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Bokade P, Bajaj A. Molecular advances in mycoremediation of polycyclic aromatic hydrocarbons: Exploring fungal bacterial interactions. J Basic Microbiol 2023; 63:239-256. [PMID: 36670077 DOI: 10.1002/jobm.202200499] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/15/2022] [Accepted: 12/18/2022] [Indexed: 01/22/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous high global concern environmental pollutants and tend to bioaccumulate due to hydrophobic properties. These xenobiotics, having variable concentrations along different matrices, gradually undergo various physical, chemical, and biological transformation processes. Myco-remediation aids accelerated degradation by effectively transforming complex ring structures to oxidized/hydroxylated intermediates, which can further funnel to bacterial degradation pathways. Exploitation of such complementing fungal-bacterial enzymatic activity can overcome certain limitations of incomplete bioremediation process. Furthermore, high-throughput molecular methods can be employed to unveil community structure, taxon abundance, coexisting community interactions, and metabolic pathways under stressed conditions. The present review critically discusses the role of different fungal phyla in PAHs biotransformation and application of fungal-bacterial cocultures for enhanced mineralization. Moreover, recent advances in bioassays for PAH residue detection, monitoring, developing xenobiotics stress-tolerant strains, and application of fungal catabolic enzymes are highlighted. Application of next-generation sequencing methods to reveal complex ecological networks based on microbial community interactions and data analysis bias in performing such studies is further discussed in detail. Conclusively, the review underscores the application of mixed-culture approach by critically highlighting in situ fungal-bacterial community nexus and its role in complete mineralization of PAHs for the management of contaminated sites.
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Affiliation(s)
- Priyanka Bokade
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Abhay Bajaj
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Czaplicki LM, Redfern LK, Cooper EM, Ferguson PL, Vilgalys R, Gunsch CK. Investigating the mycobiome of the Holcomb Creosote Superfund Site. CHEMOSPHERE 2020; 252:126208. [PMID: 32229362 PMCID: PMC7242165 DOI: 10.1016/j.chemosphere.2020.126208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 12/20/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Even though many fungi are known to degrade a range of organic chemicals and may be advantageous for targeting hydrophobic chemicals with low bioavailability due to their ability to secrete extracellular enzymes, fungi are not commonly leveraged in the context of bioremediation. Here we sought to examine the fungal microbiome (mycobiome) at a model creosote polluted site to determine if fungi were prevalent under high PAH contamination conditions as well as to identify potential mycostimulation targets. Several significant positive associations were detected between OTUs and mid-to high-molecular weight PAHs. Several OTUs were closely related to taxa that have previously been identified in culture-based studies as PAH degraders. In particular, members belonging to the Ascomycota phylum were the most diverse at higher PAH concentrations suggesting this phylum may be promising biostimulation targets. There were nearly three times more positive correlations as compared to negative correlations, suggesting that creosote-tolerance is more common than creosote-sensitivity in the fungal community. Future work including shotgun metagenomic analysis would help confirm the presence of specific degradation genes. Overall this study suggests that mycobiome and bacterial microbiome analyses should be performed in parallel to devise the most optimal in situ biostimulation treatment strategies.
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Affiliation(s)
- Lauren M Czaplicki
- Pratt School of Engineering, Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27713, USA
| | - Lauren K Redfern
- Pratt School of Engineering, Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27713, USA
| | - Ellen M Cooper
- Nicholas School of the Environment, Duke University, Durham, NC, 27713, USA
| | - P Lee Ferguson
- Nicholas School of the Environment, Duke University, Durham, NC, 27713, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC, 27713, USA
| | - Claudia K Gunsch
- Pratt School of Engineering, Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27713, USA.
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Diversity and degradative capabilities of bacteria and fungi isolated from oil-contaminated and hydrocarbon-polluted soils in Kazakhstan. Appl Microbiol Biotechnol 2019; 103:7261-7274. [PMID: 31346684 DOI: 10.1007/s00253-019-10032-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/09/2019] [Accepted: 07/13/2019] [Indexed: 01/03/2023]
Abstract
Bacteria and fungi were isolated from eight different soil samples from different regions in Kazakhstan contaminated with oil or salt or aromatic compounds. For the isolation of the organisms, we used, on the one hand, typical hydrocarbons such as the well utilizable aliphatic alkane tetradecane, the hardly degradable multiple-branched alkane pristane, and the biaromatic compound biphenyl as enrichment substrates. On the other hand, we also used oxygenated derivatives of alicyclic and monoaromatic hydrocarbons, such as cyclohexanone and p-tert-amylphenol, which are known as problematic pollutants. Seventy-nine bacterial and fungal strains were isolated, and 32 of them that were clearly able to metabolize some of these substrates, as tested by HPLC-UV/Vis and GC-MS analyses, were characterized taxonomically by DNA sequencing. Sixty-two percent of the 32 isolated strains from 14 different genera belong to well-described hydrocarbon degraders like some Rhodococci as well as Acinetobacter, Pseudomonas, Fusarium, Candida, and Yarrowia species. However, species of the bacterial genus Curtobacterium, the yeast genera Lodderomyces and Pseudozyma, as well as the filamentous fungal genera Purpureocillium and Sarocladium, which have rarely been described as hydrocarbon degrading, were isolated and shown to be efficient tetradecane degraders, mostly via monoterminal oxidation. Pristane was exclusively degraded by Rhodococcus isolates. Candida parapsilosis, Fusarium oxysporum, Fusarium solani, and Rhodotorula mucilaginosa degraded cyclohexanone, and in doing so accumulate ε-caprolactone or hexanedioic acid as metabolites. Biphenyl was transformed by Pseudomonas/Stenotrophomonas isolates. When p-tert-amylphenol was used as growth substrate, none of the isolated strains were able to use it.
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Evaluating the mycostimulation potential of select carbon amendments for the degradation of a model PAH by an ascomycete strain enriched from a superfund site. Biodegradation 2018; 29:463-471. [PMID: 30003496 DOI: 10.1007/s10532-018-9843-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/29/2018] [Indexed: 12/23/2022]
Abstract
Although ecological flexibility has been well documented in fungi, it remains unclear how this flexibility can be exploited for pollutant degradation, especially in the Ascomycota phylum. In this work, we assess three mycostimulation amendments for their ability to induce degradation in Trichoderma harzanium, a model fungus previously isolated from a Superfund site contaminated with polycyclic aromatic hydrocarbons. The amendments used in the present study were selected based on the documented ecological roles of ascomycetes. Chitin was selected to simulate the parasitic ecological role while cellulose and wood were selected to mimic bulk soil and wood saprobic conditions, respectively. Each amendment was tested in liquid basal medium in 0.1 and 1% (w/v) suspensions. Both chitin and cellulose amendments were shown to promote anthracene degradation in T. harzanium with the 0.1% chitin amendment resulting in over 90% removal of anthracene. None of the targets monitored for gene expression were found to be upregulated suggesting alternate pathways may be used in T. harzanium. Overall, our data suggest that mycostimulation amendments can be improved by understanding the ecological roles of indigenous fungi. However, further research is needed to better estimate specific amendment requirements for a broader group of target fungi and follow up studies are needed to determine whether the trends observed herein translate to more realistic soil systems.
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Delsarte I, Delattre F, Rafin C, Veignie E. Investigations of benzo[a]pyrene encapsulation and Fenton degradation by starch nanoparticles. Carbohydr Polym 2018; 186:344-349. [DOI: 10.1016/j.carbpol.2018.01.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/22/2017] [Accepted: 01/10/2018] [Indexed: 02/07/2023]
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Delsarte I, Rafin C, Mrad F, Veignie E. Lipid metabolism and benzo[a]pyrene degradation by Fusarium solani: an unexplored potential. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:12177-12182. [PMID: 29392603 DOI: 10.1007/s11356-017-1164-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/26/2017] [Indexed: 06/07/2023]
Abstract
In a search for indigenous soil saprotrophic fungi for bioremediation purposes, Fusarium solani, a saprotrophic fungus belonging to the phylum Ascomycota, was isolated from a fossil carbon contaminated soil. The effect of the carbon source, glucose or olive oil, was investigated in vitro on the biomass produced by F. solani and on the degradation of benzo[a]pyrene (BaP) in mineral medium. After only 12 days of incubation, BaP degradation by F. solani was higher (37.4%) with olive oil used as the carbon source than the one obtained with glucose (4.2%). Catalase activity increased in the presence of olive oil (3.4 μkat mg-1 protein) in comparison with glucose (2.1 μkat mg-1 protein). When olive oil was used as the carbon source, BaP degradation increased up to 76.0% in the presence of a specific catalase inhibitor, 3-Amino-1,2,4-triazole (2 mM). This metabolic engineering strategy based both on the use of olive oil as carbon source (cultivation strategy) and on the blocking of the catalase activity could be an innovative and promising approach for fungal biodegradation of BaP and consequently for bioremediation of soil contaminated with polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Isabelle Delsarte
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV EA 4492), Université du Littoral Côte d'Opale, 59140, Dunkerque, France
| | - Catherine Rafin
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV EA 4492), Université du Littoral Côte d'Opale, 59140, Dunkerque, France.
| | - Fida Mrad
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV EA 4492), Université du Littoral Côte d'Opale, 59140, Dunkerque, France
| | - Etienne Veignie
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV EA 4492), Université du Littoral Côte d'Opale, 59140, Dunkerque, France
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Czaplicki LM, Gunsch CK. Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics. JOURNAL OF ENVIRONMENTAL ENGINEERING (NEW YORK, N.Y.) 2016; 142:10.1061/(ASCE)EE.1943-7870.0001141. [PMID: 28348455 PMCID: PMC5364726 DOI: 10.1061/(asce)ee.1943-7870.0001141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/31/2016] [Indexed: 05/30/2023]
Abstract
Bioremediation is generally viewed as a cost effective and sustainable technology because it relies on microbes to transform pollutants into benign compounds. Advances in molecular biological analyses allow unprecedented microbial detection and are increasingly incorporated into bioremediation. Throughout history, state-of-the-art techniques have informed bioremediation strategies. However, the insights those techniques provided were not as in depth as those provided by recently developed omics tools. Advances in next generation sequencing (NGS) have now placed metagenomics and metatranscriptomics within reach of environmental engineers. As NGS costs decrease, metagenomics and metatranscriptomics have become increasingly feasible options to rapidly scan sites for specific degradative functions and identify microorganisms important in pollutant degradation. These omic techniques are capable of revolutionizing biological treatment in environmental engineering by allowing highly sensitive characterization of previously uncultured microorganisms. Omics enables the discovery of novel microorganisms for use in bioaugmentation and supports systematic optimization of biostimulation strategies. This review describes the omics journey from roots in biology and medicine to its current status in environmental engineering including potential future directions in commercial application.
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Affiliation(s)
- Lauren M. Czaplicki
- Ph.D. Candidate, Department of Civil & Environmental Engineering, Duke University, Durham, NC 27708-0287 USA
| | - Claudia K. Gunsch
- Associate Professor, Department of Civil & Environmental Engineering, Duke University, Durham, NC 27708-0287 USA
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Synthesis of modified potato starches for aqueous solubilization of benzo[ a ]pyrene. Carbohydr Polym 2016; 144:83-8. [DOI: 10.1016/j.carbpol.2016.01.071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 01/26/2016] [Accepted: 01/30/2016] [Indexed: 11/24/2022]
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Stefani FOP, Bell TH, Marchand C, de la Providencia IE, El Yassimi A, St-Arnaud M, Hijri M. Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils. PLoS One 2015; 10:e0128272. [PMID: 26053848 PMCID: PMC4460130 DOI: 10.1371/journal.pone.0128272] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/23/2015] [Indexed: 12/21/2022] Open
Abstract
Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA) with culture-dependent (isolation using seven different growth media) techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.
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Affiliation(s)
- Franck O. P. Stefani
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
| | - Terrence H. Bell
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
| | - Charlotte Marchand
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
| | - Ivan E. de la Providencia
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
| | - Abdel El Yassimi
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
| | - Marc St-Arnaud
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
| | - Mohamed Hijri
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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Vigueras G, Shirai K, Hernández-Guerrero M, Morales M, Revah S. Growth of the fungus Paecilomyces lilacinus with n-hexadecane in submerged and solid-state cultures and recovery of hydrophobin proteins. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.06.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Fayeulle A, Veignie E, Slomianny C, Dewailly E, Munch JC, Rafin C. Energy-dependent uptake of benzo[a]pyrene and its cytoskeleton-dependent intracellular transport by the telluric fungus Fusarium solani. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:3515-3523. [PMID: 24271730 DOI: 10.1007/s11356-013-2324-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 11/04/2013] [Indexed: 06/02/2023]
Abstract
In screening indigenous soil filamentous fungi for polycyclic aromatic hydrocarbons (PAHs) degradation, an isolate of the Fusarium solani was found to incorporate benzo[a]pyrene (BaP) into fungal hyphae before degradation and mineralization. The mechanisms involved in BaP uptake and intracellular transport remain unresolved. To address this, the incorporation of two PAHs, BaP, and phenanthrene (PHE) were studied in this fungus. The fungus incorporated more BaP into cells than PHE, despite the 400-fold higher aqueous solubility of PHE compared with BaP, indicating that PAH incorporation is not based on a simple diffusion mechanism. To identify the mechanism of BaP incorporation and transport, microscopic studies were undertaken with the fluorescence probes Congo Red, BODIPY®493/503, and FM®4-64, targeting different cell compartments respectively fungal cell walls, lipids, and endocytosis. The metabolic inhibitor sodium azide at 100 mM totally blocked BaP incorporation into fungal cells indicating an energy-requirement for PAH uptake into the mycelium. Cytochalasins also inhibited BaP uptake by the fungus and probably its intracellular transport into fungal hyphae. The perfect co-localization of BaP and BODIPY reveals that lipid bodies constitute the intracellular storage sites of BaP in F. solani. Our results demonstrate an energy-dependent uptake of BaP and its cytoskeleton-dependent intracellular transport by F. solani.
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Affiliation(s)
- Antoine Fayeulle
- Unité de Chimie Environnementale et Interactions sur le Vivant UCEIV EA 4492, ULCO, Dunkerque, 59140, France
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