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Noorjahan A, Mahesh S, Aiyamperumal B, Anantharaman P. Exploring Marine Fungal Diversity and Their Applications in Agriculture. Fungal Biol 2022. [DOI: 10.1007/978-981-16-8877-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Lacerda ALDF, Proietti MC, Secchi ER, Taylor JD. Diverse groups of fungi are associated with plastics in the surface waters of the Western South Atlantic and the Antarctic Peninsula. Mol Ecol 2020; 29:1903-1918. [DOI: 10.1111/mec.15444] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Ana L. d. F. Lacerda
- Instituto de Oceanografia Universidade Federal do Rio Grande-FURG Rio Grande Brazil
| | - Maíra C. Proietti
- Instituto de Oceanografia Universidade Federal do Rio Grande-FURG Rio Grande Brazil
| | - Eduardo R. Secchi
- Instituto de Oceanografia Universidade Federal do Rio Grande-FURG Rio Grande Brazil
| | - Joe D. Taylor
- School of Science, Engineering and Environment University of Salford Manchester UK
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Nguyen LN, Commault AS, Kahlke T, Ralph PJ, Semblante GU, Johir MAH, Nghiem LD. Genome sequencing as a new window into the microbial community of membrane bioreactors - A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135279. [PMID: 31791792 DOI: 10.1016/j.scitotenv.2019.135279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/27/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
Recent developed sequencing techniques have resulted in a new and unprecedented way to study biological wastewater treatment, in which most organisms are uncultivable. This review provides (i) an insight on state-of-the-art sequencing techniques and their limitations; (ii) a critical assessment of the microbial community in biological reactor and biofouling layer in a membrane bioreactor (MBR). The data from high-throughput sequencing has been used to infer microbial growth conditions and metabolisms of microorganisms present in MBRs at the time of sampling. These data shed new insight to two fundamental questions about a microbial community in the MBR process namely the microbial composition (who are they?) and the functions of each specific microbial assemblage (what are their function?). The results to date also highlight the complexity of the microbial community growing on MBRs. Environmental conditions are dynamic and diverse, and can influence the diversity and structural dynamics of any given microbial community for wastewater treatment. The benefits of understanding the structure of microbial communities on three major aspects of the MBR process (i.e. nutrient removal, biofouling control, and micropollutant removal) were symmetrically delineated. This review also indicates that the deployment of microbial community analysis for a practical engineering context, in terms of process design and system optimization, can be further realized.
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Affiliation(s)
- Luong N Nguyen
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, NSW 2007, Australia.
| | - Audrey S Commault
- Climate Change Cluster (C3), University of Technology Sydney, NSW 2007, Australia
| | - Tim Kahlke
- Climate Change Cluster (C3), University of Technology Sydney, NSW 2007, Australia
| | - Peter J Ralph
- Climate Change Cluster (C3), University of Technology Sydney, NSW 2007, Australia
| | - Galilee U Semblante
- Technical Services, Western Sydney University, Kingswood, NSW 2747, Australia
| | - Md Abu Hasan Johir
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, NSW 2007, Australia
| | - Long D Nghiem
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, NSW 2007, Australia; NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
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Bubnova EN, Georgieva ML, Grum-Grzhimailo OA. Method for Isolation and Enumeration of Fungi Developing in Marine Sediments. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718060061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Oppong-Danquah E, Parrot D, Blümel M, Labes A, Tasdemir D. Molecular Networking-Based Metabolome and Bioactivity Analyses of Marine-Adapted Fungi Co-cultivated With Phytopathogens. Front Microbiol 2018; 9:2072. [PMID: 30237790 PMCID: PMC6135897 DOI: 10.3389/fmicb.2018.02072] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/14/2018] [Indexed: 11/13/2022] Open
Abstract
Fungi represent a rich source of bioactive metabolites and some are marketed as alternatives to synthetic agrochemicals against plant pathogens. However, the culturability of fungal strains in artificial laboratory conditions is still limited and the standard mono-cultures do not reflect their full spectrum chemical diversity. Phytopathogenic fungi and bacteria have successfully been used in the activation of cryptic biosynthetic pathways to promote the production of new secondary metabolites in co-culture experiments. The aim of this study was to map the fungal diversity of Windebyer Noor, a brackish lake connected to Baltic Sea (Germany), to induce the chemical space of the isolated marine-adapted fungi by co-culturing with phytopathogens, and to assess their inhibitory potential against six commercially important phytopathogens. Out of 123 marine-adapted fungal isolates obtained, 21 were selected based on their phylogenetic and metabolite diversity. They were challenged with two phytopathogenic bacteria (Pseudomonas syringae and Ralstonia solanacearum) and two phytopathogenic fungi (Magnaporthe oryzae and Botrytis cinerea) on solid agar. An in-depth untargeted metabolomics approach incorporating UPLC-QToF-HRMS/MS-based molecular networking (MN), in silico MS/MS databases, and manual dereplication was employed for comparative analysis of the extracts belonging to nine most bioactive co-cultures and their respective mono-cultures. The phytopathogens triggered interspecies chemical communications with marine-adapted fungi, leading to the production of new compounds and enhanced expression of known metabolites in co-cultures. MN successfully generated a detailed map of the chemical inventory of both mono- and co-cultures. We annotated overall 18 molecular clusters (belonging to terpenes, alkaloids, peptides, and polyketides), 9 of which were exclusively produced in co-cultures. Several clusters contained compounds, which could not be annotated to any known compounds, suggesting that they are putatively new metabolites. Direct antagonistic effects of the marine-adapted fungi on the phytopathogens were observed and anti-phytopathogenic activity was demonstrated.The untargeted metabolomics approach combined with bioactivity testing allowed prioritization of two co-cultures for purification and characterization of marine fungal metabolites with crop-protective activity. To our knowledge, this is the first study employing plant pathogens to challenge marine-adapted fungi.
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Affiliation(s)
- Ernest Oppong-Danquah
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Delphine Parrot
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Antje Labes
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Department of Energy and Biotechnology, Flensburg University of Applied Sciences, Flensburg, Germany
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Kiel University, Kiel, Germany
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Papizadeh M, Wijayawardene NN, Amoozegar MA, Saba F, Fazeli SAS, Hyde KD. Neocamarosporium jorjanensis, N. persepolisi, and N. solicola spp. nov. (Neocamarosporiaceae, Pleosporales) isolated from saline lakes of Iran indicate the possible halotolerant nature for the genus. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1341-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Vera J, Gutiérrez MH, Palfner G, Pantoja S. Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile. World J Microbiol Biotechnol 2017; 33:157. [PMID: 28726124 DOI: 10.1007/s11274-017-2321-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/14/2017] [Indexed: 11/27/2022]
Abstract
Our study reports the diversity of culturable mycoplankton in the eastern South Pacific Ocean off Chile to contribute with novel knowledge on taxonomy of filamentous fungi isolated from distinct physicochemical and biological marine environments. We characterized spatial distribution of isolates, evaluated their viability and assessed the influence of organic substrate availability on fungal development. Thirty-nine Operational Taxonomic Units were identified from 99 fungal strains isolated from coastal and oceanic waters by using Automatic Barcode Gap Discovery. All Operational Taxonomic Units belonged to phylum Ascomycota and orders Eurotiales, Dothideales, Sordariales and Hypocreales, mainly Penicillium sp. (82%); 11 sequences did not match existing species in GenBank, suggesting occurrence of novel fungal taxa. Our results suggest that fungal communities in the South Pacific Ocean off Chile appear to thrive in a wide range of environmental conditions in the ocean and that substrate availability may be a factor influencing fungal viability in the ocean.
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Affiliation(s)
- Jeanett Vera
- Graduate Program in Oceanography, Department of Oceanography, University of Concepción, Concepción, Chile
| | - Marcelo H Gutiérrez
- Department of Oceanography and COPAS Sur-Austral, University of Concepción, Concepción, Chile
| | - Götz Palfner
- Department of Botany, University of Concepción, Concepción, Chile
| | - Silvio Pantoja
- Department of Oceanography and COPAS Sur-Austral, University of Concepción, Concepción, Chile.
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Yahr R, Schoch CL, Dentinger BTM. Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150336. [PMID: 27481788 PMCID: PMC4971188 DOI: 10.1098/rstb.2015.0336] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2016] [Indexed: 11/15/2022] Open
Abstract
The fungal kingdom is a hyperdiverse group of multicellular eukaryotes with profound impacts on human society and ecosystem function. The challenge of documenting and describing fungal diversity is exacerbated by their typically cryptic nature, their ability to produce seemingly unrelated morphologies from a single individual and their similarity in appearance to distantly related taxa. This multiplicity of hurdles resulted in the early adoption of DNA-based comparisons to study fungal diversity, including linking curated DNA sequence data to expertly identified voucher specimens. DNA-barcoding approaches in fungi were first applied in specimen-based studies for identification and discovery of taxonomic diversity, but are now widely deployed for community characterization based on sequencing of environmental samples. Collectively, fungal barcoding approaches have yielded important advances across biological scales and research applications, from taxonomic, ecological, industrial and health perspectives. A major outstanding issue is the growing problem of 'sequences without names' that are somewhat uncoupled from the traditional framework of fungal classification based on morphology and preserved specimens. This review summarizes some of the most significant impacts of fungal barcoding, its limitations, and progress towards the challenge of effective utilization of the exponentially growing volume of data gathered from high-throughput sequencing technologies.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
- Rebecca Yahr
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Bryn T M Dentinger
- Royal Botanic Gardens Kew, Richmond, Surrey, UK Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Cledwyn Building, Penglais, Aberystwyth SY23 3DD, UK
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Abstract
Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.
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Affiliation(s)
- Jianping Xu
- a Department of Biology, McMaster University, Hamilton, ON, Canada.,b Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan, PR China.,c Institute of Tropical Diseases, Hainan Medical University, Haikou, Hainan, PR China
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Hayashi A, Crombie A, Lacey E, Richardson AJ, Vuong D, Piggott AM, Hallegraeff G. Aspergillus Sydowii Marine Fungal Bloom in Australian Coastal Waters, Its Metabolites and Potential Impact on Symbiodinium Dinoflagellates. Mar Drugs 2016; 14:md14030059. [PMID: 26999164 PMCID: PMC4810073 DOI: 10.3390/md14030059] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/03/2016] [Accepted: 03/03/2016] [Indexed: 11/16/2022] Open
Abstract
Dust has been widely recognised as an important source of nutrients in the marine environment and as a vector for transporting pathogenic microorganisms. Disturbingly, in the wake of a dust storm event along the eastern Australian coast line in 2009, the Continuous Plankton Recorder collected masses of fungal spores and mycelia (~150,000 spores/m³) forming a floating raft that covered a coastal area equivalent to 25 times the surface of England. Cultured A. sydowii strains exhibited varying metabolite profiles, but all produced sydonic acid, a chemotaxonomic marker for A. sydowii. The Australian marine fungal strains share major metabolites and display comparable metabolic diversity to Australian terrestrial strains and to strains pathogenic to Caribbean coral. Secondary colonisation of the rafts by other fungi, including strains of Cladosporium, Penicillium and other Aspergillus species with distinct secondary metabolite profiles, was also encountered. Our bioassays revealed that the dust-derived marine fungal extracts and known A. sydowii metabolites such as sydowic acid, sydowinol and sydowinin A adversely affect photophysiological performance (Fv/Fm) of the coral reef dinoflagellate endosymbiont Symbiodinium. Different Symbiodinium clades exhibited varying sensitivities, mimicking sensitivity to coral bleaching phenomena. The detection of such large amounts of A. sydowii following this dust storm event has potential implications for the health of coral environments such as the Great Barrier Reef.
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Affiliation(s)
- Aiko Hayashi
- Institute for Marine & Antarctic Studies, University of Tasmania, Hobart, Tasmania 7004, Australia.
| | - Andrew Crombie
- Microbial Screening Technologies, Building A, 28-54 Percival Rd, Smithfield NSW 2164, Australia.
| | - Ernest Lacey
- Microbial Screening Technologies, Building A, 28-54 Percival Rd, Smithfield NSW 2164, Australia.
| | - Anthony J Richardson
- CSIRO Marine & Atmospheric Research, Ecosciences Precinct, Brisbane, Queensland 4102, Australia.
- Centre for Applications in Natural Resource Mathematics, School of Mathematics and Physics, University of Queensland, St Lucia, Queensland 4072, Australia.
| | - Daniel Vuong
- Microbial Screening Technologies, Building A, 28-54 Percival Rd, Smithfield NSW 2164, Australia.
| | - Andrew M Piggott
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia.
| | - Gustaaf Hallegraeff
- Institute for Marine & Antarctic Studies, University of Tasmania, Hobart, Tasmania 7004, Australia.
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Wang Y, Barth D, Tamminen A, Wiebe MG. Growth of marine fungi on polymeric substrates. BMC Biotechnol 2016; 16:3. [PMID: 26772742 PMCID: PMC4715362 DOI: 10.1186/s12896-016-0233-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Marine fungi are a diverse group of opportunistic and obligate organisms isolated from marine environments. These fungi are now often included in screens for novel metabolites, while less attention has been given to their production of hydrolytic enzymes. Most enzymes derived from marine microorganisms have been obtained from marine bacteria. The enzymes produced by marine fungi may have different properties than those derived from bacteria or from terrestrial fungi. Here we assess the growth of six filamentous marine fungi on a wide range of polymeric substrates as an indication of their general capacity to produce hydrolytic enzymes. RESULTS Calcarisporium sp. KF525, Tritirachium sp. LF562, Bartalinia robillardoides LF550, Penicillium pinophilum LF458, Scopulariopsis brevicaulis LF580 and Pestalotiopsis sp. KF079 all grew on both casein and gelatin as N-source, indicating secretion of proteases. All species also grew on starch, laminarin, xylan, pectin and oil, indicating production of amylases, glucanases, xylanases, pectinases and lipases. Growth on cellulose occurred but was weaker than on xylan. All strains also grew to some extent on sulphated arabinogalactan, although only LF562 could utilise arabinose. Four strains grew on the sulphated ulvans, whereas only KF525 grew on agar or carrageenan. KF525 and LF562 showed limited growth on alginate. Although fucose was used as carbon source by several species, fucoidan did not support biomass production. CONCLUSIONS Marine fungi could be excellent sources of a wide range of hydrolytic enzymes, including those able to hydrolyse various seaweed polymers. Although the native hosts may secrete only small amounts of these enzymes, the genes may provide a rich source of novel enzymes.
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Affiliation(s)
- Yanming Wang
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
| | - Dorothee Barth
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
| | - Anu Tamminen
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
| | - Marilyn G Wiebe
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
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