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Maússe-Sitoe S, Dames J. Characterization of arbuscular mycorrhizal fungal species associating with Zea mays. FRONTIERS IN PLANT SCIENCE 2024; 15:1345229. [PMID: 38774223 PMCID: PMC11106459 DOI: 10.3389/fpls.2024.1345229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/16/2024] [Indexed: 05/24/2024]
Abstract
Taxonomic identification of arbuscular mycorrhizal (AM) fungal spores extracted directly from the field is sometimes difficult because spores are often degraded or parasitized by other organisms. Single-spore inoculation of a suitable host plant allows for establishing monosporic cultures of AM fungi. This study aimed to propagate AM fungal spores isolated from maize soil using single spores for morphological characterization. First, trap cultures were established to trigger the sporulation of AM fungal species. Second, trap cultures were established with individual morphotypes by picking up only one spore under a dissecting microscope and transferring it to a small triangle of sterilized filter paper, which was then carefully inoculated below a root from germinated sorghum seeds in each pot and covered with a sterile substrate. All pots were placed in sunbags and maintained in a plant growth room for 120 days. Spores obtained from single spore trap cultures from each treatment, maize after oats (MO), maize after maize (MM), maize after peas (MP), and maize after soybean (MS), were extracted using the sieving method. Healthy spores were selected for morphological analysis. Direct PCR was conducted by crushing spores in RNAlater and applying three sets of primer pairs: ITS1 × ITS4, NS31 × AML2, and SSUmcf and LSUmBr. Nucleotide sequences obtained from Sanger sequencing were aligned on MEGA X. The phylogenetic tree showed that the closest neighbors of the propagated AM fungal species belonged to the genera Claroideoglomus, Funneliformis, Gigaspora, Paraglomus, and Rhizophagus. The morphological characteristics were compared to the descriptive features of described species posted on the INVAM website, and they included Acaulospora cavernata, Diversispora spurca, Funneliformis geosporus, Funneliformis mosseae, Gigaspora clarus, Gigaspora margarita, Glomus macrosporum, Paraglomus occultum, and Rhizophagus intraradices. These findings can provide a great contribution to crop productivity and sustainable management of the agricultural ecosystem. Also, the isolate analyzed could be grouped into efficient promoters of growth and mycorrhization of maize independent of their geographical location.
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Affiliation(s)
| | - Joanna Dames
- Mycorrhizal Research Laboratory, Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
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Navina BK, Velmurugan NK, Senthil Kumar P, Rangasamy G, Palanivelu J, Thamarai P, Vickram AS, Saravanan A, Shakoor A. Fungal bioremediation approaches for the removal of toxic pollutants: Mechanistic understanding for biorefinery applications. CHEMOSPHERE 2024; 350:141123. [PMID: 38185426 DOI: 10.1016/j.chemosphere.2024.141123] [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: 07/11/2023] [Revised: 10/30/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
Pollution is a global menace that poses harmful effects on all the living ecosystems and to the Earth. As years pass by, the available and the looming rate of pollutants increases at a faster rate. Although many treatments and processing strategies are waged for treating such pollutants, the by-products and the wastes or drain off generated by these treatments further engages in the emission of hazardous waste. Innovative and long-lasting solutions are required to address the urgent global issue of hazardous pollutant remediation from contaminated environments. Myco-remediation is a top-down green and eco-friendly tool for pollution management. It is a cost-effective and safer practice of converting pernicious substances into non-toxic forms by the use of fungi. But these pollutants can be transformed into useable products along with multiple benefits for the environment such as sequestration of carbon emissions and also to generate high valuable bioactive materials that fits as a sustainable economic model. The current study has examined the possible applications of fungi in biorefineries and their critical role in the transformation and detoxification of pollutants. The paper offers important insights into using fungal bioremediation for both economically and environmentally sound solutions in the domain of biorefinery applications by combining recent research findings.
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Affiliation(s)
- Bala Krishnan Navina
- Department of Biotechnology, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Chennai, 600062, India
| | - Nandha Kumar Velmurugan
- Department of Biotechnology, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Chennai, 600062, India
| | - P Senthil Kumar
- Centre for Pollution Control and Environmental Engineering, School of Engineering and Technology, Pondicherry University, Kalapet, Puducherry, 605014, India.
| | - Gayathri Rangasamy
- School of Engineering, Lebanese American University, Byblos, Lebanon; University Centre for Research and Development & Department of Civil Engineering, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Jeyanthi Palanivelu
- Department of Biotechnology, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Chennai, 600062, India
| | - P Thamarai
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - A S Vickram
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - A Saravanan
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - Awais Shakoor
- Hawkesbury Institute for the Environment, West Sydney University, Penrith, NSW, 2751, Australia
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Algicidal process and mechanisms of Enterobacter hormaechei F2 revealed by an integrated transcriptomic and metabolomic approach. Genomics 2023; 115:110586. [PMID: 36796656 DOI: 10.1016/j.ygeno.2023.110586] [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: 10/28/2022] [Revised: 01/27/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023]
Abstract
Controlling eutrophication with algicidal bacteria is widely recognized as an effective solution. Here, an integrated transcriptomic and metabolomic approach was used to elucidate the algicidal process of Enterobacter hormaechei F2, which exhibits substantial algicidal activity. At the transcriptome level, RNA sequencing (RNA-seq) identified 1104 differentially expressed genes in the algicidal process of the strain, thus indicating that amino acids, energy metabolism, and signaling-related genes were significantly activated during the algicidal process according to the Kyoto Encyclopedia of Genes and Genomes enrichment analysis. By analyzing the enriched amino acid and energy metabolism pathways using metabolomics, we identified 38 upregulated and 255 downregulated significantly changed metabolites in the algicidal process and an accumulation of B vitamins, peptides, and energy substances. The integrated analysis demonstrated that energy and amino acid metabolism, co-enzymes and vitamins, and bacterial chemotaxis are the most important pathways for the algicidal process of this strain, and metabolites from these pathways, such as thiomethyladenosine, isopentenyl diphosphate, hypoxanthine, xanthine, nicotinamide, and thiamine, all exhibited algicidal activity.
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Nosenko T, Zimmer I, Ghirardo A, Köllner TG, Weber B, Polle A, Rosenkranz M, Schnitzler JP. Predicting functions of putative fungal sesquiterpene synthase genes based on multiomics data analysis. Fungal Genet Biol 2023; 165:103779. [PMID: 36706978 DOI: 10.1016/j.fgb.2023.103779] [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: 09/27/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023]
Abstract
Sesquiterpenes (STs) are secondary metabolites, which mediate biotic interactions between different organisms. Predicting the species-specific ST repertoires can contribute to deciphering the language of communication between organisms of the same or different species. High biochemical plasticity and catalytic promiscuity of sesquiterpene synthases (STSs), however, challenge the homology-based prediction of the STS functions. Using integrated analyses of genomic, transcriptomic, volatilomic, and metabolomic data, we predict product profiles for 116 out of 146 putative STS genes identified in the genomes of 30 fungal species from different trophic groups. Our prediction method is based on the observation that STSs encoded by genes closely related phylogenetically are likely to share the initial enzymatic reactions of the ST biosynthesis pathways and, therefore, produce STs via the same reaction route. The classification by reaction routes allows to assign STs known to be emitted by a particular species to the putative STS genes from this species. Gene expression information helps to further specify these ST-to-STS assignments. Validation of the computational predictions of the STS functions using both in silico and experimental approaches shows that integrated multiomic analyses are able to correctly link cyclic STs of non-cadalane type to genes. In the process of the experimental validation, we characterized catalytic properties of several putative STS genes from the mycorrhizal fungus Laccaria bicolor. We show that the STSs encoded by the L.bicolor mycorrhiza-induced genes emit either nerolidol or α-cuprenene and α-cuparene, and discuss the possible roles of these STs in the mycorrhiza formation.
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Affiliation(s)
- Tetyana Nosenko
- Helmholtz Zentrum München, Research Unit Environmental Simulation, 85764 Neuherberg, Germany.
| | - Ina Zimmer
- Helmholtz Zentrum München, Research Unit Environmental Simulation, 85764 Neuherberg, Germany
| | - Andrea Ghirardo
- Helmholtz Zentrum München, Research Unit Environmental Simulation, 85764 Neuherberg, Germany
| | - Tobias G Köllner
- Max Planck Institute for Chemical Ecology, Department of Natural Product Biosynthesis, 07745 Jena, Germany
| | - Baris Weber
- Helmholtz Zentrum München, Research Unit Environmental Simulation, 85764 Neuherberg, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Göttingen, 37077 Göttingen, Germany
| | - Maaria Rosenkranz
- Helmholtz Zentrum München, Research Unit Environmental Simulation, 85764 Neuherberg, Germany
| | - Jörg-Peter Schnitzler
- Helmholtz Zentrum München, Research Unit Environmental Simulation, 85764 Neuherberg, Germany
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Li X, Lin Z, Yuan M, Zhao L, Yin P. The effects of extracellular algicidal compounds of Bacillus sp. B1 on Heterosigma akashiwo: a metabolomics approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:35635-35645. [PMID: 36534259 DOI: 10.1007/s11356-022-24255-3] [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: 07/14/2022] [Accepted: 11/13/2022] [Indexed: 06/17/2023]
Abstract
Heterosigma akashiwo (H. akashiwo), a harmful algal species, has been a global environmental problem. Extracellular algicidal compounds (EACs) extracted from Bacillus sp. B1 exhibited algicidal effects against H. akashiwo. However, little is known about the algicidal mechanism and metabolic process. In this study, metabolomics and physiological analyses were combined to investigate the cellular responses of H. akashiwo when treated with EACs. The results indicated that EACs at 10% (vEACs/vsample) showed more than 90% inhibition of H. akashiwo. EAC treatment resulted in excessive reactive oxygen species (ROS) production in algal cells, causing stress responses such as inhibition of photosynthetic pigment synthesis, reduction of sugar synthesis, imbalance of osmotic pressure in the cell membrane, disruption of cell size and morphology, and eventual cell death. The results reveal the underlying mechanism of the algicidal process and provide new insights into algae-bacteria interactions and the application of metabolomics to algal research.
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Affiliation(s)
- Xuanyue Li
- College of Chemistry and Materials Science, Jinan University, 510632, Guangzhou, People's Republic of China
| | - Zehong Lin
- Zijin Mining Group Co., Ltd., 364200, Longyan, People's Republic of China
| | - Meiyi Yuan
- School of Environment, Jinan University, 511443, Guangzhou, People's Republic of China
| | - Ling Zhao
- School of Environment, Jinan University, 511443, Guangzhou, People's Republic of China.
| | - Pinghe Yin
- College of Chemistry and Materials Science, Jinan University, 510632, Guangzhou, People's Republic of China
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Hu K, Li J, Zhao T, Zhou Q, Li Q, Hu X, Han G, Li S, Zou L, Liu S. Transcriptomic analysis reveals peripheral pathway in 3-phenoxybenzoic acid degradation by Aspergillus oryzae M-4. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116626. [PMID: 36327606 DOI: 10.1016/j.jenvman.2022.116626] [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: 09/01/2022] [Revised: 10/23/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
As a major intermediate metabolite of synthetic pyrethroids, the occurrence of 3-phenoxybenzoic acid hinders the decomposition of the parent pesticide and poses uncertain risks to environmental ecology and living organisms. Strain Aspergillus oryzae M-4 was previously reported to degrade 3-PBA and several substances were identified as downstream transformation products (TPs). But the mechanism underlying the cleavage of ether bond remains largely unclear. Here, we attempted to address such concern through identifying the peripheral TPs and analyzing transcriptomics, coupled with serial batch degradation experiments. Analysis results of chromatographic/mass spectrometry suggested that 3-PBA underwent twice hydroxylation, to yield mono- and dihydroxylated 3-PBA successively. In parallel, a mutual transformation between 3-PBA and 3-phenoxybenzyl alcohol (3-PBOH) also existed. The proposal of peripheral pathway represents an important advance towards fully understanding the whole 3-PBA metabolism in M-4. A specific altered metabolization was found for the first time, that is, resting cells of M-4 skipped the reduction step and initiate hydroxylation directly, by comparison with growing cells. Transcriptome analysis indicated that 3-PBA induced the up-regulation of genes related to energy investment, oxidative stress response, membrane transport and DNA repair. In-depth functional interpretation of differential expression genes suggested that the generation 3-PBOH and hydroxylated 3-PBA may be due to the participation of flavin-dependent monooxygenases (FMOs) and cytochrome P450 (CYP450), respectively. This study provides new insight to reveal the biodegradation mechanism of 3-PBA by A. oryzae M-4.
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Affiliation(s)
- Kaidi Hu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Jianlong Li
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Tianye Zhao
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Qiao Zhou
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Qin Li
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Xinjie Hu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Guoquan Han
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Shuhong Li
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, PR China.
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Transcriptome Analysis Reveals the Algicidal Mechanism of Brevibacillus laterosporus against Microcystis aeruginosa through Multiple Metabolic Pathways. Toxins (Basel) 2022; 14:toxins14070492. [PMID: 35878230 PMCID: PMC9320710 DOI: 10.3390/toxins14070492] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022] Open
Abstract
It is widely accepted that eutrophication has played an important role in the formation of harmful cyanobacterial blooms in recent decades, which impacts water quality and ecological environment and causes huge economic losses. Algicidal bacteria have a promising application prospect in controlling cyanobacterial blooms in aquaculture water. Here, the process of the algicidal bacterium Brevibacillus laterosporus strain Bl-zj acting on Microcystis aeruginosa was explored using transcriptome analysis to elucidate the algicidal mechanism. The results of the co-culture of bacterium and alga showed a strong alga-lysing effect of B. laterosporus against M. aeruginosa with an extreme morphology deformation of the algal cells. A total of 2744 differentially expressed genes of B. laterosporus were identified, which were mainly involved in the metabolism of amino acid, carbohydrate, and lipid. In the co-cultured group, the expression of genes mainly enriched in valine, leucine and isoleucine degradation, and fatty acid degradation were significantly increased. However, the expression of the genes related to ribosome were mainly inhibited. Transcriptome analysis showed that B. laterosporus obtained ATP and energy by the degradation of valine, leucine, isoleucine, and fatty acids, and destroyed algal cells by efflux pump transporters, secretion of hydrolytic enzymes, antibiotics, proteases, and other secondary metabolites, resulting in algal death and achieving the algicidal effect.
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Perczyk P, Broniatowski M. Membrane composition and successful bioaugmentation. Studies of the interactions of model thylakoid and plasma cyanobacterial and bacterial membranes with fungal membrane-lytic enzyme Lecitase ultra. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183888. [PMID: 35189110 DOI: 10.1016/j.bbamem.2022.183888] [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: 12/03/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Cyanobacterial/bacterial consortia are frequently inoculated to soils to increase the soil fertility and to accelerate the biodegradation of organic pollutants. Moreover, such consortia can also be successfully applied in landfills especially for the biodegradation of plastic wastes. However, the bioaugmentation techniques turn out frequently inefficient due to the competition of the indigenous microorganisms attacking directly these inoculated or secreting to their surroundings cell wall and membrane-lytic enzymes. It can be hypothesized that the resistance of the microbial membrane to the enzymatic degradation is correlated with its lipid composition. To verify this hypothesis glycolipid and phospholipid Langmuir monolayers were applied as models of thylakoid and plasma cyanobacterial and bacterial membranes. Hybrid fungal enzyme Lecitase ultra joining the activity of lipase and phospholipase A1 was applied as the model of fungal membrane-lytic enzyme. It turned out that anionic thylakoid lipids sulfoquinovosyldiacylglycerol and phosphatidylglycerols were the main targets of Lecitase ultra in the model multicomponent thylakoid membranes. The resistance of the model plasma bacterial membranes to enzymatic degradation depended significantly to their composition. The resistance increased generally when the unsaturated lipids were exchanged to their saturated counterparts. However, most resistant turned out the membranes composed of unsaturated phosphatidylamine and saturated anionic phospholipids.
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Affiliation(s)
- Paulina Perczyk
- Department of Environmental Chemistry, Faculty of Chemistry, The Jagiellonian University in Krakow, Gronostajowa 2, 30-387 Kraków, Poland
| | - Marcin Broniatowski
- Department of Environmental Chemistry, Faculty of Chemistry, The Jagiellonian University in Krakow, Gronostajowa 2, 30-387 Kraków, Poland..
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Kong Y, Wang Y, Miao L, Mo S, Li J, Zheng X. Recent Advances in the Research on the Anticyanobacterial Effects and Biodegradation Mechanisms of Microcystis aeruginosa with Microorganisms. Microorganisms 2022; 10:microorganisms10061136. [PMID: 35744654 PMCID: PMC9229865 DOI: 10.3390/microorganisms10061136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/28/2022] [Accepted: 05/29/2022] [Indexed: 02/04/2023] Open
Abstract
Harmful algal blooms (HABs) have attracted great attention around the world due to the numerous negative effects such as algal organic matters and cyanobacterial toxins in drinking water treatments. As an economic and environmentally friendly technology, microorganisms have been widely used for pollution control and remediation, especially in the inhibition/biodegradation of the toxic cyanobacterium Microcystis aeruginosa in eutrophic water; moreover, some certain anticyanobacterial microorganisms can degrade microcystins at the same time. Therefore, this review aims to provide information regarding the current status of M. aeruginosa inhibition/biodegradation microorganisms and the acute toxicities of anticyanobacterial substances secreted by microorganisms. Based on the available literature, the anticyanobacterial modes and mechanisms, as well as the in situ application of anticyanobacterial microorganisms are elucidated in this review. This review aims to enhance understanding the anticyanobacterial microorganisms and provides a rational approach towards the future applications.
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Affiliation(s)
- Yun Kong
- College of Resources and Environment, Yangtze University, Wuhan 430100, China;
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi’an University of Technology, Xi’an 710048, China; (S.M.); (J.L.); (X.Z.)
- Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310058, China
- Correspondence: ; Tel./Fax: +86-27-69111182
| | - Yue Wang
- College of Resources and Environment, Yangtze University, Wuhan 430100, China;
| | - Lihong Miao
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China;
| | - Shuhong Mo
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi’an University of Technology, Xi’an 710048, China; (S.M.); (J.L.); (X.Z.)
| | - Jiake Li
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi’an University of Technology, Xi’an 710048, China; (S.M.); (J.L.); (X.Z.)
| | - Xing Zheng
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi’an University of Technology, Xi’an 710048, China; (S.M.); (J.L.); (X.Z.)
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Kumar A, Yadav AN, Mondal R, Kour D, Subrahmanyam G, Shabnam AA, Khan SA, Yadav KK, Sharma GK, Cabral-Pinto M, Fagodiya RK, Gupta DK, Hota S, Malyan SK. Myco-remediation: A mechanistic understanding of contaminants alleviation from natural environment and future prospect. CHEMOSPHERE 2021; 284:131325. [PMID: 34216922 DOI: 10.1016/j.chemosphere.2021.131325] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
Industrialization and modernization of agricultural systems contaminated lithosphere, hydrosphere, and biosphere of the Earth. Sustainable remediation of contamination is essential for environmental sustainability. Myco-remediation is proposed to be a green, economical, and efficient technology over conventional remediation technologies to combat escalating pollution problems at a global scale. Fungi can perform remediation of pollutants through several mechanisms like biosorption, precipitation, biotransformation, and sequestration. Myco-remediation significantly removes or degrades metal metals, persistent organic pollutants, and other emerging pollutants. The current review highlights the species-specific remediation potential, influencing factors, genetic and molecular control mechanism, applicability merits to enhance the bioremediation efficiency. Structure and composition of fungal cell wall is crucial for immobilization of toxic pollutants and a subtle change on fungal cell wall structure may significantly affect the immobilization efficiency. The utilization protocol and applicability of enzyme engineering and myco-nanotechnology to enhance the bioremediation efficiency of any potential fungus was proposed. It is advocated that the association of hyper-accumulator plants with plant growth-promoting fungi could help in an effective cleanup strategy for the alleviation of persistent soil pollutants. The functions, activity, and regulation of fungal enzymes in myco-remediation practices required further research to enhance the myco-remediation potential. Study of the biotransformation mechanisms and risk assessment of the products formed are required to minimize environmental pollution. Recent advancements in molecular "Omic techniques"and biotechnological tools can further upgrade myco-remediation efficiency in polluted soils and water.
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Affiliation(s)
- Amit Kumar
- Central Muga Eri Research and Training Institute, Central Silk Board, Lahdoigarh, Jorhat, Assam, 785700, India
| | - Ajar Nath Yadav
- Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, 173101, India
| | - Raju Mondal
- Central Sericultural Germplasm Resources Centre (CSGRC), Central Silk Board, Ministry of Textiles, Thally Road, Hosur, Tamil Nadu, 635109, India
| | - Divjot Kour
- Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, 173101, India
| | - Gangavarapu Subrahmanyam
- Central Muga Eri Research and Training Institute, Central Silk Board, Lahdoigarh, Jorhat, Assam, 785700, India
| | - Aftab A Shabnam
- Central Muga Eri Research and Training Institute, Central Silk Board, Lahdoigarh, Jorhat, Assam, 785700, India
| | - Shakeel A Khan
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Krishna Kumar Yadav
- Faculty of Science and Technology, Madhyanchal Professional University, Ratibad, Bhopal, 462044, M.P., India.
| | - Gulshan Kumar Sharma
- ICAR-Indian Institute of Soil and Water Conservation, Research Centre, Dadwara Kota 324002, Rajasthan, India
| | - Marina Cabral-Pinto
- Geobiotec Research Centre, Department of Geoscience, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Ram Kishor Fagodiya
- Division of Soil and Crop Management, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India
| | - Dipak Kumar Gupta
- ICAR-Indian Agriculture Research Institute, Barhi, Hazaribagh, Jharkhand, 825411, India
| | - Surabhi Hota
- ICAR-Indian Institute of Soil and Water Conservation, Research Centre, Dadwara Kota 324002, Rajasthan, India
| | - Sandeep K Malyan
- Research Management and Outreach Division, National Institute of Hydrology, Jalvigyan Bhawan, Roorkee, Uttarakhand, 247667, India
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Mohamed ZA, Hashem M, Alamri S, Campos A, Vasconcelos V. Fungal biodegradation and removal of cyanobacteria and microcystins: potential applications and research needs. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:37041-37050. [PMID: 34053035 DOI: 10.1007/s11356-021-14623-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/25/2021] [Indexed: 05/26/2023]
Abstract
Harmful cyanobacterial blooms (HCB) have severe impacts on marine and freshwater systems worldwide. They cause oxygen depletion and produce potent cyanotoxins that have detrimental effects on human and environmental health and deteriorate the water quality. Biological treatment of the water for control of cyanobacterial blooms and removal of cyanotoxins can be a more economical and environment-friendly way, as they do not result in production of undesirable by-products. Most biological treatments of cyanobacteria and cyanotoxins have concentrated largely on bacteria, with little attention paid to algicidal fungi. Therefore, this review aims to provide an overview of the current status and the main progresses achieved in fungal biodegradation of HCB and cyanotoxin research. The available data revealed that 15 fungal species had high lytic activity against cyanobacteria, and 6 species were capable of degrading microcystins (MCs). Some fungal species (e.g., Aurobasidium pullulans and Trichoderma citrinoviride) have been identified to selectively inhibit the growth of cyanobacteria rather than beneficial species of other algal groups. Interestingly, some fungal strains (Trichaptum abietinum, Trichoderma citrinoviride) exhibited di-functional trait, being efficient in lysing cyanobacteria and degrading MCs released from the cells after decay. Beyond a comprehensive review of algicidal and toxin-degrading activities of fungi, this paper also identifies and prioritizes research gaps in algicidal fungi. The review also gives insights to the potential applications of algicidal fungi for removal of cyanobacterial blooms and their cyanotoxins from the aquatic environment.
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Affiliation(s)
- Zakaria A Mohamed
- Department of Botany, Faculty of Science, Sohag University, Sohag, 82524, Egypt.
| | - Mohamed Hashem
- College of Science, Department of Biology, King Khalid University, Abha, 61413, Saudi Arabia
- Faculty of Science, Botany and Microbiology Department, Assiut University, Assiut, 71516, Egypt
| | - Saad Alamri
- College of Science, Department of Biology, King Khalid University, Abha, 61413, Saudi Arabia
| | - Alexandre Campos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
| | - Vitor Vasconcelos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
- Departament of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, 4169-007, Porto, Portugal
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12
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Han G, Ma H, Ren S, Gao X, He X, Zhu S, Deng R, Zhang S. Insights into the mechanism of cyanobacteria removal by the algicidal fungi Bjerkandera adusta and Trametes versicolor. Microbiologyopen 2020; 9:e1042. [PMID: 32529805 PMCID: PMC7424253 DOI: 10.1002/mbo3.1042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 03/19/2020] [Accepted: 03/28/2020] [Indexed: 01/14/2023] Open
Abstract
Fungal mycelia can eliminate almost all cocultured cyanobacterial cells within a short time. However, molecular mechanisms of algicidal fungi are poorly understood. In this study, a time‐course transcriptomic analysis of algicidal fungus Bjerkandera adusta T1 was applied to investigate gene expression and regulation. A total of 132, 300, 422, and 823 differentially expressed genes (DEGs) were identified at 6, 12, 24, and 48 hr, respectively. Most DEGs exhibited high endopeptidase activity, cellulose catabolic process, and transmembrane transporter activity by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Many decomposition genes encoding endopeptidases were induced a little later in B. adusta T1 when compared with previously investigated algicidal fungus Trametes versicolor F21a. Besides, the accumulated expression of Polysaccharide lyases8 (PL8) gene with peptidoglycan and alginate decomposition abilities was greatly delayed in B. adusta T1 relative to T. versicolor F21a. It was implied that endopeptidases and enzymes of PL8 might be responsible for the strong algicidal ability of B. adusta T1 as well as T. versicolor F21a.
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Affiliation(s)
- Guomin Han
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
| | - Hui Ma
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Shenrong Ren
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xueyan Gao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiaolong He
- Institute of Applied Mathematics, Anhui Agricultural University, Hefei, China
| | - Suwen Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
| | - Ruining Deng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Shihua Zhang
- Institute of Applied Mathematics, Anhui Agricultural University, Hefei, China
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13
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Akhtar N, Mannan MAU. Mycoremediation: Expunging environmental pollutants. ACTA ACUST UNITED AC 2020; 26:e00452. [PMID: 32617263 PMCID: PMC7322808 DOI: 10.1016/j.btre.2020.e00452] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 04/04/2020] [Accepted: 04/04/2020] [Indexed: 01/27/2023]
Abstract
Mycoremediation of polycyclic aromatic hydrocarbons, challenges, and strategies to overcome. Role of the fungi in eradicating heavy metal contamination from the polluted sites. Mycoremediation of agricultural wastes including pesticides, herbicides, and cyanotoxins. Pharmaceutical wastes and strategies for its remediation using white-rot and ligninolytic fungus.
The ever-increasing population, rapid rate of urbanization, and industrialization are exacerbating the pollution-related problems. Soil and water pollution affect human health and the ecosystem. Thus, it is crucial to develop strategies to combat this ever-growing problem. Mycoremediation, employing fungi or its derivatives for remediation of environmental pollutants, is a comparatively cost-effective, eco-friendly, and effective method. It has advantages over other conventional and bioremediation methods. In this review, we have elucidated the harmful effects of common pollutants on public health and the environment. The role of several fungi in degrading these pollutants such as heavy metals, agricultural, pharmaceutical wastes, including polycyclic aromatic hydrocarbons, is enumerated. Future strategies to improve the rate and efficiency of mycoremediation are suggested. The manuscript describes the strategies which can be used as a future framework to address the global problem of pollution.
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Affiliation(s)
- Nahid Akhtar
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi, G.T. Road, Punjab 144401, India
| | - M Amin-Ul Mannan
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi, G.T. Road, Punjab 144401, India.,Department of Trans-Disciplinary Research, Division of Research and Development, Lovely Professional University, Jalandhar-Delhi, G.T. Road, Punjab 144401, India
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14
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Zhang Y, Wang J, Yajun C, Zhou M, Wang W, Geng M, Xu D, Xu Z. Comparative Genomics Uncovers the Genetic Diversity and Synthetic Biology of Secondary Metabolite Production of Trametes. MYCOBIOLOGY 2020; 48:104-114. [PMID: 32363038 PMCID: PMC7178859 DOI: 10.1080/12298093.2020.1725361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 01/02/2020] [Accepted: 01/22/2020] [Indexed: 05/27/2023]
Abstract
The carbohydrate-active enzyme (CAZyme) genes of Trametes contribute to polysaccharide degradation. However, the comprehensive analysis of the composition of CAZymes and the biosynthetic gene clusters (BGCs) of Trametes remain unclear. Here, we conducted comparative analysis, detected the CAZyme genes, and predicted the BGCs for nine Trametes strains. Among the 82,053 homologous clusters obtained for Trametes, we identified 8518 core genes, 60,441 accessory genes, and 13,094 specific genes. A large proportion of CAZyme genes were cataloged into glycoside hydrolases, glycosyltransferases, and carbohydrate esterases. The predicted BGCs of Trametes were divided into six strategies, and the nine Trametes strains harbored 47.78 BGCs on average. Our study revealed that Trametes exhibits an open pan-genome structure. These findings provide insights into the genetic diversity and explored the synthetic biology of secondary metabolite production for Trametes.
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Affiliation(s)
- Yan Zhang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Jingjing Wang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Chen Yajun
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Minghui Zhou
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Wei Wang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Ming Geng
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Decong Xu
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Zhongdong Xu
- School of Life Sciences, Hefei Normal University, Hefei, China
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15
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Han G, Cheng C, Zheng Y, Wang X, Xu Y, Wang W, Zhu S, Cheng B. Identification of Long Non-Coding RNAs and the Regulatory Network Responsive to Arbuscular Mycorrhizal Fungi Colonization in Maize Roots. Int J Mol Sci 2019; 20:E4491. [PMID: 31514333 PMCID: PMC6769569 DOI: 10.3390/ijms20184491] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/22/2019] [Accepted: 09/09/2019] [Indexed: 02/06/2023] Open
Abstract
Recently, long noncoding RNAs (lncRNAs) have emerged as vital regulators of many biological processes in animals and plants. However, to our knowledge no investigations on plant lncRNAs which respond to arbuscular mycorrhizal (AM) fungi have been reported thus far. In this study, maize roots colonized with AM fungus were analyzed by strand-specific RNA-Seq to identify AM fungi-responsive lncRNAs and construct an associated regulatory network. A total of 1837 differentially expressed protein coding genes (DEGs) were identified from maize roots with Rhizophagus irregularis inoculation. Many AM fungi-responsive genes were homologs to MtPt4, STR, STR2, MtFatM, and enriched pathways such as fatty acid biosynthesis, response to phosphate starvation, and nitrogen metabolism are consistent with previous studies. In total, 5941 lncRNAs were identified, of which more than 3000 were new. Of those, 63 lncRNAs were differentially expressed. The putative target genes of differentially expressed lncRNAs (DELs) were mainly related to phosphate ion transmembrane transport, cellular response to potassium ion starvation, and lipid catabolic processes. Regulatory network analysis showed that DELs might be involved in the regulation of bidirectional nutrient exchange between plant and AM fungi as mimicry of microRNA targets. The results of this study can broaden our knowledge on the interaction between plant and AM fungi.
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Affiliation(s)
- Guomin Han
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China.
| | - Chen Cheng
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Yanmei Zheng
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
| | - Yunjian Xu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Wei Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China.
| | - Suwen Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China.
| | - Beijiu Cheng
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China.
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