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Ebsa G, Gizaw B, Admassie M, Degu T, Alemu T. The role and mechanisms of microbes in dichlorodiphenyltrichloroethane (DDT) and its residues bioremediation. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2024; 42:e00835. [PMID: 38560709 PMCID: PMC10972831 DOI: 10.1016/j.btre.2024.e00835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/09/2024] [Accepted: 03/09/2024] [Indexed: 04/04/2024]
Abstract
Environmental contamination with dichlorodiphenyltrichloroethane (DDT) has sever effects on the ecosystem worldwide. DDT is a recalcitrant synthetic chemical with high toxicity and lipophilicity. It is also bioaccumulated in the food chain and causes genotoxic, estrogenic, carcinogenic, and mutagenic effects on aquatic organisms and humans. Microbial remediation mechanism and its enzymes are very important for removing DDT from environment. DDT and its main residues dichlorodiphenyldichloroethylene (DDE) and dichlorodiphenyldichloroethane (DDD) can biodegrade slowly in soil and water. To enhance this process, a number of strategies are proposed, such as bio-attenuation, biostimulation, bioaugmentation and the manipulation of environmental conditions to enhance the activity of microbial enzymes. The addition of organic matter and flooding of the soil enhance DDT degradation. Microbial candidates for DDT remediation include micro-algae, fungi and bacteria. This review provide brief information and recommendation on microbial DDT remediation and its mechanisms.
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Affiliation(s)
- Girma Ebsa
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P. O. Box: 1176, Addis Ababa, Ethiopia
| | - Birhanu Gizaw
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P. O. Box: 1176, Addis Ababa, Ethiopia
| | - Mesele Admassie
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P. O. Box: 1176, Addis Ababa, Ethiopia
| | - Tizazu Degu
- Department of Crop Protection, Ethiopian Institute of Agricultural Research, P. O. Box: 2003, Addis Ababa, Ethiopia
| | - Tesfaye Alemu
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P. O. Box: 1176, Addis Ababa, Ethiopia
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Lodi RS, Peng C, Dong X, Deng P, Peng L. Trichoderma hamatum and Its Benefits. J Fungi (Basel) 2023; 9:994. [PMID: 37888250 PMCID: PMC10607699 DOI: 10.3390/jof9100994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Trichoderma hamatum (Bonord.) Bainier (T. hamatum) belongs to Hypocreaceae family, Trichoderma genus. Trichoderma spp. are prominently known for their biocontrol activities and plant growth promotion. Hence, T. hamatum also possess several beneficial activities, such as antimicrobial activity, antioxidant activity, insecticidal activity, herbicidal activity, and plant growth promotion; in addition, it holds several other beneficial properties, such as resistance to dichlorodiphenyltrichloroethane (DDT) and degradation of DDT by certain enzymes and production of certain polysaccharide-degrading enzymes. Hence, the current review discusses the beneficial properties of T. hamatum and describes the gaps that need to be further considered in future studies, such as T. hamatum's potentiality against human pathogens and, in contrast, its role as an opportunistic human pathogen. Moreover, there is a need for substantial study on its antiviral and antioxidant activities.
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Affiliation(s)
| | | | | | | | - Lizeng Peng
- Key Laboratory of Agro-Products Processing Technology of Shandong Province, Key Laboratory of Novel Food Resources Processing Ministry of Agriculture, Institute of Food & Nutrition Science and Technology, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (R.S.L.); (C.P.); (X.D.); (P.D.)
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Ansari M, Devi BM, Sarkar A, Chattopadhyay A, Satnami L, Balu P, Choudhary M, Shahid MA, Jailani AAK. Microbial Exudates as Biostimulants: Role in Plant Growth Promotion and Stress Mitigation. J Xenobiot 2023; 13:572-603. [PMID: 37873814 PMCID: PMC10594471 DOI: 10.3390/jox13040037] [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: 08/02/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/25/2023] Open
Abstract
Microbes hold immense potential, based on the fact that they are widely acknowledged for their role in mitigating the detrimental impacts of chemical fertilizers and pesticides, which were extensively employed during the Green Revolution era. The consequence of this extensive use has been the degradation of agricultural land, soil health and fertility deterioration, and a decline in crop quality. Despite the existence of environmentally friendly and sustainable alternatives, microbial bioinoculants encounter numerous challenges in real-world agricultural settings. These challenges include harsh environmental conditions like unfavorable soil pH, temperature extremes, and nutrient imbalances, as well as stiff competition with native microbial species and host plant specificity. Moreover, obstacles spanning from large-scale production to commercialization persist. Therefore, substantial efforts are underway to identify superior solutions that can foster a sustainable and eco-conscious agricultural system. In this context, attention has shifted towards the utilization of cell-free microbial exudates as opposed to traditional microbial inoculants. Microbial exudates refer to the diverse array of cellular metabolites secreted by microbial cells. These metabolites enclose a wide range of chemical compounds, including sugars, organic acids, amino acids, peptides, siderophores, volatiles, and more. The composition and function of these compounds in exudates can vary considerably, depending on the specific microbial strains and prevailing environmental conditions. Remarkably, they possess the capability to modulate and influence various plant physiological processes, thereby inducing tolerance to both biotic and abiotic stresses. Furthermore, these exudates facilitate plant growth and aid in the remediation of environmental pollutants such as chemicals and heavy metals in agroecosystems. Much like live microbes, when applied, these exudates actively participate in the phyllosphere and rhizosphere, engaging in continuous interactions with plants and plant-associated microbes. Consequently, they play a pivotal role in reshaping the microbiome. The biostimulant properties exhibited by these exudates position them as promising biological components for fostering cleaner and more sustainable agricultural systems.
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Affiliation(s)
- Mariya Ansari
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; (M.A.); (A.S.); (L.S.)
| | - B. Megala Devi
- Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India;
| | - Ankita Sarkar
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; (M.A.); (A.S.); (L.S.)
| | - Anirudha Chattopadhyay
- Pulses Research Station, S.D. Agricultural University, Sardarkrushinagar 385506, Gujarat, India;
| | - Lovkush Satnami
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; (M.A.); (A.S.); (L.S.)
| | - Pooraniammal Balu
- Department of Biotechnology, Sastra Deemed University, Thanjavur 613401, Tamil Nadu, India;
| | - Manoj Choudhary
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA;
| | - Muhammad Adnan Shahid
- Horticultural Science Department, North Florida Research and Education Center, University of Florida/IFAS, Quincy, FL 32351, USA;
| | - A. Abdul Kader Jailani
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA;
- Plant Pathology Department, North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA
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Champramary S, Indic B, Szűcs A, Tyagi C, Languar O, Hasan KMF, Szekeres A, Vágvölgyi C, Kredics L, Sipos G. The mycoremediation potential of the armillarioids: a comparative genomics analysis. Front Bioeng Biotechnol 2023; 11:1189640. [PMID: 37662429 PMCID: PMC10470841 DOI: 10.3389/fbioe.2023.1189640] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/03/2023] [Indexed: 09/05/2023] Open
Abstract
Genes involved in mycoremediation were identified by comparative genomics analysis in 10 armillarioid species and selected groups of white-rot Basidiomycota (14) and soft-rot Ascomycota (12) species to confine the distinctive bioremediation capabilities of the armillarioids. The genomes were explored using phylogenetic principal component analysis (pPCA), searching for genes already documented in a biocatalysis/biodegradation database. The results underlined a distinct, increased potential of aromatics-degrading genes/enzymes in armillarioids, with particular emphasis on a high copy number and diverse spectrum of benzoate 4-monooxygenase [EC:1.14.14.92] homologs. In addition, other enzymes involved in the degradation of various monocyclic aromatics were more abundant in the armillarioids than in the other white-rot basidiomycetes, and enzymes involved in the degradation of polycyclic aromatic hydrocarbons (PAHs) were more prevailing in armillarioids and other white-rot species than in soft-rot Ascomycetes. Transcriptome profiling of A. ostoyae and A. borealis isolates confirmed that several genes involved in the degradation of benzoates and other monocyclic aromatics were distinctively expressed in the wood-invading fungal mycelia. Data were consistent with armillarioid species offering a more powerful potential in degrading aromatics. Our results provide a reliable, practical solution for screening the likely fungal candidates for their full biodegradation potential, applicability, and possible specialization based on their genomics data.
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Affiliation(s)
- Simang Champramary
- Functional Genomics and Bioinformatics Group, Institute of Forest and Natural Resource Management, Faculty of Forestry, University of Sopron, Sopron, Hungary
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Boris Indic
- Functional Genomics and Bioinformatics Group, Institute of Forest and Natural Resource Management, Faculty of Forestry, University of Sopron, Sopron, Hungary
| | - Attila Szűcs
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Omar Languar
- Functional Genomics and Bioinformatics Group, Institute of Forest and Natural Resource Management, Faculty of Forestry, University of Sopron, Sopron, Hungary
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - K. M. Faridul Hasan
- Fibre and Nanotechnology Program, Faculty of Wood Engineering and Creative Industries, University of Sopron, Sopron, Hungary
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - György Sipos
- Functional Genomics and Bioinformatics Group, Institute of Forest and Natural Resource Management, Faculty of Forestry, University of Sopron, Sopron, Hungary
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Schalamun M, Schmoll M. Trichoderma - genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1002161. [PMID: 37746224 PMCID: PMC10512326 DOI: 10.3389/ffunb.2022.1002161] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/25/2022] [Indexed: 09/26/2023]
Abstract
The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted. The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.
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Affiliation(s)
- Miriam Schalamun
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Monika Schmoll
- Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
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Miglani R, Parveen N, Kumar A, Ansari MA, Khanna S, Rawat G, Panda AK, Bisht SS, Upadhyay J, Ansari MN. Degradation of Xenobiotic Pollutants: An Environmentally Sustainable Approach. Metabolites 2022; 12:818. [PMID: 36144222 PMCID: PMC9505297 DOI: 10.3390/metabo12090818] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/21/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
The ability of microorganisms to detoxify xenobiotic compounds allows them to thrive in a toxic environment using carbon, phosphorus, sulfur, and nitrogen from the available sources. Biotransformation is the most effective and useful metabolic process to degrade xenobiotic compounds. Microorganisms have an exceptional ability due to particular genes, enzymes, and degradative mechanisms. Microorganisms such as bacteria and fungi have unique properties that enable them to partially or completely metabolize the xenobiotic substances in various ecosystems.There are many cutting-edge approaches available to understand the molecular mechanism of degradative processes and pathways to decontaminate or change the core structure of xenobiotics in nature. These methods examine microorganisms, their metabolic machinery, novel proteins, and catabolic genes. This article addresses recent advances and current trends to characterize the catabolic genes, enzymes and the techniques involved in combating the threat of xenobiotic compounds using an eco-friendly approach.
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Affiliation(s)
- Rashi Miglani
- Department of Zoology, D.S.B Campus, Kumaun University, Nainital 263002, Uttarakhand, India
| | - Nagma Parveen
- Department of Zoology, D.S.B Campus, Kumaun University, Nainital 263002, Uttarakhand, India
| | - Ankit Kumar
- Department of Pharmaceutical Sciences, Sir J. C Bose Technical Campus, Bhimtal, Nainital 263136, Uttarakhand, India
| | - Mohd. Arif Ansari
- Department of Forestry and Environmental Science, D.S.B Campus, Kumaun University, Nainital 263002, Uttarakhand, India
| | - Soumya Khanna
- Department of Anatomy, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Gaurav Rawat
- Department of Zoology, D.S.B Campus, Kumaun University, Nainital 263002, Uttarakhand, India
| | - Amrita Kumari Panda
- Department of Biotechnology, Sant Gahira Guru University, Ambikapur 497001, Chhattisgarh, India
| | - Satpal Singh Bisht
- Department of Zoology, D.S.B Campus, Kumaun University, Nainital 263002, Uttarakhand, India
| | - Jyoti Upadhyay
- Department of Pharmaceutical Sciences, School of Health Sciences and Technology, University of Petroleum and Energy Studies, Energy Acre Campus Bidholi, Dehradun 248007, Uttarakhand, India
| | - Mohd Nazam Ansari
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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Novotný Č, Fojtík J, Mucha M, Malachová K. Biodeterioration of Compost-Pretreated Polyvinyl Chloride Films by Microorganisms Isolated From Weathered Plastics. Front Bioeng Biotechnol 2022; 10:832413. [PMID: 35223795 PMCID: PMC8867010 DOI: 10.3389/fbioe.2022.832413] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/21/2022] [Indexed: 11/29/2022] Open
Abstract
Polyvinyl chloride (PVC) is a petroleum-based plastic used in various applications, polluting the environment because of its recalcitrance, large content of additives, and the presence of halogen. In our case study, a new, two-stage biodegradation technology that combined composting process used for PVC pretreatment with a subsequent PVC attack by newly-isolated fungal and bacterial strains under SSF conditions was used for biodegradation of commercial PVC films. The novelty consisted in a combined effect of the two biodegradation processes and the use for augmentation of microbial strains isolated from plastic-polluted environments. First, the ability of the newly-isolated strains to deteriorate PVC was tested in individual, liquid-medium- and SSF cultures. Higher mass-reductions of PVC films were obtained in the former cultures, probably due to a better mass transfer in liquid phase. Using the two-stage biodegradation technology the highest cumulative mass-reductions of 29.3 and 33.2% of PVC films were obtained after 110 days with Trichoderma hamatum and Bacillus amyloliquefaciens applied in the second stage in the SSF culture, respectively. However, FTIR analysis showed that the mass-reductions obtained represented removal of significant amounts of additives but the PVC polymer chain was not degraded.
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Affiliation(s)
- Čenek Novotný
- Laboratory of Environmental Biotechnology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Horticulture, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic.,Institute of Environmental Technology, CEET, VSB-Technical University of Ostrava, Ostrava, Czech Republic
| | - Jindřich Fojtík
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Mucha
- Department of Chemistry, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Kateřina Malachová
- Institute of Environmental Technology, CEET, VSB-Technical University of Ostrava, Ostrava, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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Sustainable Application of Biosorption and Bioaccumulation of Persistent Pollutants in Wastewater Treatment: Current Practice. Processes (Basel) 2021. [DOI: 10.3390/pr9101696] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Persistent toxic substances including persistent organic pollutants and heavy metals have been released in high quantities in surface waters by industrial activities. Their presence in environmental compartments is causing harmful effects both on the environment and human health. It was shown that their removal from wastewaters using conventional methods and adsorbents is not always a sustainable process. In this circumstance, the use of microorganisms for pollutants uptake can be seen as being an environmentally-friendly and cost-effective strategy for the treatment of industrial effluents. However, in spite of their confirmed potential in the remediation of persistent pollutants, microorganisms are not yet applied at industrial scale. Thus, the current paper aims to synthesize and analyze the available data from literature to support the upscaling of microbial-based biosorption and bioaccumulation processes. The industrial sources of persistent pollutants, the microbial mechanisms for pollutant uptake and the significant results revealed so far in the scientific literature are identified and covered in this review. Moreover, the influence of different parameters affecting the performance of the discussed systems and also very important in designing of treatment processes are highly considered. The analysis performed in the paper offers an important perspective in making decisions for scaling-up and efficient operation, from the life cycle assessment point of view of wastewater microbial bioremediation. This is significant since the sustainability of the microbial-based remediation processes through standardized methodologies such as life cycle analysis (LCA), hasn’t been analyzed yet in the scientific literature.
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