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El Ayari T, Bouhdida R, Ouzari HI, El Menif NT. Bioremediation of petroleum refinery wastewater by fungal stains isolated from the fishing harbour of Bizerte (Mediterranean Sea). Biodegradation 2024; 35:755-767. [PMID: 38687419 DOI: 10.1007/s10532-024-10083-4] [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: 02/27/2024] [Accepted: 04/13/2024] [Indexed: 05/02/2024]
Abstract
The study was conducted in order to explore the potential of fungi isolated from surface and bottom seawater collected from the fishing harbour of Bizerte on the bioremediation of industrial effluent (IE) contaminated by petroleum hydrocarbon. Among the 128 fungal isolates, 11 were isolated from surface seawater and 7 from bottom seawater, representing 18 taxa in total. The gas chromatography mass spectrometry (GC-MS) was used for the determination of hydrocarbon compounds in IE. An initial screening of fungal growth using six concentrations ranged between 20 and 70% (v/v) IE has allowed the identification of the optimal concentration for fungal growth as well as selection of species able to tolerate high amounts of hydrocarbon. Colorimetric test employing 2,6-dichlorophenol indophenol and gravimetric method was applied for the assessment of fungal growth using 20% EI. By checking the phylogenetic affiliation of the high-performing stains as identified using ITSr DNA sequence, a dominance of Ascomycetes was detected. Indeed, Aspergillus terreus and Penicillium expansum may degrade 82.07 and 81.76% of residual total petroleum hydrocarbon (TPH), respectively. Both species were collected from surface seawater. While, Aspergillus niger, Colletotrichum sp and Fusarium annulatum displayed comparable degradation rates 40.43%, 41.3%, and 42.03%, respectively. The lowest rate of degradation 33.62% was detected in Emericellopsis phycophila. All those species were isolated from bottom seawater, excepting A. niger isolated from surface water. This work highlighted the importance of exploring the potential of fungi isolated from the natural environment on the bioremediation of industrial effluent. Our results promoted the investigation of the potential of the high-performing isolates A. terreus and P. expansum on the bioremediation of IE at pilot-scale and then in situ.
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Affiliation(s)
- Tahani El Ayari
- Laboratory of Environment Biomonitoring, Group of Fundamental and Applied Malacology (LEB/GFAM), Faculty of Sciences of Bizerte, University of Carthage, Zarzouna, 7021, Bizerte, Tunisia.
| | - Rihab Bouhdida
- Société Tunisienne de Lubrifiants, désignée par son acronyme SOTULUB, rue Lac Mälaren, Les Berges du Lac, 1053, Tunis, Tunisia
| | - Hadda Imene Ouzari
- Laboratoire de Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université Tunis Manar, 2092, Tunis, Tunisia
| | - Najoua Trigui El Menif
- Laboratory of Environment Biomonitoring, Group of Fundamental and Applied Malacology (LEB/GFAM), Faculty of Sciences of Bizerte, University of Carthage, Zarzouna, 7021, Bizerte, Tunisia
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Wang H, Sui Y, Liu J, Liu H, Qin L, Kong B, Chen Q. Screening and evaluating microorganisms with broad-spectrum biogenic amine-degrading ability from naturally fermented dry sausage collected from Northeast China. Meat Sci 2024; 210:109438. [PMID: 38290305 DOI: 10.1016/j.meatsci.2024.109438] [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] [Revised: 12/01/2023] [Accepted: 01/22/2024] [Indexed: 02/01/2024]
Abstract
This study aimed to screen autochthonous strains with broad-spectrum biogenic amine (BA) degradation ability from traditional dry sausages and to evaluate their BA-degrading ability in dry sausages. A total of 120 strains were isolated from dry sausages collected from various regions in Northeast China, and 35 of 120 isolates were identified as non-BA producing strains by the in vitro agar method. The random amplified polymorphic DNA polymerase chain reaction technique genotyped these 35 isolates into 18 biotypes. Moreover, high performance liquid chromatography (HPLC) quantification showed that six strains (Latilactobacillus sakei MDJ6; Lactiplantibacillus plantarum SH7; Weissella hellenica DQ9; Staphylococcus saprophyticus JX18 and SYS8; and Macrococcus caseolyticus SYS11) of the 18 biotypes exhibited broad-spectrum BA-degrading ability, all of which had various levels of amine oxidase activity with monoamine oxidase and diamine oxidase activities ranged of 6.60-619.04 and 26.32-352.81 U/mg protein, respectively. These six strains were subsequently inoculated into dry sausages and the results showed that they exhibited varying degrees of BA-degrading ability, of which strain Lat. sakei MDJ6 allowed to have less BA production on dry sausage with a final concentration of 61.33 mg/kg.
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Affiliation(s)
- Huiping Wang
- Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Yumeng Sui
- Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Jiaqi Liu
- Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Haotian Liu
- Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Ligang Qin
- Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Baohua Kong
- Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
| | - Qian Chen
- Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
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Li Z, Zhao C, Zhou Y, Zheng S, Hu Q, Zou Y. Label-free comparative proteomic analysis of Pleurotus eryngii grown on sawdust, bagasse, and peanut shell substrates. J Proteomics 2024; 294:105074. [PMID: 38199305 DOI: 10.1016/j.jprot.2024.105074] [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: 10/05/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
The white rot fungi Pleurotus eryngii are environmental microorganisms that can effectively break down lignocellulosic biomass. However, understanding of the mechanisms by which P. eryngii is effective in degrading lignocellulose is still limited. This work aimed to examine the extracellular secretory proteins implicated in the breakdown of lignocellulose in P. eryngii and identify degradation tactics across various cultivation substrates. Thus, a comparative analysis of the secretory proteins based on Nanoliquid chromatography combined with tandem mass spectrometry was conducted among P. eryngii cultivated on sawdusts, bagasse, peanut shells, and glucose. In total, 647, 616, 604, and 511 proteins were identified from the four samples, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis of protein expression differences identified pathways (hydrolytic enzymes, catalytic activity, metabolic processes, cellular processes, and response to stimuli) significantly enriched in proteins associated with lignocellulose degradation in P. eryngii. An integrated analysis of proteome data revealed specifically or differentially expressed genes secreted by P. eryngii in different cultivation substrates. The most prevalent carbohydrate-active enzymes involved in lignocellulose degradation in the secretome of the four samples were laccase (Lac), manganese peroxidase (MnP), aryl alcohol oxidase (AaO), and copper radical oxidase (CRO). Among them, Lac 2 mainly involved in the lignin degradation of sawdust peanut shells, and bagasse by P. eryngii, and Mnp 3 was mainly involved in the degradation of peanut shells. AaO and Lac 4 were mainly involved in glucose substrate defense and oxidative stress. It was found that exogenous addition of sawdust and peanut shells significantly increased lignolytic enzyme abundance. These findings provide insight and guidance for improving agricultural waste resource recovery. In this study, the secretomes of P. eryngii grown on four different carbon sources were compared. The findings revealed the extracellular enzymes implicated in the degradation of lignocellulose, offering avenues for further investigation into the biotransformation mechanisms of P. eryngii biomass and the potential utilization of agricultural wastes. SIGNIFICANCE: The cost of the substrate for mushroom cultivation has increased as the production of edible fungus has risen year after year. Therefore, the use of these locally available lignocellulosic wastes as substrates offers a cost-cutting option. Further, the overuse of wood for the cultivation of edible mushrooms is also detrimental to the conservation of forest resources or the ecological environment. Consequently, the use of other agricultural wastes as an alternative to sawdust or other woody substrates is a viable approach for cultivating P. eryngii. The distribution of extracellular lignocellulosic degrading enzymes, inferred in the present study could help improve the cultivation efficiency of P. eryngii vis-à-vis managing agricultural waste.
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Affiliation(s)
- Zihao Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China; Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cuimin Zhao
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China; Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Department of Gardens and Ecological Engineering, Hebei University of Engineering, Handan, China; Liaocheng Academy of Agricultural Sciences, Liaocheng, China
| | - Yuanyuan Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China; Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Suyue Zheng
- Department of Gardens and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Qingxiu Hu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China; Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yajie Zou
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China; Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Maucourt F, Doumèche B, Nazaret S, Fraissinet-Tachet L. Under explored roles of microbial ligninolytic enzymes in aerobic polychlorinated biphenyl transformation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:19071-19084. [PMID: 38372925 DOI: 10.1007/s11356-024-32291-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/28/2024] [Indexed: 02/20/2024]
Abstract
Polychlorinated biphenyls (PCBs) are persistent organic pollutants in the environment that are responsible for many adverse health effects. Bioremediation appears to be a healthy and cost-effective alternative for remediating PCB-contaminated environments. While some microbial species have been observed to be capable of transforming PCBs, only two different microbial pathways (rdh and bph pathways) have been described to be involved in PCB transformations. Ligninolytic enzymes have been observed or are under suspicion in some microbial PCB transformations. However, the role of these promising PCB-transforming enzymes, which are produced by fungi and some aerobic bacteria, is still unclear. The present review describes their role by identifying microbial PCB-transforming species and their reported ligninolytic enzymes whether proven or suspected to be involved in PCB transformations. There are several lines of evidence that ligninolytic enzymes are responsible for PCB transformations such as (1) the ability of purified laccases from Myceliophthora thermophila, Pycnoporus cinnabarinus, Trametes versicolor, Cladosporium sp, and Coprinus cumatus to transform hydroxy-PCBs; (2) the increased production of laccases and peroxidases by many fungi in the presence of PCBs; and (3) the enhanced PCB transformation by Pseudomonas stutzeri and Sinorhizobium meliloti NM after the addition of ligninolytic enzyme enhancers. However, if the involvement of ligninolytic enzymes in PCB transformation is clearly demonstrated in some fungal species, it does not seem to be implicated in all microbial species suggesting other still unknown metabolic pathways involved in PCB transformation and different from the bph and rdh pathways. Therefore, PCB transformation may involve several metabolic pathways, some involving ligninolytic enzymes, bph or rdh genes, and some still unknown, depending on the microbial species. In addition, current knowledge does not fully clarify the role of ligninolytic enzymes in PCB oxidation and dechlorination. Therefore, further studies focusing on purified ligninolytic enzymes are needed to clearly elucidate their role in PCB transformation.
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Affiliation(s)
- Flavien Maucourt
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-7 69622, Villeurbanne, France
- ENVISOL, 2-4 rue Hector Berlioz, F-38110, La Tour du Pin, France
| | - Bastien Doumèche
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS 5246 ICBMS, F-7 69622, Villeurbanne, France
| | - Sylvie Nazaret
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-7 69622, Villeurbanne, France
| | - Laurence Fraissinet-Tachet
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-7 69622, Villeurbanne, France.
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Li Z, Zhou Y, Xu C, Pan J, Li H, Zhou Y, Zou Y. Genome-wide analysis of the Pleurotus eryngii laccase gene (PeLac) family and functional identification of PeLac5. AMB Express 2023; 13:104. [PMID: 37768391 PMCID: PMC10539258 DOI: 10.1186/s13568-023-01608-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The laccase gene family encodes multiple isozymes that are crucial for the degradation of substrates and the regulation of developmental processes in fungi. Pleurotus eryngii is an important edible and medicinal fungus belonging to the Basidiomycota phylum and can grow on a variety of natural substrates. In the present study, genome-wide profiling of P. eryngii identified 10 genes encoding its laccase isoenzymes. Conservative sequence analysis demonstrated that all PeLacs possess classical laccase structural domains. Phylogenetic analysis yielded four major subgroups, the members of which are similar with respect to conserved gene organization, protein domain architecture, and consensus motifs. The 10 PeLacs formed three groups together with 12 PoLacs in Pleurotus ostreatus, indicating that they share a high level of evolutionary homology. Cis-responsive element analysis implied that PeLacs genes play a role in growth and development and lignocellulose degradation. Targeted overexpression of PeLac5 reduced the time to primordia formation and their development to fruiting bodies. Gene expression patterns in the presence of different lignocellulosic substrates indicate that three PeLacs genes (2, 4, and 9) are key to lignocellulose degradation. This work presents the first inventory of laccase genes in P. eryngii and preliminarily explores their functions, which may help to uncover the manner by which these proteins utilize substrates.
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Affiliation(s)
- Zihao Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, 100081, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuanyuan Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, 100081, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Congtao Xu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, 100081, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinlong Pan
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, 100081, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haikang Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, 100081, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yi Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, 100081, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yajie Zou
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, 100081, China.
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Maucourt F, Doumèche B, Chapulliot D, Vallon L, Nazaret S, Fraissinet-Tachet L. Polychlorinated Biphenyl Transformation, Peroxidase and Oxidase Activities of Fungi and Bacteria Isolated from a Historically Contaminated Site. Microorganisms 2023; 11:1887. [PMID: 37630447 PMCID: PMC10457763 DOI: 10.3390/microorganisms11081887] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
Causing major health and ecological disturbances, polychlorinated biphenyls (PCBs) are persistent organic pollutants still recovered all over the world. Microbial PCB biotransformation is a promising technique for depollution, but the involved molecular mechanisms remain misunderstood. Ligninolytic enzymes are suspected to be involved in many PCB transformations, but their assessments remain scarce. To further inventory the capabilities of microbes to transform PCBs through their ligninolytic enzymes, we investigated the role of oxidase and peroxidase among a set of microorganisms isolated from a historically PCB-contaminated site. Among 29 isolated fungi and 17 bacteria, this work reports for the first time the PCB-transforming capabilities from fungi affiliated to Didymella, Dothiora, Ilyonectria, Naganishia, Rhodoturula, Solicoccozyma, Thelebolus and Truncatella genera and bacteria affiliated to Peribacillus frigotolerans, Peribacillus muralis, Bacillus mycoides, Bacillus cereus, Bacillus toyonensis, Pseudarthrobacter sp., Pseudomonas chlororaphis, Erwinia aphidicola and Chryseobacterium defluvii. In the same way, this is the first report of fungal isolates affiliated to the Dothiora maculans specie and Cladosporium genus that displayed oxidase (putatively laccase) and peroxidase activity, respectively, enhanced in the presence of PCBs (more than 4-fold and 20-fold, respectively, compared to controls). Based on these results, the observed activities are suspected to be involved in PCB transformation.
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Affiliation(s)
- Flavien Maucourt
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
- ENVISOL, 2-4 Rue Hector Berlioz, F-38110 La Tour du Pin, France
| | - Bastien Doumèche
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS 5246 ICBMS, F-69622 Villeurbanne, France
| | - David Chapulliot
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Laurent Vallon
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Sylvie Nazaret
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Laurence Fraissinet-Tachet
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
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Zhong J, Liu J, Hu R, Pan D, Shao S, Wu X. Performance of nitrification-denitrification and denitrifying phosphorus removal driven by in-situ generated biogenic manganese oxides in a moving bed biofilm reactor. BIORESOURCE TECHNOLOGY 2023; 377:128957. [PMID: 36965588 DOI: 10.1016/j.biortech.2023.128957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 06/18/2023]
Abstract
Simultaneous removal of NH4+-N, NO3--N, COD, and P by manganese redox cycling in nutrient wastewater was established with two moving bed biofilm reactors (MBBRs) with in-situ generated biogenic manganese oxides (BioMnOx) and non-BioMnOx. In-situ generated BioMnOx preferentially promoted the denitrification, and the average removal of NO3--N, NH4+-N, and TN in the experimental MBBR with BioMnOx increased to 89.00%, 70.64%, and 76.06% compared with the control MBBR with non-BioMnOx. The relevant enzymes activity, extracellular polymeric substance (EPS), electron transport system activity (ETSA), and reactive oxygen species (ROS) were investigated. The element valence and morphology of purified BioMnOx were characterized by X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM), as well as the effect of BioMnOx on nitrogen and phosphorus removal. The results suggested that BioMnOx could improve nitrogen conversion. Electrochemical characteristic and microbial community were detected. This study provided a new strategy for nutrients removal in BioMnOx-mediated wastewater treatment.
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Affiliation(s)
- Jinfeng Zhong
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China
| | - Jiamin Liu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China
| | - Rui Hu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China
| | - Dandan Pan
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China
| | - Sicheng Shao
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China.
| | - Xiangwei Wu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China
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Virués-Segovia JR, Muñoz-Mira S, Durán-Patrón R, Aleu J. Marine-derived fungi as biocatalysts. Front Microbiol 2023; 14:1125639. [PMID: 36922968 PMCID: PMC10008910 DOI: 10.3389/fmicb.2023.1125639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/08/2023] [Indexed: 03/03/2023] Open
Abstract
Marine microorganisms account for over 90% of ocean biomass and their diversity is believed to be the result of their ability to adapt to extreme conditions of the marine environment. Biotransformations are used to produce a wide range of high-added value materials, and marine-derived fungi have proven to be a source of new enzymes, even for activities not previously discovered. This review focuses on biotransformations by fungi from marine environments, including bioremediation, from the standpoint of the chemical structure of the substrate, and covers up to September 2022.
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Affiliation(s)
- Jorge R Virués-Segovia
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4ª Planta, Universidad de Cádiz, Cádiz, Spain
| | - Salvador Muñoz-Mira
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4ª Planta, Universidad de Cádiz, Cádiz, Spain
| | - Rosa Durán-Patrón
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4ª Planta, Universidad de Cádiz, Cádiz, Spain
| | - Josefina Aleu
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4ª Planta, Universidad de Cádiz, Cádiz, Spain
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Euglena gracilis can grow in the mixed culture containing Cladosporium westerdijkiae, Lysinibacillus boronitolerans and Pseudobacillus badius without the addition of vitamins B1 and B12. J Biotechnol 2022; 351:50-59. [DOI: 10.1016/j.jbiotec.2022.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/15/2022]
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A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications. Int J Mol Sci 2022; 23:ijms23063135. [PMID: 35328559 PMCID: PMC8954581 DOI: 10.3390/ijms23063135] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/11/2022] [Accepted: 03/11/2022] [Indexed: 12/20/2022] Open
Abstract
The production of biochemicals requires the use of microbial strains with efficient substrate conversion and excellent environmental robustness, such as Weizmannia coagulans species. So far, the genomes of 47 strains have been sequenced. Herein, we report a comparative genomic analysis of nine strains on the full repertoire of Carbohydrate-Active enZymes (CAZymes), secretion systems, and resistance mechanisms to environmental challenges. Moreover, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immune system along with CRISPR-associated (Cas) genes, was also analyzed. Overall, this study expands our understanding of the strain's genomic diversity of W. coagulans to fully exploit its potential in biotechnological applications.
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Brugnari T, Braga DM, Dos Santos CSA, Torres BHC, Modkovski TA, Haminiuk CWI, Maciel GM. Laccases as green and versatile biocatalysts: from lab to enzyme market-an overview. BIORESOUR BIOPROCESS 2021; 8:131. [PMID: 38650295 PMCID: PMC10991308 DOI: 10.1186/s40643-021-00484-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/07/2021] [Indexed: 11/10/2022] Open
Abstract
Laccases are multi-copper oxidase enzymes that catalyze the oxidation of different compounds (phenolics and non-phenolics). The scientific literature on laccases is quite extensive, including many basic and applied research about the structure, functions, mechanism of action and a variety of biotechnological applications of these versatile enzymes. Laccases can be used in various industries/sectors, from the environmental field to the cosmetics industry, including food processing and the textile industry (dyes biodegradation and synthesis). Known as eco-friendly or green enzymes, the application of laccases in biocatalytic processes represents a promising sustainable alternative to conventional methods. Due to the advantages granted by enzyme immobilization, publications on immobilized laccases increased substantially in recent years. Many patents related to the use of laccases are available, however, the real industrial or environmental use of laccases is still challenged by cost-benefit, especially concerning the feasibility of producing this enzyme on a large scale. Although this is a compelling point and the enzyme market is heated, articles on the production and application of laccases usually neglect the economic assessment of the processes. In this review, we present a description of laccases structure and mechanisms of action including the different sources (fungi, bacteria, and plants) for laccases production and tools for laccases evolution and prediction of potential substrates. In addition, we both compare approaches for scaling-up processes with an emphasis on cost reduction and productivity and critically review several immobilization methods for laccases. Following the critical view on production and immobilization, we provide a set of applications for free and immobilized laccases based on articles published within the last five years and patents which may guide future strategies for laccase use and commercialization.
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Affiliation(s)
- Tatiane Brugnari
- Biotechnology Laboratory, Department of Chemistry and Biology, Graduate Program in Environmental Science and Technology, Federal University of Technology, Paraná, Curitiba, Brazil.
| | - Dayane Moreira Braga
- Biotechnology Laboratory, Department of Chemistry and Biology, Graduate Program in Environmental Science and Technology, Federal University of Technology, Paraná, Curitiba, Brazil
| | - Camila Souza Almeida Dos Santos
- Biotechnology Laboratory, Department of Chemistry and Biology, Graduate Program in Environmental Science and Technology, Federal University of Technology, Paraná, Curitiba, Brazil
| | - Bruno Henrique Czelusniak Torres
- Biotechnology Laboratory, Department of Chemistry and Biology, Graduate Program in Environmental Science and Technology, Federal University of Technology, Paraná, Curitiba, Brazil
| | - Tatiani Andressa Modkovski
- Biotechnology Laboratory, Department of Chemistry and Biology, Graduate Program in Environmental Science and Technology, Federal University of Technology, Paraná, Curitiba, Brazil
| | - Charles Windson Isidoro Haminiuk
- Biotechnology Laboratory, Department of Chemistry and Biology, Graduate Program in Environmental Science and Technology, Federal University of Technology, Paraná, Curitiba, Brazil
| | - Giselle Maria Maciel
- Biotechnology Laboratory, Department of Chemistry and Biology, Graduate Program in Environmental Science and Technology, Federal University of Technology, Paraná, Curitiba, Brazil
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Zafeiropoulos H, Gioti A, Ninidakis S, Potirakis A, Paragkamian S, Angelova N, Antoniou A, Danis T, Kaitetzidou E, Kasapidis P, Kristoffersen JB, Papadogiannis V, Pavloudi C, Ha QV, Lagnel J, Pattakos N, Perantinos G, Sidirokastritis D, Vavilis P, Kotoulas G, Manousaki T, Sarropoulou E, Tsigenopoulos CS, Arvanitidis C, Magoulas A, Pafilis E. 0s and 1s in marine molecular research: a regional HPC perspective. Gigascience 2021; 10:6353916. [PMID: 34405237 PMCID: PMC8371273 DOI: 10.1093/gigascience/giab053] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/07/2021] [Accepted: 07/20/2021] [Indexed: 01/23/2023] Open
Abstract
High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade's experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility's future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.
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Affiliation(s)
- Haris Zafeiropoulos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.,Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013, Heraklion, Crete, Greece
| | - Anastasia Gioti
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Stelios Ninidakis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Antonis Potirakis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Savvas Paragkamian
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.,Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013, Heraklion, Crete, Greece
| | - Nelina Angelova
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Aglaia Antoniou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Theodoros Danis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.,School of Medicine, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Eliza Kaitetzidou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Panagiotis Kasapidis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Jon Bent Kristoffersen
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Vasileios Papadogiannis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Christina Pavloudi
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Quoc Viet Ha
- Bull SAS, Rue du Gros Caillou, 78340 Les Clayes-sous-Bois, France
| | - Jacques Lagnel
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche Provence-Alpes-Côte d'Azur, Domaine Saint Maurice, CS60094, 84143 Montfavet Cedex, France
| | - Nikos Pattakos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Giorgos Perantinos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Dimitris Sidirokastritis
- Hellenic Centre for Marine Research, Network Operation Center, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Panagiotis Vavilis
- Hellenic Centre for Marine Research, Network Operation Center, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Georgios Kotoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Tereza Manousaki
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Elena Sarropoulou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Costas S Tsigenopoulos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Christos Arvanitidis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.,LifeWatch European Research Infrastructure Consortium, Sector II-III Plaza de España, 41071, Seville, Spain
| | - Antonios Magoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Evangelos Pafilis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
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Šrédlová K, Šírová K, Stella T, Cajthaml T. Degradation Products of Polychlorinated Biphenyls and Their In Vitro Transformation by Ligninolytic Fungi. TOXICS 2021; 9:toxics9040081. [PMID: 33918084 PMCID: PMC8070434 DOI: 10.3390/toxics9040081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 02/08/2023]
Abstract
Metabolites of polychlorinated biphenyls (PCBs)—hydroxylated PCBs (OH-PCBs), chlorobenzyl alcohols (CB-OHs), and chlorobenzaldehydes (CB-CHOs)—were incubated in vitro with the extracellular liquid of Pleurotus ostreatus, which contains mainly laccase and low manganese-dependent peroxidase (MnP) activity. The enzymes were able to decrease the amount of most of the tested OH-PCBs by > 80% within 1 h; the removal of more recalcitrant OH-PCBs was greatly enhanced by the addition of the laccase mediator syringaldehyde. Conversely, glutathione substantially hindered the reaction, suggesting that it acted as a laccase inhibitor. Hydroxylated dibenzofuran and chlorobenzoic acid were identified as transformation products of OH-PCBs. The extracellular enzymes also oxidized the CB-OHs to the corresponding CB-CHOs on the order of hours to days; however, the mediated and nonmediated setups exhibited only slight differences, and the participating enzymes could not be determined. When CB-CHOs were used as the substrates, only partial transformation was observed. In an additional experiment, the extracellular liquid of Irpex lacteus, which contains predominantly MnP, was able to efficiently transform CB-CHOs with the aid of glutathione; mono- and di-chloroacetophenones were detected as transformation products. These results demonstrate that extracellular enzymes of ligninolytic fungi can act on a wide range of PCB metabolites, emphasizing their potential for bioremediation.
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Affiliation(s)
- Kamila Šrédlová
- Faculty of Science, Institute for Environmental Studies, Charles University, Benátská 2, 12801 Prague 2, Czech Republic; (K.Š.); (K.Š.)
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague 4, Czech Republic;
| | - Kateřina Šírová
- Faculty of Science, Institute for Environmental Studies, Charles University, Benátská 2, 12801 Prague 2, Czech Republic; (K.Š.); (K.Š.)
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague 4, Czech Republic;
| | - Tatiana Stella
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague 4, Czech Republic;
- M3R S.r.l., University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Tomáš Cajthaml
- Faculty of Science, Institute for Environmental Studies, Charles University, Benátská 2, 12801 Prague 2, Czech Republic; (K.Š.); (K.Š.)
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague 4, Czech Republic;
- Correspondence:
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