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Zucconi L, Cavallini G, Canini F. Trends in Antarctic soil fungal research in the context of environmental changes. Braz J Microbiol 2024; 55:1625-1634. [PMID: 38652442 PMCID: PMC11153391 DOI: 10.1007/s42770-024-01333-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Antarctic soils represent one of the most pristine environments on Earth, where highly adapted and often endemic microbial species withstand multiple extremes. Specifically, fungal diversity is extremely low in Antarctic soils and species distribution and diversity are still not fully characterized in the continent. Despite the unique features of this environment and the international interest in its preservation, several factors pose severe threats to the conservation of inhabiting ecosystems. In this light, we aimed to provide an overview of the effects on fungal communities of the main changes endangering the soils of the continent. Among these, the increasing human presence, both for touristic and scientific purposes, has led to increased use of fuels for transport and energy supply, which has been linked to an increase in unintentional environmental contamination. It has been reported that several fungal species have evolved cellular processes in response to these soil contamination episodes, which may be exploited for restoring contaminated areas at low temperatures. Additionally, the effects of climate change are another significant threat to Antarctic ecosystems, with the expected merging of previously isolated ecosystems and their homogenization. A possible reduction of biodiversity due to the disappearance of well-adapted, often endemic species, as well as an increase of biodiversity, due to the spreading of non-native, more competitive species have been suggested. Despite some studies describing the specialization of fungal communities and their correlation with environmental parameters, our comprehension of how soil communities may respond to these changes remains limited. The majority of studies attempting to precisely define the effects of climate change, including in situ and laboratory simulations, have mainly focused on the bacterial components of these soils, and further studies are necessary, including the other biotic components.
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Affiliation(s)
- Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.
- National Research Council, Institute of Polar Sciences, Messina, Italy.
| | - Giorgia Cavallini
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
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2
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da Silva MK, Barreto DLC, Vieira R, Neto AA, de Oliveira FS, Convey P, Rosa CA, Duarte AWF, Rosa LH. Diversity and enzymatic, biosurfactant and phytotoxic activities of culturable Ascomycota fungi present in marine sediments obtained near the South Shetland Islands, maritime Antarctica. Extremophiles 2024; 28:20. [PMID: 38493412 DOI: 10.1007/s00792-024-01336-4] [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: 12/09/2023] [Accepted: 02/11/2024] [Indexed: 03/18/2024]
Abstract
We studied the culturable fungal community recovered from deep marine sediments in the maritime Antarctic, and assessed their capabilities to produce exoenzymes, emulsifiers and metabolites with phytotoxic activity. Sixty-eight Ascomycota fungal isolates were recovered and identified. The most abundant taxon recovered was the yeast Meyerozyma guilliermondii, followed by the filamentous fungi Penicillium chrysogenum, P. cf. palitans, Pseudeurotium cf. bakeri, Thelebolus balaustiformis, Antarctomyces psychrotrophicus and Cladosporium sp. Diversity indices displayed low values overall, with the highest values obtained at shallow depth, decreasing to the deepest location sampled. Only M. guilliermondii and P. cf. palitans were detected in the sediments at all depths sampled, and were the most abundant taxa at all sample sites. The most abundant enzymes detected were proteases, followed by invertases, cellulases, lipases, carrageenases, agarases, pectinases and esterases. Four isolates showed good biosurfactant activity, particularly the endemic species A. psychrotrophicus. Twenty-four isolates of P. cf. palitans displayed strong phytotoxic activities against the models Lactuca sativa and Allium schoenoprasum. The cultivable fungi recovered demonstrated good biosynthetic activity in the production of hydrolytic exoenzymes, biosurfactant molecules and metabolites with phytotoxic activity, reinforcing the importance of documenting the taxonomic, ecological and biotechnological properties of fungi present in deep oceanic sediments of the Southern Ocean.
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Affiliation(s)
- Mayanne Karla da Silva
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Débora Luiza Costa Barreto
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rosemary Vieira
- Instituto de Geociências, Universidade Federal Fluminense, Rio de Janeiro, RJ, Brazil
| | - Arthur Ayres Neto
- Instituto de Geociências, Universidade Federal Fluminense, Rio de Janeiro, RJ, Brazil
| | | | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Las Palmeras 3425, Santiago, Chile
- Cape Horn International Center (CHIC), Puerto Williams, Chile
| | - Carlos Augusto Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Luiz Henrique Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, P. O. Box 486, Belo Horizonte, MG, CEP 31270-901, Brazil.
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de Melo Carlos L, Camacho KF, Duarte AW, de Oliveira VM, Boroski M, Rosa LH, Vieira R, Neto AA, Ottoni JR, Passarini MRZ. Bioprospecting the potential of the microbial community associated to Antarctic marine sediments for hydrocarbon bioremediation. Braz J Microbiol 2024; 55:471-485. [PMID: 38052770 PMCID: PMC10920520 DOI: 10.1007/s42770-023-01199-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/27/2023] [Indexed: 12/07/2023] Open
Abstract
Microorganisms that inhabit the cold Antarctic environment can produce ligninolytic enzymes potentially useful in bioremediation. Our study focused on characterizing Antarctic bacteria and fungi from marine sediment samples of King George and Deception Islands, maritime Antarctica, potentially affected by hydrocarbon influence, able to produce enzymes for use in bioremediation processes in environments impacted with petroleum derivatives. A total of 168 microorganism isolates were obtained: 56 from sediments of King George Island and 112 from Deception Island. Among them, five bacterial isolates were tolerant to cell growth in the presence of diesel oil and gasoline and seven fungal were able to discolor RBBR dye. In addition, 16 isolates (15 bacterial and one fungal) displayed enzymatic emulsifying activities. Two isolates were characterized taxonomically by showing better biotechnological results. Psychrobacter sp. BAD17 and Cladosporium sp. FAR18 showed pyrene tolerance (cell growth of 0.03 g mL-1 and 0.2 g mL-1) and laccase enzymatic activity (0.006 UL-1 and 0.10 UL-1), respectively. Our results indicate that bacteria and fungi living in sediments under potential effect of hydrocarbon pollution may represent a promising alternative to bioremediate cold environments contaminated with polluting compounds derived from petroleum such as polycyclic aromatic hydrocarbons and dyes.
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Affiliation(s)
- Layssa de Melo Carlos
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000 - Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Karine Fernandes Camacho
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000 - Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | | | | | - Marcela Boroski
- Programa de Pós-Graduação Em Energia & Sustentabilidade, Universidade Federal da Integração Latino-Americana - UNILA, Foz Do Iguaçu, Brazil
| | - Luiz Henrique Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rosemary Vieira
- Instituto de Geociências, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Arthur A Neto
- Instituto de Geociências, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Júlia Ronzella Ottoni
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000 - Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Michel R Z Passarini
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Av. Tarquínio Joslin dos Santos, 1000 - Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil.
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Li M, Raza M, Song S, Hou L, Zhang ZF, Gao M, Huang JE, Liu F, Cai L. Application of culturomics in fungal isolation from mangrove sediments. MICROBIOME 2023; 11:272. [PMID: 38082427 PMCID: PMC10712113 DOI: 10.1186/s40168-023-01708-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 10/19/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Fungi play a crucial role in ecosystems, and they have been widely considered a promising source for natural compounds that are crucial for drug discovery. Fungi have a high diversity, but about 95% of them remain unknown to science. The description rate of fungi is very low, mainly due to the inability of most fungi to grow in artificial media, which could not provide a sufficiently similar environment to their natural habitats. Moreover, many species in nature are in a state of low metabolic activity which cannot readily proliferate without proper resuscitation. Previously developed culturomics techniques are mostly designed and applicable for bacteria, with few attempts for fungal isolation because of their significantly larger cell size and hyphal growth properties. RESULTS This study attempted to isolate previously uncultured and rare fungi from mangrove sediments using newly developed fungal enrichment culture method (FECM) and fungal isolation chips (FiChips). Comparison of fungal community composition at different enrichment stages showed that FECM had great influence on fungal community composition, with rare taxa increased significantly, thus improving the isolation efficiency of previously uncultured fungi. Similarly, in situ cultivation using FiChips has a significant advantage in detecting and culturing rare fungi, as compared to the conventional dilution plate method (DPM). In addition, based on morphological comparisons and phylogenetic analyses, we described and proposed 38 new ascomycetous taxa, including three new families, eight new genera, 25 new species, and two new combinations (presented in additional file 1). CONCLUSIONS Our study demonstrated that mangrove sediments harbor a high diversity of fungi, and our new isolation approaches (FECM and FiChips) presented a high efficiency in isolating hitherto uncultured fungi, which is potentially usable for fungal isolation in other similar environments. Video Abstract.
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Affiliation(s)
- Meng Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mubashar Raza
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Integrated Pest Management On Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Shuang Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingwei Hou
- Key Lab of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Zhi-Feng Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Min Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-En Huang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Lin Y, Fang L, Chen H, Sun X, He Y, Duan B, Li R, Cao C, Chen J. Sex-specific competition differently regulates the response of the rhizosphere fungal community of Hippophae rhamnoides-A dioecious plant, under Mn stress. Front Microbiol 2023; 14:1102904. [PMID: 36744096 PMCID: PMC9892859 DOI: 10.3389/fmicb.2023.1102904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023] Open
Abstract
In this study, we investigated the soil physicochemical parameters and responses of rhizospheric fungal communities of Hippophae rhamnoides to Mn stress under different sexual competition patterns. The results showed that competition significantly affects soil physicochemical properties, enzyme activity, and rhizosphere-associated fungal community structures. Under Mn stress, soils with intersexual competition had higher levels of N supply than those with the intrasexual competition. Moreover, fungal communities under intersexual interaction were more positive to Mn stress than intrasexual interaction. Under intrasexual competition, female plants had higher total phosphorus content, neutral phosphatase activity, and relative abundance of symbiotic fungi in soils to obtain phosphorus nutrients to alleviate Mn stress. In contrast, male plants had relatively stable fungal communities in soils. In the intersexual competition, rhizosphere fungal diversity and relative abundance of saprophytic fungi in male plants were significantly higher than in female plants under Mn stress. In addition, female plants showed greater plasticity in the response of rhizosphere microorganisms to their neighbors of different sexes. The microbial composition in soils of female plants varied more than male plants between intrasexual and intersexual competition. These results indicated that sex-specific competition and neighbor effects regulate the microbial community structure and function of dioecious plants under heavy metal stress, which might affect nutrient cycling and phytoremediation potential in heavy metal-contaminated soils.
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Affiliation(s)
- Yuhu Lin
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China,School of Resources and Environmental Engineering, Mianyang Teachers’ College, Mianyang, China
| | - Ling Fang
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China,School of Resources and Environmental Engineering, Mianyang Teachers’ College, Mianyang, China
| | - Hao Chen
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China,School of Resources and Environmental Engineering, Mianyang Teachers’ College, Mianyang, China
| | - Xudong Sun
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China
| | - Yunxiao He
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China
| | - Baoli Duan
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Rui Li
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China
| | - Chuntao Cao
- Northwest Sichuan Geological Team, Sichuan Provincial Bureau of Geology and Mineral Resources Exploration and Development, Mianyang, China
| | - Juan Chen
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Teachers’College of Sichuan Province, Mianyang Teachers’ College, Mianyang, China,*Correspondence: Juan Chen, ✉
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6
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Younginger BS, Stewart NU, Balkan MA, Ballhorn DJ. Stable coexistence or competitive exclusion? Fern endophytes demonstrate rapid turnover favouring a dominant fungus. Mol Ecol 2023; 32:244-257. [PMID: 36218009 DOI: 10.1111/mec.16732] [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: 10/05/2020] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 12/29/2022]
Abstract
Fungal endophytes are critical members of the plant microbiome, but their community dynamics throughout an entire growing season are underexplored. Additionally, most fungal endophyte research has centred on seed-reproducing hosts, while spore-reproducing plants also host endophytes and may be colonized by unique community members. In order to examine annual fungal endophyte community dynamics in a spore-reproducing host, we explored endophytes in a single population of ferns, Polystichum munitum, in the Pacific Northwest. Through metabarcoding, we characterized the community assembly and temporal turnover of foliar endophytes throughout a growing season. From these results, we selected endophytes with outsized representations in sequence data and performed in vitro competition assays. Finally, we inoculated sterile fern gametophytes with dominant fungi observed in the field and determined their effects on host performance. Sequencing demonstrated that ferns were colonized by a diverse community of fungal endophytes in newly emerged tissue, but diversity decreased throughout the season leading to the preponderance of a single fungus in later sampling months. This previously undescribed endophyte appears to abundantly colonize the host to the detriment of other microfungi. Competition assays on a variety of media types failed to demonstrate that the dominant fungus was competitive against other fungi isolated from the same hosts, and inoculation onto sterile fern gametophytes did not alter growth compared to sterile controls, suggesting its effects are not antagonistic. The presence of this endophyte in the fern population probably demonstrates a case of repeated colonization driving competitive exclusion of other fungal community members.
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Affiliation(s)
| | - Nathan U Stewart
- Department of Biology, Portland State University, Portland, Oregon, USA
| | - Mehmet A Balkan
- Department of Biology, Portland State University, Portland, Oregon, USA
| | - Daniel J Ballhorn
- Department of Biology, Portland State University, Portland, Oregon, USA
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7
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Ordóñez-Enireb E, Cucalón RV, Cárdenas D, Ordóñez N, Coello S, Elizalde P, Cárdenas WB. Antarctic fungi with antibiotic potential isolated from Fort William Point, Antarctica. Sci Rep 2022; 12:21477. [PMID: 36509821 PMCID: PMC9744802 DOI: 10.1038/s41598-022-25911-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
The Antarctic continent is one of the most inhospitable places on earth, where living creatures, mostly represented by microorganisms, have specific physiological characteristics that allow them to adapt to the extreme environmental conditions. These physiological adaptations can result in the production of unique secondary metabolites with potential biotechnological applications. The current study presents a genetic and antibacterial characterization of four Antarctic fungi isolated from soil samples collected in Pedro Vicente Maldonado Scientific Station, at Fort William Point, Greenwich Island, Antarctica. Based on the sequences of the internal transcribed spacer (ITS) region, the fungi were identified as Antarctomyces sp., Thelebolus sp., Penicillium sp., and Cryptococcus gilvescens. The antibacterial activity was assessed against four clinical bacterial strains: Escherichia coli, Klebsiella pneumoniae, Enterococcus faecalis, and Staphylococcus aureus, by a modified bacterial growth inhibition assay on agar plates. Results showed that C. gilvescens and Penicillium sp. have potential antibiotic activity against all bacterial strains. Interestingly, Thelebolus sp. showed potential antibiotic activity only against E. coli. In contrast, Antarctomyces sp. did not show antibiotic activity against any of the bacteria tested under our experimental conditions. This study highlights the importance of conservation of Antarctica as a source of metabolites with important biomedical applications.
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Affiliation(s)
- Eunice Ordóñez-Enireb
- grid.442143.40000 0001 2107 1148Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Roberto V. Cucalón
- grid.442143.40000 0001 2107 1148Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador ,grid.35403.310000 0004 1936 9991Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Natural Resources Building 607 E. Peabody Dr., Champaign, IL 61820 USA
| | - Diana Cárdenas
- grid.442143.40000 0001 2107 1148Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Nadia Ordóñez
- grid.442143.40000 0001 2107 1148Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador ,grid.420044.60000 0004 0374 4101Biochemistry and Biosupport, Research and Development, Crop Science, Bayer AG, Monheim, Germany
| | - Santiago Coello
- grid.442143.40000 0001 2107 1148Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Paola Elizalde
- grid.442143.40000 0001 2107 1148Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador ,grid.25152.310000 0001 2154 235XVaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK S7N5E3 Canada ,grid.25152.310000 0001 2154 235XSchool of Public Health, University of Saskatchewan, Saskatoon, SK S7N5E5 Canada
| | - Washington B. Cárdenas
- grid.442143.40000 0001 2107 1148Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
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Taxonomic and functional trait-based approaches suggest that aerobic and anaerobic soil microorganisms allow the natural attenuation of oil from natural seeps. Sci Rep 2022; 12:7245. [PMID: 35508504 PMCID: PMC9068923 DOI: 10.1038/s41598-022-10850-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/31/2022] [Indexed: 12/02/2022] Open
Abstract
Natural attenuation, involving microbial adaptation, helps mitigating the effect of oil contamination of surface soils. We hypothesized that in soils under fluctuating conditions and receiving oil from seeps, aerobic and anaerobic bacteria as well as fungi could coexist to efficiently degrade hydrocarbons and prevent the spread of pollution. Microbial community diversity was studied in soil longitudinal and depth gradients contaminated with petroleum seeps for at least a century. Hydrocarbon contamination was high just next to the petroleum seeps but this level drastically lowered from 2 m distance and beyond. Fungal abundance and alpha-diversity indices were constant along the gradients. Bacterial abundance was constant but alpha-diversity indices were lower next to the oil seeps. Hydrocarbon contamination was the main driver of microbial community assemblage. 281 bacterial OTUs were identified as indicator taxa, tolerant to hydrocarbon, potentially involved in hydrocarbon-degradation or benefiting from the degradation by-products. These taxa belonging to lineages of aerobic and anaerobic bacteria, have specific functional traits indicating the development of a complex community adapted to the biodegradation of petroleum hydrocarbons and to fluctuating conditions. Fungi are less impacted by oil contamination but few taxa should contribute to the metabolic complementary within the microbial consortia forming an efficient barrier against petroleum dissemination.
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Likar M, Grašič M, Stres B, Regvar M, Gaberščik A. Original Leaf Colonisers Shape Fungal Decomposer Communities of Phragmites australis in Intermittent Habitats. J Fungi (Basel) 2022; 8:284. [PMID: 35330286 PMCID: PMC8951327 DOI: 10.3390/jof8030284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 01/29/2023] Open
Abstract
Common reed (Phragmites australis) has high biomass production and is primarily subjected to decomposition processes affected by multiple factors. To predict litter decomposition dynamics in intermittent lakes, it is critical to understand how communities of fungi, as the primary decomposers, form under different habitat conditions. This study reports the shotgun metagenomic sequencing of the initial fungal communities on common reed leaves decomposing under different environmental conditions. We demonstrate that a complex network of fungi forms already on the plant persists into the decomposition phase. Phragmites australis leaves contained at least five fungal phyla, with abundant Ascomycota (95.7%) and Basidiomycota (4.1%), identified as saprotrophs (48.6%), pathotrophs (22.5%), and symbiotrophs (12.6%). Most of the correlations between fungi in fresh and decomposing leaves were identified as co-occurrences (positive correlations). The geographic source of litter and leaf age did not affect the structure and diversity of fungal communities. Keystone taxa were mostly moisture-sensitive. Our results suggest that habitat has a strong effect on the formation of the fungal communities through keystone taxa. Nevertheless, it can also alter the proportions of individual fungal groups in the community through indirect effects on competition between the fungal taxa and their exploitation of favourable conditions.
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Affiliation(s)
- Matevž Likar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
| | - Mateja Grašič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
| | - Blaž Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Marjana Regvar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
| | - Alenka Gaberščik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
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Kazemzadeh S, Emami‐Karvani Z, Naghavi NS, Emtiazi G. Production of surface‐active sophorolipid biosurfactant and crude oil degradability by novel
Rhodotorula mucilaginosa
strain
SKF2. J SURFACTANTS DETERG 2022. [DOI: 10.1002/jsde.12572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Somayeh Kazemzadeh
- Department of Microbiology, Falavarjan Branch Islamic Azad University Isfahan Iran
| | | | | | - Giti Emtiazi
- Department of Biotechnology, Faculty of Biological Science and Technology Shahid Ashrafi Esfahani University Isfahan Iran
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11
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Wolińska A, Podlewski J, Słomczewski A, Grządziel J, Gałązka A, Kuźniar A. Fungal Indicators of Sensitivity and Resistance to Long-Term Maize Monoculture: A Culture-Independent Approach. Front Microbiol 2022; 12:799378. [PMID: 35046921 PMCID: PMC8761758 DOI: 10.3389/fmicb.2021.799378] [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: 10/21/2021] [Accepted: 12/07/2021] [Indexed: 01/04/2023] Open
Abstract
Although fungi are regarded as very important components of soils, the knowledge of their community in agricultural (monocultural) soils is still limited. This indicates that soil fungal communities are investigated less intensively than bacteria. Therefore, the main goal of this paper was to evaluate the fungal mycobiome structure in monoculture soils in a culture-independent approach. Firstly, the study was conducted to identify the core mycobiome composition and its variability at different stages of the maize growing season (spring, summer, and autumn). Secondly, we identified and recommended fungal indicators of both sensitivity and resistance to long-term maize monoculture. Two neighboring fields from the Potulicka Foundation area were selected for the study: K20 sown with a Gorzow mixture (intercropping mixture) to improve soil quality after a maize monoculture in 2020 and K21, where long-term (over 30 years) monoculture cultivation was continued. The basic chemical features [acidity, redox potential, total organic carbon (TOC), and moisture] of soils were determined, fungal genetic diversity was assessed by ITS next generation sequencing (NGS) analyses, and biodiversity indices were calculated. The results of the NGS technique facilitated recognition and classification of the fungal mycobiome to the taxonomic genus level and changes in the fungal structure in the three periods (spring, summer, and autumn) were assessed. It was evidenced that the mycobiome composition was dependent on both the seasons and the agricultural practices. It was also found that even a 1-year break in the monoculture in favor of an intercropping mixture improved soil properties thus contributing to higher biodiversity. Mortierella was recommended as a potential indicator of sensitivity to long-term maize cultivation, whereas Solicoccozyma and Exophiala were proposed as indicators of resistance to long-term maize cultivation. We proved that the precision farming principles applied on the Potulicka Foundation farm had a very positive effect on fungal biodiversity, which was high even in the long-term maize monoculture field. Therefore, the monoculture cultivation carried out in this way does not induce biological degradation of monoculture soils but preserves their good biological quality.
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Affiliation(s)
- Agnieszka Wolińska
- Department of Biology and Biotechnology of Microorganisms, Institute of Biological Sciences, The John Paul II Catholic University of Lublin, Lublin, Poland
| | | | | | - Jarosław Grządziel
- Department of Agriculture Microbiology, Institute of Soil Science and Plant Cultivation in Pulawy, Puławy, Poland
| | - Anna Gałązka
- Department of Agriculture Microbiology, Institute of Soil Science and Plant Cultivation in Pulawy, Puławy, Poland
| | - Agnieszka Kuźniar
- Department of Biology and Biotechnology of Microorganisms, Institute of Biological Sciences, The John Paul II Catholic University of Lublin, Lublin, Poland
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12
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Bianco A, Fancello F, Garau M, Deroma M, Atzori AS, Castaldi P, Zara G, Budroni M. Microbial and chemical dynamics of brewers' spent grain during a low-input pre-vermicomposting treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 802:149792. [PMID: 34464790 DOI: 10.1016/j.scitotenv.2021.149792] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/09/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
The eco-sustainability of industrial processes relies on the proper exploitation of by-products and wastes. Recently, brewers' spent grain (BSG), the main by-product of brewing, was successfully recycled through vermicomposting to produce an organic soil conditioner. However, the pre-processing step there applied (oven-drying) resulted in high costs and the suppression of microbial species beneficial for soil fertility. To overcome these limitations, a low-input pre-processing step was here applied to better exploit BSG microbiota and to make BSG suitable for vermicomposting. During 51 days of pre-treatment, the bacterial and fungal communities of BSG were monitored by denaturing gradient gel electrophoresis (DGGE). Chemical (carbon, nitrogen, ammonium, nitrate content, dissolved organic carbon) and biochemical (dehydrogenase activity) parameters were also evaluated. Mature vermicompost obtained from pre-processed BSG was characterized considering its legal requirements (e.g., absence of pathogens and mycotoxins, lack of phytotoxicity on seeds), microbiota composition, and chemical properties. Results obtained showed that throughout the pre-process, the BSG microbiota was enriched in bacterial and fungal species of significant biotechnological and agronomic potential, including lactic acid bacteria (Weissella, Pediococcus), plant growth-promoting bacteria (Bacillus, Pseudomonas, Pseudoxhantomonas), and biostimulant yeasts (Pichia fermentans, Trichoderma reesei, Beauveria bassiana). Pre-processing increased the suitability of BSG for earthworms' activity to produce high-quality mature vermicompost.
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Affiliation(s)
- Angela Bianco
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100 Sassari, Italy - Associated Member of the JRU MIRRI-IT
| | - Francesco Fancello
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100 Sassari, Italy
| | - Matteo Garau
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100 Sassari, Italy
| | - Mario Deroma
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100 Sassari, Italy
| | - Alberto S Atzori
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100 Sassari, Italy
| | - Paola Castaldi
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100 Sassari, Italy
| | - Giacomo Zara
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100 Sassari, Italy - Associated Member of the JRU MIRRI-IT.
| | - Marilena Budroni
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100 Sassari, Italy - Associated Member of the JRU MIRRI-IT
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Salicylate or Phthalate: The Main Intermediates in the Bacterial Degradation of Naphthalene. Processes (Basel) 2021. [DOI: 10.3390/pr9111862] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widely presented in the environment and pose a serious environmental threat due to their toxicity. Among PAHs, naphthalene is the simplest compound. Nevertheless, due to its high toxicity and presence in the waste of chemical and oil processing industries, naphthalene is one of the most critical pollutants. Similar to other PAHs, naphthalene is released into the environment via the incomplete combustion of organic compounds, pyrolysis, oil spills, oil processing, household waste disposal, and use of fumigants and deodorants. One of the main ways to detoxify such compounds in the natural environment is through their microbial degradation. For the first time, the pathway of naphthalene degradation was investigated in pseudomonades. The salicylate was found to be a key intermediate. For some time, this pathway was considered the main, if not the only one, in the bacterial destruction of naphthalene. However, later, data emerged which indicated that gram-positive bacteria in the overwhelming majority of cases are not capable of the formation/destruction of salicylate. The obtained data made it possible to reveal that protocatechoate, phthalate, and cinnamic acids are predominant intermediates in the destruction of naphthalene by rhodococci. Pathways of naphthalene degradation, the key enzymes, and genetic regulation are the main subjects of the present review, representing an attempt to summarize the current knowledge about the mechanism of the microbial degradation of PAHs. Modern molecular methods are also discussed in the context of the development of “omics” approaches, namely genomic, metabolomic, and proteomic, used as tools for studying the mechanisms of microbial biodegradation. Lastly, a comprehensive understanding of the mechanisms of the formation of specific ecosystems is also provided.
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The Mycobiota of High Altitude Pear Orchards Soil in Colombia. BIOLOGY 2021; 10:biology10101002. [PMID: 34681101 PMCID: PMC8533231 DOI: 10.3390/biology10101002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 01/04/2023]
Abstract
Simple Summary Soil fungi are extremely important in the agro-environment. They are among the main decomposers of organic matter, contributing to carbon, nitrogen, and phosphorous cycles. They often establish positive relationships with plants, protecting them from pathogens and abiotic stresses. This study aimed to uncover the soil fungal communities of two high altitude pear orchards with biomolecular techniques. We found a rich and diverse assemblage, dominated by fungi belonging to Ascomycota and Mortierellomycota. Most of the found species were novel records for soil fungi in Colombia. The most common fungal genera were Mortierella, Fusarium, Pseudaleria and Cylindrocarpon. Among the identified fungi, some species are known to be bioactive, with promising activities as biocontrol agents, plant-growth promoters, and producers of valuable substances. These results could contribute for a more attentive management of Colombian pear orchards in future and an enrichment of knowledge on Colombian biodiversity. Abstract In Colombia, the cultivation of deciduous fruit trees such as pear is expanding for socio-economic reasons and is becoming more and more important for the local population. Since organized cultivation is slowly replacing sustenance cultivation, scientific information on the present agro-environment is needed to proceed in this change in an organic and environmentally friendly way. In particular, this study is an accurate description of the mycobiota present in the bulk soil of two different high altitude pear orchards in the Colombian Andes. The metabarcoding of soil samples allowed an in-depth analysis of the whole fungal community. The fungal assemblage was generally dominated by Ascomycota and secondly by Mortierellomycota. As observed in other studies in Colombia, the genus Mortierella was found to be especially abundant. The soil of the different pear orchards appeared to host quite different fungal communities according to the soil physico-chemical properties. The common mycobiota contained 35 fungal species, including several species of Mortierella, Humicola, Solicoccozyma and Exophiala. Moreover, most of the identified fungal species (79%) were recorded for the first time in Colombian soils, thus adding important information on soil biodiversity regarding both Colombia and pear orchards.
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Lemmel F, Maunoury-Danger F, Leyval C, Cébron A. Altered fungal communities in contaminated soils from French industrial brownfields. JOURNAL OF HAZARDOUS MATERIALS 2021; 406:124296. [PMID: 33268205 DOI: 10.1016/j.jhazmat.2020.124296] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 05/20/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and metals are contaminants of industrial brownfield soils. Pollutants can have harmful effects on fungi, which are major actors of soil functioning. Our objective was to highlight fungal selection following long-term contamination of soils. Fungal diversity was assessed on 30 top-soil samples from ten sites gathered in three groups with different contamination levels and physico-chemical characteristics: 1) uncontaminated controls, 2) slag heaps displaying high PAH and moderate metal contaminations, and 3) settling ponds displaying high metal and intermediate PAH contaminations. Although fungal abundance and richness were similar among the soil groups, the diversity and evenness indices were lower for the slag heap group. Fungal diversity differed among soil groups at the phylum and OTU levels, and indicator species were identified. The relative abundance of Agaricomycetes, Saccharomycetes, Leotiomycetes and Chytridiomycota was higher in the control soils than in the two groups of contaminated soils. Cryptomycota LKM11 representatives were favoured in the slag heap and settling pond groups, and their relative abundance was correlated to the zinc and lead contamination levels. Dothideomycetes - positively linked to PAH contamination - and Eurotiomycetes were specific to the slag heap group. Pucciniomycetes and especially Gymnosporangium members were favoured in the settling pond soils.
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Affiliation(s)
- Florian Lemmel
- Université de Lorraine, CNRS, LIEC, Nancy F-54000, France
| | | | - Corinne Leyval
- Université de Lorraine, CNRS, LIEC, Nancy F-54000, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, Nancy F-54000, France.
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Wong RR, Lim ZS, Shaharuddin NA, Zulkharnain A, Gomez-Fuentes C, Ahmad SA. Diesel in Antarctica and a Bibliometric Study on Its Indigenous Microorganisms as Remediation Agent. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18041512. [PMID: 33562609 PMCID: PMC7915771 DOI: 10.3390/ijerph18041512] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/03/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Diesel acts as a main energy source to complement human activities in Antarctica. However, the increased expedition in Antarctica has threatened the environment as well as its living organisms. While more efforts on the use of renewable energy are being done, most activities in Antarctica still depend heavily on the use of diesel. Diesel contaminants in their natural state are known to be persistent, complex and toxic. The low temperature in Antarctica worsens these issues, making pollutants more significantly toxic to their environment and indigenous organisms. A bibliometric analysis had demonstrated a gradual increase in the number of studies on the microbial hydrocarbon remediation in Antarctica over the year. It was also found that these studies were dominated by those that used bacteria as remediating agents, whereas very little focus was given on fungi and microalgae. This review presents a summary of the collective and past understanding to the current findings of Antarctic microbial enzymatic degradation of hydrocarbons as well as its genotypic adaptation to the extreme low temperature.
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Affiliation(s)
- Rasidnie Razin Wong
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
| | - Zheng Syuen Lim
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, Shibaura Institute of Technology, College of Systems Engineering and Science, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan;
| | - Claudio Gomez-Fuentes
- Department of Chemical Engineering, Universidad de Magallanes, Avda. Bulnes, Punta Arenas, Región de Magallanes y Antártica Chilena 01855, Chile;
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes, Punta Arenas, Región de Magallanes y Antártica Chilena 01855, Chile
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (R.R.W.); (Z.S.L.); (N.A.S.)
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes, Punta Arenas, Región de Magallanes y Antártica Chilena 01855, Chile
- National Antarctic Research Centre, Universiti Malaya B303 Level 3, Block B, IPS Building, Kuala Lumpur 50603, Malaysia
- Correspondence:
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17
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Zucconi L, Canini F, Temporiti ME, Tosi S. Extracellular Enzymes and Bioactive Compounds from Antarctic Terrestrial Fungi for Bioprospecting. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17186459. [PMID: 32899827 PMCID: PMC7558612 DOI: 10.3390/ijerph17186459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022]
Abstract
Antarctica, one of the harshest environments in the world, has been successfully colonized by extremophilic, psychrophilic, and psychrotolerant microorganisms, facing a range of extreme conditions. Fungi are the most diverse taxon in the Antarctic ecosystems, including soils. Genetic adaptation to this environment results in the synthesis of a range of metabolites, with different functional roles in relation to the biotic and abiotic environmental factors, some of which with new biological properties of potential biotechnological interest. An overview on the production of cold-adapted enzymes and other bioactive secondary metabolites from filamentous fungi and yeasts isolated from Antarctic soils is here provided and considerations on their ecological significance are reported. A great number of researches have been carried out to date, based on cultural approaches. More recently, metagenomics approaches are expected to increase our knowledge on metabolic potential of these organisms, leading to the characterization of unculturable taxa. The search on fungi in Antarctica deserves to be improved, since it may represent a useful strategy for finding new metabolic pathways and, consequently, new bioactive compounds.
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Affiliation(s)
- Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università snc, 01100 Viterbo, Italy
- Correspondence: (L.Z.); (F.C.); Tel.: +39-328-2741247 (L.Z.); +39-347-9288247 (F.C.)
| | - Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università snc, 01100 Viterbo, Italy
- Correspondence: (L.Z.); (F.C.); Tel.: +39-328-2741247 (L.Z.); +39-347-9288247 (F.C.)
| | - Marta Elisabetta Temporiti
- Department of Earth and Environmental Sciences, University of Pavia, via S. Epifanio 14, 27100 Pavia, Italy; (M.E.T.); (S.T.)
| | - Solveig Tosi
- Department of Earth and Environmental Sciences, University of Pavia, via S. Epifanio 14, 27100 Pavia, Italy; (M.E.T.); (S.T.)
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Fungal Planet description sheets: 1042-1111. Persoonia - Molecular Phylogeny and Evolution of Fungi 2020; 44:301-459. [PMID: 33116344 PMCID: PMC7567971 DOI: 10.3767/persoonia.2020.44.11] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/30/2020] [Indexed: 12/31/2022]
Abstract
Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii.Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis.Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica.Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens.Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias.India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii.Poland, Lecanicillium praecognitum on insects’ frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.) from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa.Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae.UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis.USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.) on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.) from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes.
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Khan AR, Reichmann LG, Ibal JC, Shin JH, Liu Y, Collins H, LePage B, Terry N. Variation in pickleweed root-associated microbial communities at different locations of a saline solid waste management unit contaminated with petroleum hydrocarbons. PLoS One 2019; 14:e0222901. [PMID: 31581244 PMCID: PMC6776359 DOI: 10.1371/journal.pone.0222901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 09/10/2019] [Indexed: 12/03/2022] Open
Abstract
The main purpose of this study was to explore the potential influences of pickleweed vegetation on the abundance, diversity and metabolic activities of microbial communities in four distinct areas of a petroleum-contaminated solid waste management unit (SWMU) located in Contra Costa County, northern California. The four areas sampled include two central areas, one of which is central vegetated (CV) and one unvegetated (UV), and two peripheral vegetated areas, one of which is located to the west side of the SWMU (V-West) and one located to the east side (V-East). Measurements were made of total petroleum hydrocarbons (TPH), polyaromatic hydrocarbons (PAH), soil physicochemical properties, and various aspects of microbial communities including metabolic activities, microbial abundances (PLFAs), diversity and composition based on amplicon sequencing. The peripheral V-East and V-West sites had 10-times lower electrical conductivity (EC) than that of the CV and UV sites. The high salinity levels of the CV and UV sites were associated with significant reductions in bacterial and fungal abundances (PLFA) when compared to V-East but not when compared to V-West. TPH levels of CV and UV were not significantly different from those of V-West but were substantially lower than V-East TPH (19,311 mg/kg of dry soil), the high value of which may have been associated with a pipeline that ran through the area. Microbial activities (in terms of soil respiration and the activities of three soil enzymes, i.e., urease, lipase, and phosphatase) were greatest in the vegetated sites compared to the UV site. The prokaryotic community was not diverse as revealed by the Shannon index with no significant variation among the four groups of samples. However, the fungal community of the peripheral sites, V-East and V-West had significantly higher OTU richness and Shannon index. Structure of prokaryotic communities inhabiting the rhizosphere of pickleweed plants at the three sites differed significantly and were also different from those found in the UV region of the central site according to pairwise, global PERMANOVA and ANOSIM analyses. The differences in OTU-based rhizosphere-associated bacterial and fungal communities’ composition were explained mainly by the changes in soil EC and pH. The results suggest that saline TPH-contaminated areas that are vegetated with pickleweed are likely to have increased abundances, diversity and metabolic activities in the rhizosphere compared to unvegetated areas, even in the presence of high salinity.
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Affiliation(s)
- Abdur Rahim Khan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
- * E-mail: (NT); , (ARK)
| | - L. G. Reichmann
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - J. C. Ibal
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - J. H. Shin
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Y. Liu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - H. Collins
- USDA-ARS Grassland Soil and Water Research Laboratory, Temple, TX, United States of America
| | - B. LePage
- Pacific Gas and Electric Company, San Ramon, CA, United States of America
- The Academy of Natural Science, Philadelphia, PA, United States of America
| | - N. Terry
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
- * E-mail: (NT); , (ARK)
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Zhang C, Sirijovski N, Adler L, Ferrari BC. Exophiala macquariensis sp. nov., a cold adapted black yeast species recovered from a hydrocarbon contaminated sub-Antarctic soil. Fungal Biol 2019; 123:151-158. [DOI: 10.1016/j.funbio.2018.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 11/29/2022]
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Errington I, King CK, Wilkins D, Spedding T, Hose GC. Ecosystem effects and the management of petroleum-contaminated soils on subantarctic islands. CHEMOSPHERE 2018; 194:200-210. [PMID: 29207352 DOI: 10.1016/j.chemosphere.2017.11.157] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/26/2017] [Indexed: 06/07/2023]
Abstract
Human activity in the Polar Regions has resulted in petroleum contamination of soils. In this context, subantarctic islands are a unique management challenge for climatic, biological and logistical reasons. In this review we identify the main abiotic factors affecting petroleum-contaminated soils in the subantarctic environment, the primary effects of such contamination on biota, and lessons learned with regards to remediation techniques in this region. The sensitivity of biota to contamination depends on organism life stage, on soil properties, and on the degree of contaminant weathering. Initial studies using species endemic to subantarctic islands suggest that for fresh diesel fuel, sensitivities may range between 103 and 20 000 mg total petroleum hydrocarbons (TPH) kg -1 soil. Diesel that has undergone a short period of weathering is generally more toxic, with sensitivities ranging between 52 and 13 000 mg TPH kg-1 soil for an earthworm and a grass respectively (based on EC20 and IC50 values). A sufficient body of data from which to develop remediation targets for existing spills in the region does not yet exist for the region, but there has been a recent increase in research attention to address this data gap. A range of remediation methods have also now been trialled, and techniques such as in-ground aeration and nutrient addition have achieved some success. Passive management techniques such as permeable reactive barriers and phytoremediation are in preliminary stages of investigation for the region and show promise, not least because they cause less collateral disturbance than other methods.
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Affiliation(s)
- Ingrid Errington
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Catherine K King
- Antarctic Conservation and Management, Australian Antarctic Division, Kingston, Australia
| | - Daniel Wilkins
- Antarctic Conservation and Management, Australian Antarctic Division, Kingston, Australia
| | - Tim Spedding
- Antarctic Conservation and Management, Australian Antarctic Division, Kingston, Australia
| | - Grant C Hose
- Department of Biological Sciences, Macquarie University, Sydney, Australia.
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Duarte AWF, Dos Santos JA, Vianna MV, Vieira JMF, Mallagutti VH, Inforsato FJ, Wentzel LCP, Lario LD, Rodrigues A, Pagnocca FC, Pessoa Junior A, Durães Sette L. Cold-adapted enzymes produced by fungi from terrestrial and marine Antarctic environments. Crit Rev Biotechnol 2017; 38:600-619. [PMID: 29228814 DOI: 10.1080/07388551.2017.1379468] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Antarctica is the coldest, windiest, and driest continent on Earth. In this sense, microorganisms that inhabit Antarctica environments have to be adapted to harsh conditions. Fungal strains affiliated with Ascomycota and Basidiomycota phyla have been recovered from terrestrial and marine Antarctic samples. They have been used for the bioprospecting of molecules, such as enzymes. Many reports have shown that these microorganisms produce cold-adapted enzymes at low or mild temperatures, including hydrolases (e.g. α-amylase, cellulase, chitinase, glucosidase, invertase, lipase, pectinase, phytase, protease, subtilase, tannase, and xylanase) and oxidoreductases (laccase and superoxide dismutase). Most of these enzymes are extracellular and their production in the laboratory has been carried out mainly under submerged culture conditions. Several studies showed that the cold-adapted enzymes exhibit a wide range in optimal pH (1.0-9.0) and temperature (10.0-70.0 °C). A myriad of methods have been applied for cold-adapted enzyme purification, resulting in purification factors and yields ranging from 1.70 to 1568.00-fold and 0.60 to 86.20%, respectively. Additionally, some fungal cold-adapted enzymes have been cloned and expressed in host organisms. Considering the enzyme-producing ability of microorganisms and the properties of cold-adapted enzymes, fungi recovered from Antarctic environments could be a prolific genetic resource for biotechnological processes (industrial and environmental) carried out at low or mild temperatures.
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Affiliation(s)
- Alysson Wagner Fernandes Duarte
- a Universidade Federal de Alagoas, Campus Arapiraca , Arapiraca , Brazil.,b Divisão de Recursos Microbianos , Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Universidade Estadual de Campinas , Paulínia , Brazil
| | - Juliana Aparecida Dos Santos
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Marina Vitti Vianna
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Juliana Maíra Freitas Vieira
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Vitor Hugo Mallagutti
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Fabio José Inforsato
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Lia Costa Pinto Wentzel
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Luciana Daniela Lario
- d Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario , Rosario , Argentina.,e Departamento de Tecnologia Bioquímico-Farmacêutica , Faculdade de Ciências Farmacêuticas, Universidade de São Paulo , São Paulo , Brazil
| | - Andre Rodrigues
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Fernando Carlos Pagnocca
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Adalberto Pessoa Junior
- e Departamento de Tecnologia Bioquímico-Farmacêutica , Faculdade de Ciências Farmacêuticas, Universidade de São Paulo , São Paulo , Brazil
| | - Lara Durães Sette
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
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Iffis B, St-Arnaud M, Hijri M. Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities. FRONTIERS IN PLANT SCIENCE 2017; 8:1381. [PMID: 28848583 PMCID: PMC5550799 DOI: 10.3389/fpls.2017.01381] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/25/2017] [Indexed: 05/30/2023]
Abstract
Phytoremediation is a promising in situ green technology based on the use of plants to cleanup soils from organic and inorganic pollutants. Microbes, particularly bacteria and fungi, that closely interact with plant roots play key roles in phytoremediation processes. In polluted soils, the root-associated microbes contribute to alleviation of plant stress, improve nutrient uptake and may either degrade or sequester a large range of soil pollutants. Therefore, improving the efficiency of phytoremediation requires a thorough knowledge of the microbial diversity living in the rhizosphere and in close association with plant roots in both the surface and the endosphere. This study aims to assess fungal ITS and bacterial 16S rRNA gene diversity using high-throughput sequencing in rhizospheric soils and roots of three plant species (Solidago canadensis, Populus balsamifera, and Lycopus europaeus) growing spontaneously in three petroleum hydrocarbon polluted sedimentation basins. Microbial community structures of rhizospheric soils and roots were compared with those of microbes associated with arbuscular mycorrhizal fungal (AMF) spores to determine the links between the root and rhizosphere communities and those associated with AMF. Our results showed a difference in OTU richness and community structure composition between soils and roots for both bacteria and fungi. We found that petroleum hydrocarbon pollutant (PHP) concentrations have a significant effect on fungal and bacterial community structures in both soils and roots, whereas plant species identity showed a significant effect only on the roots for bacteria and fungi. Our results also showed that the community composition of bacteria and fungi in soil and roots varied from those associated with AMF spores harvested from the same plants. This let us to speculate that in petroleum hydrocarbon contaminated soils, AMF may release chemical compounds by which they recruit beneficial microbes to tolerate or degrade the PHPs present in the soil.
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Biotechnological Advances for Restoring Degraded Land for Sustainable Development. Trends Biotechnol 2017; 35:847-859. [PMID: 28606405 DOI: 10.1016/j.tibtech.2017.05.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 04/27/2017] [Accepted: 05/01/2017] [Indexed: 01/24/2023]
Abstract
Global land resources are under severe threat due to pollution and unsustainable land use practices. Restoring degraded land is imperative for regaining ecosystem services, such as biodiversity maintenance and nutrient and water cycling, and to meet the food, feed, fuel, and fibre requirements of present and future generations. While bioremediation is acknowledged as a promising technology for restoring polluted and degraded lands, its field potential is limited for various reasons. However, recent biotechnological advancements, including producing efficient microbial consortia, applying enzymes with higher degrees of specificity, and designing plants with specific microbial partners, are opening new prospects in remediation technology. This review provides insights into such promising ways to harness biotechnology as ecofriendly methods for remediation and restoration.
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Moghimi H, Heidary Tabar R, Hamedi J. Assessing the biodegradation of polycyclic aromatic hydrocarbons and laccase production by new fungus Trematophoma sp. UTMC 5003. World J Microbiol Biotechnol 2017; 33:136. [PMID: 28585171 DOI: 10.1007/s11274-017-2304-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/27/2017] [Indexed: 11/26/2022]
Abstract
Environmental pollution caused by petroleum compounds has become a global concern. The aim of this study was to evaluate the indigenous fungal isolates in Iran for biodegradation of crude oil pollutants. In order to isolate fungal strains, the soil samples were enriched in minimal salts medium (MSM) with 1% crude oil and then the crude oil degradation was measured by total petroleum hydrocarbon (TPH) assay. The degradation of hydrocarbons compounds was also analysed by FT-IR and HPLC, and the activity of peroxidase enzyme and biosurfactant production were also measured. We isolated 40 fungal strains and selected the isolate G-05 with 70% degradation ability of petroleum hydrocarbons as a premium isolate after 15 days. Residual crude oil analysis with FT-IR spectrophotometry and HPLC showed that G-05 is able to degrade 90 and 100% of aliphatic compounds and some polycyclic aromatic hydrocarbons (PAH), respectively. Evaluation of enzymatic activity showed that this isolate can produce 4 U L-1 of Laccase enzyme for oil removal; it is capable of producing biosurfactant and reducing the surface tension of the medium to 25.95 ± 0.1 m Nm-1. This strain was identified as a member of Trematophoma genus and the obtained results showed that this strain is a highly potent strain in bioremediation of soils contaminated by crude oil.
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Affiliation(s)
- Hamid Moghimi
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| | - Rezvan Heidary Tabar
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Javad Hamedi
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran
- Microbial Technology and Products Research Center, University of Tehran, Tehran, Iran
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Pudasaini S, Wilson J, Ji M, van Dorst J, Snape I, Palmer AS, Burns BP, Ferrari BC. Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods. Front Microbiol 2017; 8:591. [PMID: 28439263 PMCID: PMC5383709 DOI: 10.3389/fmicb.2017.00591] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 03/22/2017] [Indexed: 01/07/2023] Open
Abstract
Browning Peninsula is an ice-free polar desert situated in the Windmill Islands, Eastern Antarctica. The entire site is described as a barren landscape, comprised of frost boils with soils dominated by microbial life. In this study, we explored the microbial diversity and edaphic drivers of community structure across this site using traditional cultivation methods, a novel approach the soil substrate membrane system (SSMS), and culture-independent 454-tag pyrosequencing. The measured soil environmental and microphysical factors of chlorine, phosphate, aspect and elevation were found to be significant drivers of the bacterial community, while none of the soil parameters analyzed were significantly correlated to the fungal community. Overall, Browning Peninsula soil harbored a distinctive microbial community in comparison to other Antarctic soils comprised of a unique bacterial diversity and extremely limited fungal diversity. Tag pyrosequencing data revealed the bacterial community to be dominated by Actinobacteria (36%), followed by Chloroflexi (18%), Cyanobacteria (14%), and Proteobacteria (10%). For fungi, Ascomycota (97%) dominated the soil microbiome, followed by Basidiomycota. As expected the diversity recovered from culture-based techniques was lower than that detected using tag sequencing. However, in the SSMS enrichments, that mimic the natural conditions for cultivating oligophilic “k-selected” bacteria, a larger proportion of rare bacterial taxa (15%), such as Blastococcus, Devosia, Herbaspirillum, Propionibacterium and Methylocella and fungal (11%) taxa, such as Nigrospora, Exophiala, Hortaea, and Penidiella were recovered at the genus level. At phylum level, a comparison of OTU's showed that the SSMS shared 21% of Acidobacteria, 11% of Actinobacteria and 10% of Proteobacteria OTU's with soil. For fungi, the shared OTUs was 4% (Basidiomycota) and <0.5% (Ascomycota). This was the first known attempt to culture microfungi using the SSMS which resulted in an increase in diversity from 14 to 57 microfungi OTUs compared to standard cultivation. Furthermore, the SSMS offers the opportunity to retrieve a greater diversity of bacterial and fungal taxa for future exploitation.
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Affiliation(s)
- Sarita Pudasaini
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - John Wilson
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Mukan Ji
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Josie van Dorst
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Ian Snape
- Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and CommunitiesKingston, TAS, Australia
| | - Anne S Palmer
- Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and CommunitiesKingston, TAS, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
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Mercier A, Gravouil K, Aucher W, Brosset-Vincent S, Kadri L, Colas J, Bouchon D, Ferreira T. Fate of Eight Different Polymers under Uncontrolled Composting Conditions: Relationships Between Deterioration, Biofilm Formation, and the Material Surface Properties. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:1988-1997. [PMID: 28112955 DOI: 10.1021/acs.est.6b03530] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
With the ever-increasing volume of polymer wastes and their associated detrimental impacts on the environment, the plastic life cycle has drawn increasing attention. Here, eight commercial polymers selected from biodegradable to environmentally persistent materials, all formulated under a credit card format, were incubated in an outdoor compost to evaluate their fate over time and to profile the microbial communities colonizing their surfaces. After 450 days in compost, the samples were all colonized by multispecies biofilms, these latest displaying different amounts of adhered microbial biomass and significantly distinct bacterial and fungal community compositions depending on the substrate. Interestingly, colonization experiments on the eight polymers revealed a large core of shared microbial taxa, predominantly composed of microorganisms previously reported from environments contaminated with petroleum hydrocarbons or plastics debris. These observations suggest that biofilms may contribute to the alteration process of all the polymers studied. Actually, four substrates, independently of their assignment to a polymer group, displayed a significant deterioration, which might be attributed to biologically mediated mechanisms. Relevantly, the deterioration appears strongly associated with the formation of a high-cell density biofilm onto the polymer surfaces. The analysis of various surface properties revealed that roughness and hydrophilicity are likely prominent parameters for driving the biological interactions with the polymers.
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Affiliation(s)
- Anne Mercier
- Laboratoire coopératif ThanaplastSP-Carbios, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, and ‡Equipe Ecologie Evolution Symbiose, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, Université de Poitiers , 86073 Poitiers, France
| | - Kevin Gravouil
- Laboratoire coopératif ThanaplastSP-Carbios, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, and ‡Equipe Ecologie Evolution Symbiose, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, Université de Poitiers , 86073 Poitiers, France
| | - Willy Aucher
- Laboratoire coopératif ThanaplastSP-Carbios, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, and ‡Equipe Ecologie Evolution Symbiose, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, Université de Poitiers , 86073 Poitiers, France
| | - Sandra Brosset-Vincent
- Laboratoire coopératif ThanaplastSP-Carbios, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, and ‡Equipe Ecologie Evolution Symbiose, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, Université de Poitiers , 86073 Poitiers, France
| | - Linette Kadri
- Laboratoire coopératif ThanaplastSP-Carbios, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, and ‡Equipe Ecologie Evolution Symbiose, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, Université de Poitiers , 86073 Poitiers, France
| | - Jenny Colas
- Laboratoire coopératif ThanaplastSP-Carbios, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, and ‡Equipe Ecologie Evolution Symbiose, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, Université de Poitiers , 86073 Poitiers, France
| | - Didier Bouchon
- Laboratoire coopératif ThanaplastSP-Carbios, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, and ‡Equipe Ecologie Evolution Symbiose, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, Université de Poitiers , 86073 Poitiers, France
| | - Thierry Ferreira
- Laboratoire coopératif ThanaplastSP-Carbios, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, and ‡Equipe Ecologie Evolution Symbiose, Ecologie et Biologie des Interactions, Centre National de la Recherche Scientifique, UMR 7267, Université de Poitiers , 86073 Poitiers, France
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Iffis B, St-Arnaud M, Hijri M. Petroleum hydrocarbon contamination, plant identity and arbuscular mycorrhizal fungal (AMF) community determine assemblages of the AMF spore-associated microbes. Environ Microbiol 2016; 18:2689-704. [DOI: 10.1111/1462-2920.13438] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bachir Iffis
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal; 4101 Rue Sherbrooke Est Montréal QC H1X 2B2 Canada
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal; 4101 Rue Sherbrooke Est Montréal QC H1X 2B2 Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal; 4101 Rue Sherbrooke Est Montréal QC H1X 2B2 Canada
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Bourdel G, Roy-Bolduc A, St-Arnaud M, Hijri M. Concentration of Petroleum-Hydrocarbon Contamination Shapes Fungal Endophytic Community Structure in Plant Roots. Front Microbiol 2016; 7:685. [PMID: 27433155 PMCID: PMC4922216 DOI: 10.3389/fmicb.2016.00685] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/26/2016] [Indexed: 11/24/2022] Open
Abstract
Plant-root inhabiting fungi are a universal phenomenon found in all ecosystems where plants are able to grow, even in harsh environments. Interactions between fungi and plant roots can vary widely from mutualism to parasitism depending on many parameters. The role of fungal endophytes in phytoremediation of polluted sites, and characterization of the endophytic diversity and community assemblages in contaminated areas remain largely unexplored. In this study, we investigated the composition of endophytic fungal communities in the roots of two plant species growing spontaneously in petroleum-contaminated sedimentation basins of a former petro-chemical plant. The three adjacent basins showed a highly heterogeneous pattern of pollutant concentrations. We combined a culture-based isolation approach with the pyrosequencing of fungal ITS ribosomal DNA. We selected two species, Eleocharis erythropoda Steud. and Populus balsamifera L., and sampled three individuals of each species from each of three adjacent basins, each with a different concentration of petroleum hydrocarbons. We found that contamination level significantly shaped endophytic fungal diversity and community composition in E. erythropoda, with only 9.9% of these fungal Operational Taxonomic Units (OTUs) retrieved in all three basins. However, fungal community structure associated with P. balsamifera remained unaffected by the contamination level with 28.2% of fungal OTUs shared among all three basins. This could be explained by the smaller differences of pollutant concentrations in the soil around our set of P. balsamifera sampless compared to that around our set of E. erythropoda samples. Our culture-based approach allowed isolation of 11 and 30 fungal endophytic species from surface-sterilized roots of E. erythropoda and P. balsamifera, respectively. These isolates were ribotyped using ITS, and all were found in pyrosequensing datasets. Our results demonstrate that extreme levels of pollution reduce fungal diversity and shape community composition in E. erythropoda. Our findings shed light on the effect of soil petroleum contamination on fungal endophytic communities and could help to develop strategies for improving phytoremediation using fungal endophytes.
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Affiliation(s)
- Guillaume Bourdel
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal QC, Canada
| | - Alice Roy-Bolduc
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal QC, Canada
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal QC, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal QC, Canada
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Vida C, Bonilla N, de Vicente A, Cazorla FM. Microbial Profiling of a Suppressiveness-Induced Agricultural Soil Amended with Composted Almond Shells. Front Microbiol 2016; 7:4. [PMID: 26834725 PMCID: PMC4722121 DOI: 10.3389/fmicb.2016.00004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/05/2016] [Indexed: 12/12/2022] Open
Abstract
This study focused on the microbial profile present in an agricultural soil that becomes suppressive after the application of composted almond shells (AS) as organic amendments. For this purpose, we analyzed the functions and composition of the complex communities present in an experimental orchard of 40-year-old avocado trees, many of them historically amended with composted almond shells. The role of microbes in the suppression of Rosellinia necatrix, the causative agent of avocado white root rot, was determined after heat-treatment and complementation experiments with different types of soil. Bacterial and fungal profiles obtained from natural soil samples based on the 16S rRNA gene and ITS sequencing revealed slight differences among the amended (AS) and unamended (CT) soils. When the soil was under the influence of composted almond shells as organic amendments, an increase in Proteobacteria and Ascomycota groups was observed, as well as a reduction in Acidobacteria and Mortierellales. Complementary to these findings, functional analysis by GeoChip 4.6 confirmed these subtle differences, mainly present in the relative abundance of genes involved in the carbon cycle. Interestingly, a group of specific probes included in the "soil benefit" category was present only in AS-amended soils, corresponding to specific microorganisms previously described as potential biocontrol agents, such as Pseudomonas spp., Burkholderia spp., or Actinobacteria. Considering the results of both analyses, we determined that AS-amendments to the soil led to an increase in some orders of Gammaproteobacteria, Betaproteobacteria, and Dothideomycetes, as well as a reduction in the abundance of Xylariales fungi (where R. necatrix is allocated). The combination of microbial action and substrate properties of suppressiveness are discussed.
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Affiliation(s)
| | | | | | - Francisco M. Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones CientíficasMálaga, Spain
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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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Abstract
Fungi contribute extensively to a wide range of ecosystem processes, including decomposition of organic carbon, deposition of recalcitrant carbon, and transformations of nitrogen and phosphorus. In this review, we discuss the current knowledge about physiological and morphological traits of fungi that directly influence these processes, and we describe the functional genes that encode these traits. In addition, we synthesize information from 157 whole fungal genomes in order to determine relationships among selected functional genes within fungal taxa. Ecosystem-related traits varied most at relatively coarse taxonomic levels. For example, we found that the maximum amount of variance for traits associated with carbon mineralization, nitrogen and phosphorus cycling, and stress tolerance could be explained at the levels of order to phylum. Moreover, suites of traits tended to co-occur within taxa. Specifically, the genetic capacities for traits that improve stress tolerance-β-glucan synthesis, trehalose production, and cold-induced RNA helicases-were positively related to one another, and they were more evident in yeasts. Traits that regulate the decomposition of complex organic matter-lignin peroxidases, cellobiohydrolases, and crystalline cellulases-were also positively related, but they were more strongly associated with free-living filamentous fungi. Altogether, these relationships provide evidence for two functional groups: stress tolerators, which may contribute to soil carbon accumulation via the production of recalcitrant compounds; and decomposers, which may reduce soil carbon stocks. It is possible that ecosystem functions, such as soil carbon storage, may be mediated by shifts in the fungal community between stress tolerators and decomposers in response to environmental changes, such as drought and warming.
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Affiliation(s)
- Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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Krishnan A, Convey P, Gonzalez-Rocha G, Alias SA. Production of extracellular hydrolase enzymes by fungi from King George Island. Polar Biol 2014. [DOI: 10.1007/s00300-014-1606-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Endophytic fungi from the Amazonian plant Paullinia cupana and from Olea europaea isolated using cassava as an alternative starch media source. SPRINGERPLUS 2013; 2:579. [PMID: 25674409 PMCID: PMC4320186 DOI: 10.1186/2193-1801-2-579] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/28/2013] [Indexed: 11/10/2022]
Abstract
Endophytic fungi live inside plants, apparently do not cause any harm to their hosts and may play important roles in defense and growth promotion. Fungal growth is a routine practice at microbiological laboratories, and the Potato Dextrose Agar (PDA) is the most frequently used medium because it is a rich source of starch. However, the production of potatoes in some regions of the world can be costly. Aiming the development of a new medium source to tropical countries, in the present study, we used leaves from the guarana (a tropical plant from the Amazon region) and the olive (which grows in subtropical and temperate regions) to isolate endophytic fungi using PDA and Manihot Dextrose Agar (MDA). Cassava (Manihot esculenta) was evaluated as a substitute starch source. For guarana, the endophytic incidence (EI) was 90% and 98% on PDA and MDA media, respectively, and 65% and 70% for olive, respectively. The fungal isolates were sequenced using the ITS- rDNA region. The fungal identification demonstrated that the isolates varied according to the host plant and media source. In the guarana plant, 13 fungal genera were found using MDA and six were found using PDA. In the olive plant, six genera were obtained using PDA and 4 were obtained using MDA. The multivariate analysis results demonstrated the highest fungal diversity from guarana when using MDA medium. Interestingly, some genera were isolated from one specific host or in one specific media, suggesting the importance of these two factors in fungal isolation specificity. Thus, this study indicated that cassava is a feasible starch source that could serve as a potential alternative medium to potato medium.
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38
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Linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny. ISME JOURNAL 2013; 8:331-43. [PMID: 23985744 DOI: 10.1038/ismej.2013.149] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 07/16/2013] [Accepted: 07/24/2013] [Indexed: 11/08/2022]
Abstract
Phytoremediation is an attractive alternative to excavating and chemically treating contaminated soils. Certain plants can directly bioremediate by sequestering and/or transforming pollutants, but plants may also enhance bioremediation by promoting contaminant-degrading microorganisms in soils. In this study, we used high-throughput sequencing of bacterial 16S rRNA genes and the fungal internal transcribed spacer (ITS) region to compare the community composition of 66 soil samples from the rhizosphere of planted willows (Salix spp.) and six unplanted control samples at the site of a former petrochemical plant. The Bray-Curtis distance between bacterial communities across willow cultivars was significantly correlated with the distance between fungal communities in uncontaminated and moderately contaminated soils but not in highly contaminated (HC) soils (>2000 mg kg(-1) hydrocarbons). The mean dissimilarity between fungal, but not bacterial, communities from the rhizosphere of different cultivars increased substantially in the HC blocks. This divergence was partly related to high fungal sensitivity to hydrocarbon contaminants, as demonstrated by reduced Shannon diversity, but also to a stronger influence of willows on fungal communities. Abundance of the fungal class Pezizomycetes in HC soils was directly related to willow phylogeny, with Pezizomycetes dominating the rhizosphere of a monophyletic cluster of cultivars, while remaining in low relative abundance in other soils. This has implications for plant selection in phytoremediation, as fungal associations may affect the health of introduced plants and the success of co-inoculated microbial strains. An integrated understanding of the relationships between fungi, bacteria and plants will enable the design of treatments that specifically promote effective bioremediating communities.
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Çabuk A, Aytar P, Gedikli S, Özel YK, Kocabıyık E. Biosorption of acidic textile dyestuffs from aqueous solution by Paecilomyces sp. isolated from acidic mine drainage. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:4540-4550. [PMID: 23263759 DOI: 10.1007/s11356-012-1396-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 11/30/2012] [Indexed: 06/01/2023]
Abstract
Removal of textile dyestuffs from aqueous solution by biosorption onto a dead fungal biomass isolated from acidic mine drainage in the Çanakkale Region of Turkey was investigated. The fungus was found to be a promising biosorbent and identified as Paecilomyces sp. The optimal conditions for bioremediation were as follows: pH, 2.0; initial dyestuff concentration, 50 mg l(-1) for Reactive Yellow 85 and Reactive Orange 12, and 75 mg l(-1) for Reactive Black 8; biomass dosage, 2 g l(-1) for Reactive Yellow 85, 3 g l(-1) for Reactive Orange 12, 4 g l(-1) for Reactive Black 8; temperature, 25 °C; and agitation rate, 100 rpm. Zeta potential measurements indicated an electrostatic interaction between the binding sites and dye anions. Fourier transform infrared spectroscopy showed that amine, hydroxyl, carbonyl, and amide bonds were involved in the dyestuff biosorption. A toxicity investigation was also carried out before and after the biosorption process. These results showed that the toxicities for the reactive dyestuffs in aqueous solutions after biosorption studies decreased. The Freundlich and Langmuir adsorption models were used for the mathematical description of the biosorption equilibrium, and isotherm constants were evaluated for each dyestuff. Equilibrium data of biosorption of RY85 and RO12 dyestuffs fitted well to both models at the studied concentration and temperature.
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Affiliation(s)
- Ahmet Çabuk
- Department of Biology, Faculty of Arts and Science, Eskişehir Osmangazi University, Eskişehir, Turkey.
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