortech.2015.02.078] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/18/2015] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
Nitriles are common environmental pollutants, and their removal has attracted increasing attention. Microbial degradation is considered to be the most acceptable method for removal. In this work, we investigated the biodegradation of three aliphatic nitriles (acetonitrile, acrylonitrile and crotononitrile) by Rhodococcus rhodochrous BX2 and the expression of their corresponding metabolic enzymes. This organism can utilize all three aliphatic nitriles as sole carbon and nitrogen sources, resulting in the complete degradation of these compounds. The degradation kinetics were described using a first-order model. The degradation efficiency was ranked according to t1/2 as follows: acetonitrile>trans-crotononitrile>acrylonitrile>cis-crotononitrile. Only ammonia accumulated following the three nitriles degradation, while amides and carboxylic acids were transient and disappeared by the end of the assay. mRNA expression and enzyme activity indicated that the tested aliphatic nitriles were degraded via both the inducible NHase/amidase and the constitutive nitrilase pathways, with the former most likely preferred.
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Affiliation(s)
- Shumei Fang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China; College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 16339, Heilongjiang, PR China
| | - Xuejiao An
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Hongyuan Liu
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Yi Cheng
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Ning Hou
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Lu Feng
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Xinning Huang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Chunyan Li
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
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15
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Angelini LML, da Silva ARM, Rocco LDFC, Milagre CDDF. A high-throughput screening assay for distinguishing nitrile hydratases from nitrilases. Braz J Microbiol 2015. [PMID: 26221095 PMCID: PMC4512080 DOI: 10.1590/s1517-838246120130851] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A modified colorimetric high-throughput screen based on pH changes combined with an amidase inhibitor capable of distinguishing between nitrilases and nitrile hydratases. This enzymatic screening is based on a binary response and is suitable for the first step of hierarchical screening projects.
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Affiliation(s)
- Leticia Mara Lima Angelini
- Instituto de of Biociências, Universidade Estadual Paulista "Julio de Mesquita Filho", Rio Claro, SP, Brazil
| | | | - Lucas de Freitas Coli Rocco
- Instituto de of Biociências, Universidade Estadual Paulista "Julio de Mesquita Filho", Rio Claro, SP, Brazil
| | - Cintia Duarte de Freitas Milagre
- Departamento de Química Orgânia, Instituto de Química, Universidade Estadual Paulista "Julio de Mesquita Filho", Araraquara, SP, Brazil
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16
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Alcolea Palafox M, Bhat D, Goyal Y, Ahmad S, Hubert Joe I, Rastogi VK. FT-IR and FT-Raman spectra, MEP and HOMO-LUMO of 2,5-dichlorobenzonitrile: DFT study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:464-472. [PMID: 25448947 DOI: 10.1016/j.saa.2014.09.058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/11/2014] [Accepted: 09/18/2014] [Indexed: 06/04/2023]
Abstract
The experimental FT-IR and FT-Raman spectra of 2,5-dichlorobenzonitrile molecule were recorded at room temperature, and the results compared with quantum chemical theoretical values using MP2 and DFT methods. Molecular geometry, vibrational wavenumbers and thermodynamic parameters were calculated. With the help of specific scaling procedures for the computed wavenumbers, the experimentally observed FTIR and FT-Raman bands were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range and the error obtained was in general very low. Several general conclusions were deduced. The NBO analysis has been done and Molecular Electrostatic Potential (MEP) has been plotted.
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Affiliation(s)
- M Alcolea Palafox
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Madrid 28040, Spain.
| | - Daisy Bhat
- R.D. Foundation Group of Institutions, NH-58, Kadrabad, Modinagar (Ghaziabad), India
| | - Yasha Goyal
- R.D. Foundation Group of Institutions, NH-58, Kadrabad, Modinagar (Ghaziabad), India
| | - Shabbir Ahmad
- Department of Physics, Aligarh Muslim University, Aligarh, India
| | - I Hubert Joe
- Department of Physics, Mar Ivanios College, Thiruvananthapuram 6959 015, Kerala, India
| | - V K Rastogi
- R.D. Foundation Group of Institutions, NH-58, Kadrabad, Modinagar (Ghaziabad), India; Indian Spectroscopy Society, KC 68/1, Old Kavinagar, Ghaziabad 201 002, India.
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17
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Royston KJ, Tollefsbol TO. The Epigenetic Impact of Cruciferous Vegetables on Cancer Prevention. CURRENT PHARMACOLOGY REPORTS 2015; 1:46-51. [PMID: 25774338 PMCID: PMC4354933 DOI: 10.1007/s40495-014-0003-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The answer to chemoprevention has perhaps been available to the general public since the dawn of time. The epigenetic diet is of extreme interest, for research suggests that cruciferous vegetables are not only an important source of nutrients, but perhaps a key to eliminating cancer as life threatening disease. Cruciferous vegetables such as kale, cabbage, Brussels sprouts, and broccoli sprouts contain chemical components, such as sulforaphane (SFN) and indole-3-carbinol (I3C), which have been revealed to be regulators of microRNAs (miRNAs) and inhibitors of histone deacetylases (HDACs) and DNA methyltransferases (DNMTs). The mis-regulation and overexpression of these genes are responsible for the uncontrolled cellular proliferation and viability of various types of cancer cells. The field of epigenetics and its incorporation into modern medicinal investigation is an exponentially growing field of interest and it is becoming increasingly apparent that the incorporation of an epigenetic diet may in fact be the key to chemoprevention.
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Affiliation(s)
- Kendra J. Royston
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA
| | - Trygve O. Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA
- Comprehensive Center for Healthy Aging, University of Alabama Birmingham, 1530 3 Avenue South, Birmingham, AL 35294, USA
- Comprehensive Cancer Center, University of Alabama Birmingham, 1802 6 Avenue South, Birmingham, AL 35294, USA
- Nutrition Obesity Research Center, University of Alabama Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA
- Comprehensive Diabetes Center, University of Alabama Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
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18
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Pasquarelli F, Spera A, Cantarella L, Cantarella M. Biodegradation of bromoxynil using the cascade enzymatic system nitrile hydratase/amidase from Microbacterium imperiale CBS 498-74. Comparison between free enzymes and resting cells. RSC Adv 2015. [DOI: 10.1039/c5ra01438g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This work investigates the biodegradation of bromoxynil to the corresponding acid to reduce its acute toxicity.
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Affiliation(s)
- Fabrizia Pasquarelli
- Department of Industrial and Information Engineering and Economics
- University of L'Aquila
- 67100 L'Aquila
- Italy
| | - Agata Spera
- Department of Industrial and Information Engineering and Economics
- University of L'Aquila
- 67100 L'Aquila
- Italy
| | - Laura Cantarella
- Department of Civil and Mechanical Engineering
- University of Cassino and Southern Lazio
- 03043 Cassino
- Italy
| | - Maria Cantarella
- Department of Industrial and Information Engineering and Economics
- University of L'Aquila
- 67100 L'Aquila
- Italy
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19
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Expression control of nitrile hydratase and amidase genes in Rhodococcus erythropolis and substrate specificities of the enzymes. Antonie Van Leeuwenhoek 2014; 105:1179-90. [DOI: 10.1007/s10482-014-0179-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 04/16/2014] [Indexed: 10/25/2022]
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20
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Pukkila V, Kontro MH. Dichlobenil and 2,6-dichlorobenzamide (BAM) dissipation in topsoil and deposits from groundwater environment within the boreal region in southern Finland. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:2289-2297. [PMID: 24057965 DOI: 10.1007/s11356-013-2164-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 09/11/2013] [Indexed: 05/12/2023]
Abstract
BAM (2,6-dichlorobenzamide) is a metabolite of pesticide dichlobenil and a common groundwater contaminant. Dichlobenil and BAM half-lives were determined in five Finnish subsurface deposits and in topsoil. Aerobic and anaerobic conditions with sterilized controls were included in this 1.4-year incubation experiment. In subsurface deposits, dichlobenil half-life varied from 157 days to no degradation and that of BAM from 314 days to no degradation. Microbes and oxygen enhanced dichlobenil and BAM dissipation rates in some deposits. However, dichlobenil and BAM concentrations were most significantly affected by deposit characteristics, especially carbon and nitrogen amounts. Also low pH, cadmium, iron, zinc, manganese and lead correlated with low dichlobenil and/or BAM concentrations. In mineral topsoil, dissipation was faster with half-lives of 41-54 days for dichlobenil, and 182-261 days for BAM. Dichlobenil was depleted completely in surface soil, but BAM was not dissipated below 55-81 % of the initial concentration. Generally, dichlobenil and BAM dissipation in samples from the northern boreal region was similar to that reported for the temperate region. BAM was persistent in topsoil and subsurface deposits, indicating long-term persistence problems in groundwater also within the northern boreal region.
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Affiliation(s)
- Veera Pukkila
- Department of Environmental Sciences, University of Helsinki, Niemenkatu 73, 15140, Lahti, Finland.
| | - Merja H Kontro
- Department of Environmental Sciences, University of Helsinki, Niemenkatu 73, 15140, Lahti, Finland
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21
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Neumann J, Pawlik M, Bryniok D, Thöming J, Stolte S. Biodegradation potential of cyano-based ionic liquid anions in a culture of Cupriavidus spp. and their in vitro enzymatic hydrolysis by nitrile hydratase. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 21:9495-505. [PMID: 24338070 PMCID: PMC4133019 DOI: 10.1007/s11356-013-2341-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 11/04/2013] [Indexed: 05/25/2023]
Abstract
Biodegradation tests with bacteria from activated sludge revealed the probable persistence of cyano-based ionic liquid anions when these leave waste water treatment plants. A possible biological treatment using bacteria capable of biodegrading similar compounds, namely cyanide and cyano-complexes, was therefore examined. With these bacteria from the genera Cupriavidus, the ionic liquid anions B(CN)₄(-), C(CN)₃(-), N(CN)₂(-) combined with alkaline cations were tested in different growth media using ion chromatography for the examination of their primary biodegradability. However, no enhanced biodegradability of the tested cyano-based ionic liquids was observed. Therefore, an in vitro enzymatic hydrolysis test was additionally run showing that all tested ionic liquid (IL) anions can be hydrolysed to their corresponding amides by nitrile hydratase, but not by nitrilase under the experimental conditions. The biological stability of the cyano-based anions is an advantage in technological application, but the occurrence of enzymes that are able to hydrolyse the parent compound gives a new perspective on future cyano-based IL anion treatment.
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Affiliation(s)
- Jennifer Neumann
- Department 3 Sustainable Chemistry, UFT - Centre for Environmental Research and Sustainable Technology, University of Bremen, Leobener Straße, 28359 Bremen, Germany
| | - Magdalena Pawlik
- Polish AGH University of Science and Technology, A. Mickiewicza 30 Ave. 30-059, Kraków, Poland
| | - Dieter Bryniok
- Department of Environmental Biotechnology and Bioprocess Engineering, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Nobelstraße 12, 70569 Stuttgart, Germany
| | - Jorg Thöming
- Department 4 Chemical Engineering - Recovery and Recycling, UFT - Centre for Environmental Research and Sustainable Technology, University of Bremen, Leobener Straße, 28359 Bremen, Germany
| | - Stefan Stolte
- Department 3 Sustainable Chemistry, UFT - Centre for Environmental Research and Sustainable Technology, University of Bremen, Leobener Straße, 28359 Bremen, Germany
- Department of Environmental Analysis, University of Gdańsk, ul. Sobieskiego 18/19, 80-952 Gdańsk, Poland
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22
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Kolvenbach BA, Helbling DE, Kohler HPE, Corvini PFX. Emerging chemicals and the evolution of biodegradation capacities and pathways in bacteria. Curr Opin Biotechnol 2013; 27:8-14. [PMID: 24863891 DOI: 10.1016/j.copbio.2013.08.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/12/2013] [Accepted: 08/26/2013] [Indexed: 11/24/2022]
Abstract
The number of new chemicals produced is increasing daily by the thousands, and it is inevitable that many of these chemicals will reach the environment. Current research provides an understanding of how the evolution of promiscuous enzymes and the recruitment of enzymes available from the metagenome allows for the assembly of these pathways. Nevertheless, physicochemical constraints including bioavailability, bioaccessibility, and the structural variations of similar chemicals limit the evolution of biodegradation pathways. Similarly, physiological constraints related to kinetics and substrate utilization at low concentrations likewise limit chemical-enzyme interactions and consequently evolution. Considering these new data, the biodegradation decalogue still proves valid while at the same time the underlying mechanisms are better understood.
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Affiliation(s)
- Boris A Kolvenbach
- University of Applied Sciences and Arts Northwestern Switzerland, School for Life Sciences, Institute for Ecopreneurship, Gruendenstrasse 40, Muttenz 4132, Switzerland
| | - Damian E Helbling
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Environmental Microbiology, Ueberlandstrasse 133, P.O. Box 611, Duebendorf 8600, Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Environmental Microbiology, Ueberlandstrasse 133, P.O. Box 611, Duebendorf 8600, Switzerland
| | - Philippe F-X Corvini
- University of Applied Sciences and Arts Northwestern Switzerland, School for Life Sciences, Institute for Ecopreneurship, Gruendenstrasse 40, Muttenz 4132, Switzerland; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University Xianlin Campus, Xianlin Avenue 163, Nanjing 210023, China.
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23
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Kaplan O, Veselá AB, Petříčková A, Pasquarelli F, Pičmanová M, Rinágelová A, Bhalla TC, Pátek M, Martínková L. A Comparative Study of Nitrilases Identified by Genome Mining. Mol Biotechnol 2013; 54:996-1003. [DOI: 10.1007/s12033-013-9656-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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