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Yi X, Lu H, Liu X, He J, Li B, Wang Z, Zhao Y, Zhang X, Yu X. Unravelling the enigma of the human microbiome: Evolution and selection of sequencing technologies. Microb Biotechnol 2024; 17:e14364. [PMID: 37929823 PMCID: PMC10832515 DOI: 10.1111/1751-7915.14364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023] Open
Abstract
The human microbiome plays a crucial role in maintaining health, with advances in high-throughput sequencing technology and reduced sequencing costs triggering a surge in microbiome research. Microbiome studies generally incorporate five key phases: design, sampling, sequencing, analysis, and reporting, with sequencing strategy being a crucial step offering numerous options. Present mainstream sequencing strategies include Amplicon sequencing, Metagenomic Next-Generation Sequencing (mNGS), and Targeted Next-Generation Sequencing (tNGS). Two innovative technologies recently emerged, namely MobiMicrobe high-throughput microbial single-cell genome sequencing technology and 2bRAD-M simplified metagenomic sequencing technology, compensate for the limitations of mainstream technologies, each boasting unique core strengths. This paper reviews the basic principles and processes of these three mainstream and two novel microbiological technologies, aiding readers in understanding the benefits and drawbacks of different technologies, thereby guiding the selection of the most suitable method for their research endeavours.
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Affiliation(s)
- Xin Yi
- Department of PharmacyShanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Hong Lu
- Department of Clinical laboratoryThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xiang Liu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Junyi He
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Bing Li
- Department of Public HealthShanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Zhelong Wang
- Department of PharmacyGuangdong Pharmaceutical UniversityGuangzhouPeople's Republic of China
| | - Yujing Zhao
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xinri Zhang
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xiao Yu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
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Kempken F. Marine fungi: A treasure trove of novel natural products and for biological discovery. PLoS Pathog 2023; 19:e1011624. [PMID: 37733683 PMCID: PMC10513230 DOI: 10.1371/journal.ppat.1011624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Affiliation(s)
- Frank Kempken
- Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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Arfken AM, Frey JF, Carrillo NI, Dike NI, Onyeachonamm O, Rivera DN, Davies CP, Summers KL. Porcine fungal mock community analyses: Implications for mycobiome investigations. Front Cell Infect Microbiol 2023; 13:928353. [PMID: 36844394 PMCID: PMC9945231 DOI: 10.3389/fcimb.2023.928353] [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: 04/25/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction The gut microbiome is an integral partner in host health and plays a role in immune development, altered nutrition, and pathogen prevention. The mycobiome (fungal microbiome) is considered part of the rare biosphere but is still a critical component in health. Next generation sequencing has improved our understanding of fungi in the gut, but methodological challenges remain. Biases are introduced during DNA isolation, primer design and choice, polymerase selection, sequencing platform selection, and data analyses, as fungal reference databases are often incomplete or contain erroneous sequences. Methods Here, we compared the accuracy of taxonomic identifications and abundances from mycobiome analyses which vary among three commonly selected target gene regions (18S, ITS1, or ITS2) and the reference database (UNITE - ITS1, ITS2 and SILVA - 18S). We analyze multiple communities including individual fungal isolates, a mixed mock community created from five common fungal isolates found in weanling piglet feces, a purchased commercial fungal mock community, and piglet fecal samples. In addition, we calculated gene copy numbers for the 18S, ITS1, and ITS2 regions of each of the five isolates from the piglet fecal mock community to determine whether copy number affects abundance estimates. Finally, we determined the abundance of taxa from several iterations of our in-house fecal community to assess the effects of community composition on taxon abundance. Results Overall, no marker-database combination consistently outperformed the others. Internal transcribed space markers were slightly superior to 18S in the identification of species in tested communities, but Lichtheimia corymbifera, a common member of piglet gut communities, was not amplified by ITS1 and ITS2 primers. Thus, ITS based abundance estimates of taxa in piglet mock communities were skewed while 18S marker profiles were more accurate. Kazachstania slooffiae displayed the most stable copy numbers (83-85) while L. corymbifera displayed significant variability (90-144) across gene regions. Discussion This study underscores the importance of preliminary studies to assess primer combinations and database choice for the mycobiome sample of interest and raises questions regarding the validity of fungal abundance estimates.
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Affiliation(s)
- Ann M. Arfken
- Oak Ridge Institute for Science and Education, Center for Disease Control, Atlanta, GA, United States
| | - Juli Foster Frey
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Nora Isabel Carrillo
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Nneka Ijeoma Dike
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Ogechukwu Onyeachonamm
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Daniela Nieves Rivera
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Cary Pirone Davies
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Katie Lynn Summers
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States,*Correspondence: Katie Lynn Summers,
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Stengel A, Stanke KM, Quattrone AC, Herr JR. Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics. Front Microbiol 2022; 13:847067. [PMID: 35250961 PMCID: PMC8892103 DOI: 10.3389/fmicb.2022.847067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 01/28/2022] [Indexed: 01/04/2023] Open
Abstract
Species concepts have long provided a source of debate among biologists. These lively debates have been important for reaching consensus on how to communicate across scientific disciplines and for advancing innovative strategies to study evolution, population biology, ecology, natural history, and disease epidemiology. Species concepts are also important for evaluating variability and diversity among communities, understanding biogeographical distributions, and identifying causal agents of disease across animal and plant hosts. While there have been many attempts to address the concept of species in the fungi, there are several concepts that have made taxonomic delimitation especially challenging. In this review we discuss these major challenges and describe methodological approaches that show promise for resolving ambiguity in fungal taxonomy by improving discrimination of genetic and functional traits. We highlight the relevance of eco-evolutionary theory used in conjunction with integrative taxonomy approaches to improve the understanding of interactions between environment, ecology, and evolution that give rise to distinct species boundaries. Beyond recent advances in genomic and phenomic methods, bioinformatics tools and modeling approaches enable researchers to test hypothesis and expand our knowledge of fungal biodiversity. Looking to the future, the pairing of integrative taxonomy approaches with multi-locus genomic sequencing and phenomic techniques, such as transcriptomics and proteomics, holds great potential to resolve many unknowns in fungal taxonomic classification.
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Affiliation(s)
- Ashley Stengel
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Kimberly M. Stanke
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Amanda C. Quattrone
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Joshua R. Herr
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
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5
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Extremophilic Fungi from Marine Environments: Underexplored Sources of Antitumor, Anti-Infective and Other Biologically Active Agents. Mar Drugs 2022; 20:md20010062. [PMID: 35049917 PMCID: PMC8781577 DOI: 10.3390/md20010062] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/07/2023] Open
Abstract
Marine environments are underexplored terrains containing fungi that produce a diversity of natural products given unique environmental pressures and nutrients. While bacteria are commonly the most studied microorganism for natural products in the marine world, marine fungi are also abundant but remain an untapped source of bioactive metabolites. Given that their terrestrial counterparts have been a source of many blockbuster antitumor agents and anti-infectives, including camptothecin, the penicillins, and cyclosporin A, marine fungi also have the potential to produce new chemical scaffolds as leads to potential drugs. Fungi are more phylogenetically diverse than bacteria and have larger genomes that contain many silent biosynthetic gene clusters involved in making bioactive compounds. However, less than 5% of all known fungi have been cultivated under standard laboratory conditions. While the number of reported natural products from marine fungi is steadily increasing, their number is still significantly lower compared to those reported from their bacterial counterparts. Herein, we discuss many varied cytotoxic and anti-infective fungal metabolites isolated from extreme marine environments, including symbiotic associations as well as extreme pressures, temperatures, salinity, and light. We also discuss cultivation strategies that can be used to produce new bioactive metabolites or increase their production. This review presents a large number of reported structures though, at times, only a few of a large number of related structures are shown.
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Han Y, Guo C, Guan X, McMinn A, Liu L, Zheng G, Jiang Y, Liang Y, Shao H, Tian J, Wang M. Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench. MICROBIAL ECOLOGY 2022; 83:34-47. [PMID: 33811505 DOI: 10.1007/s00248-021-01747-2] [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: 10/27/2020] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Diversity of microbial eukaryotes is estimated largely based on sequencing analysis of the hypervariable regions of 18S rRNA genes. But the use of different regions of 18S rRNA genes as molecular markers may generate bias in diversity estimation. Here, we compared the differences between the two most widely used markers, V4 and V9 regions of the 18S rRNA gene, in describing the diversity of epipelagic, bathypelagic, and hadal picoeukaryotes in the Challenger Deep of the Mariana Trench, which is a unique and little explored environment. Generally, the V9 region identified more OTUs in deeper waters than V4, while the V4 region provided greater Shannon diversity than V9. In the epipelagic zone, where Alveolata was the dominant group, picoeukaryotic community compositions identified by V4 and V9 markers are similar at different taxonomic levels. However, in the deep waters, the results of the two datasets show clear differences. These differences were mainly contributed by Retaria, Fungi, and Bicosoecida. The primer targeting the V9 region has an advantage in amplifying Bicosoecids in the bathypelagic and hadal zone of the Mariana Trench, and its high abundance in V9 dataset pointed out the possibility of Bicosoecids as a dominant group in this environment. Chrysophyceae, Fungi, MALV-I, and Retaria were identified as the dominant picoeukaryotes in the bathypelagic and hadal zone and potentially play important roles in deep-sea microbial food webs and biogeochemical cycling by their phagotrophic, saprotrophic, and parasitic life styles. Overall, the use of different markers of 18S rRNA gene allows a better assessment and understanding of the picoeukaryotic diversity in deep-sea environments.
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Affiliation(s)
- Yuye Han
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Xuran Guan
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Lu Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Guiliang Zheng
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, China
- Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
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Mohamed GA, Ibrahim SRM. Untapped Potential of Marine-Associated Cladosporium Species: An Overview on Secondary Metabolites, Biotechnological Relevance, and Biological Activities. Mar Drugs 2021; 19:645. [PMID: 34822516 PMCID: PMC8622643 DOI: 10.3390/md19110645] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022] Open
Abstract
The marine environment is an underexplored treasure that hosts huge biodiversity of microorganisms. Marine-derived fungi are a rich source of novel metabolites with unique structural features, bioactivities, and biotechnological applications. Marine-associated Cladosporium species have attracted considerable interest because of their ability to produce a wide array of metabolites, including alkaloids, macrolides, diketopiperazines, pyrones, tetralones, sterols, phenolics, terpenes, lactones, and tetramic acid derivatives that possess versatile bioactivities. Moreover, they produce diverse enzymes with biotechnological and industrial relevance. This review gives an overview on the Cladosporium species derived from marine habitats, including their metabolites and bioactivities, as well as the industrial and biotechnological potential of these species. In the current review, 286 compounds have been listed based on the reported data from 1998 until July 2021. Moreover, more than 175 references have been cited.
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Affiliation(s)
- Gamal A. Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sabrin R. M. Ibrahim
- Preparatory Year Program, Batterjee Medical College, Jeddah 21442, Saudi Arabia;
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
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Calado MDL, Silva J, Alves C, Susano P, Santos D, Alves J, Martins A, Gaspar H, Pedrosa R, Campos MJ. Marine endophytic fungi associated with Halopteris scoparia (Linnaeus) Sauvageau as producers of bioactive secondary metabolites with potential dermocosmetic application. PLoS One 2021; 16:e0250954. [PMID: 33983974 PMCID: PMC8118457 DOI: 10.1371/journal.pone.0250954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/17/2021] [Indexed: 12/16/2022] Open
Abstract
Marine fungi and, particularly, endophytic species have been recognised as one of the most prolific sources of structurally new and diverse bioactive secondary metabolites with multiple biotechnological applications. Despite the increasing number of bioprospecting studies, very few have already evaluated the cosmeceutical potential of marine fungal compounds. Thus, this study focused on a frequent seaweed in the Portuguese coast, Halopteris scoparia, to identify the endophytic marine fungi associated with this host, and assess their ability to biosynthesise secondary metabolites with antioxidative, enzymatic inhibitory (hyaluronidase, collagenase, elastase and tyrosinase), anti-inflammatory, photoprotective, and antimicrobial (Cutibacterium acnes, Staphylococcus epidermidis and Malassezia furfur) activities. The results revealed eight fungal taxa included in the Ascomycota, and in the most representative taxonomic classes in marine ecosystems (Eurotiomycetes, Sordariomycetes and Dothideomycetes). These fungi were reported for the first time in Portugal and in association with H. scoparia, as far as it is known. The screening analyses showed that most of these endophytic fungi were producers of compounds with relevant biological activities, though those biosynthesised by Penicillium sect. Exilicaulis and Aspergillus chevalieri proved to be the most promising ones for being further exploited by dermocosmetic industry. The chemical analysis of the crude extract from an isolate of A. chevalieri revealed the presence of two bioactive compounds, echinulin and neoechinulin A, which might explain the high antioxidant and UV photoprotective capacities exhibited by the extract. These noteworthy results emphasised the importance of screening the secondary metabolites produced by these marine endophytic fungal strains for other potential bioactivities, and the relevance of investing more efforts in understanding the ecology of halo/osmotolerant fungi.
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Affiliation(s)
- Maria da Luz Calado
- MARE–Marine and Environmental Sciences Centre, Polytechnic of Leiria, Peniche, Portugal
| | - Joana Silva
- MARE–Marine and Environmental Sciences Centre, Polytechnic of Leiria, Peniche, Portugal
| | - Celso Alves
- MARE–Marine and Environmental Sciences Centre, Polytechnic of Leiria, Peniche, Portugal
| | - Patrícia Susano
- MARE–Marine and Environmental Sciences Centre, Polytechnic of Leiria, Peniche, Portugal
| | - Débora Santos
- MARE–Marine and Environmental Sciences Centre, Polytechnic of Leiria, Peniche, Portugal
| | - Joana Alves
- MARE–Marine and Environmental Sciences Centre, Polytechnic of Leiria, Peniche, Portugal
| | - Alice Martins
- MARE–Marine and Environmental Sciences Centre, Polytechnic of Leiria, Peniche, Portugal
| | - Helena Gaspar
- MARE–Marine and Environmental Sciences Centre, Polytechnic of Leiria, Peniche, Portugal
- MARE–Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, Peniche, Portugal
| | - Rui Pedrosa
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, Lisbon, Portugal
| | - Maria Jorge Campos
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, Lisbon, Portugal
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Yang Y, Banos S, Gerdts G, Wichels A, Reich M. Mycoplankton Biome Structure and Assemblage Processes Differ Along a Transect From the Elbe River Down to the River Plume and the Adjacent Marine Waters. Front Microbiol 2021; 12:640469. [PMID: 33967979 PMCID: PMC8102988 DOI: 10.3389/fmicb.2021.640469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/12/2021] [Indexed: 11/25/2022] Open
Abstract
Rivers are transport systems and supply adjacent ecosystems with nutrients. They also serve human well-being, for example as a source of food. Microorganism biodiversity is an important parameter for the ecological balance of river ecosystems. Despite the knowledge that fungi are key players in freshwater nutrient cycling and food webs, data on planktonic fungi of streams with higher stream order are scarce. This study aims to fill this knowledge gap by a fungi-specific 18S ribosomal RNA (rRNA) gene tag sequencing approach, investigating mycoplankton diversity in the Elbe River along a transect from shallow freshwater, to the estuary and river plume down to the adjacent marine waters (sections of seventh stream order number). Using multivariate analyses and the quantitative process estimates (QPEs) method, questions (i) of how mycoplankton communities as part of the river continuum change along the transect, (ii) what factors, spatial and environmental, play a role, and (iii) what assembly processes, such as selection or dispersion, operate along the transect, were addressed. The partitioning of mycoplankton communities into three significant distant biomes was mainly driven by local environmental conditions that were partly under spatial control. The assembly processes underlying the biomes also differed significantly. Thus, variable selection dominated the upstream sections, while undominated processes like ecological drift dominated the sections close to the river mouth and beyond. Dispersal played a minor role. The results suggest that the ecological versatility of the mycoplankton communities changes along the transect as response, for example, to a drastic change from an autotrophic to a heterotrophic system caused by an abrupt increase in the river depth. Furthermore, a significant salinity-dependent occurrence of diverse basal fungal groups was observed, with no clade found exclusively in marine waters. These results provide an important framework to help understand patterns of riverine mycoplankton communities and serve as basis for a further in-depth work so that fungi, as an important ecological organism group, can be integrated into models of, e.g., usage-balance considerations of rivers.
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Affiliation(s)
- Yanyan Yang
- Molecular Ecology Group, University of Bremen, FB2, Bremen, Germany
| | - Stefanos Banos
- Molecular Ecology Group, University of Bremen, FB2, Bremen, Germany
| | - Gunnar Gerdts
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Antje Wichels
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Marlis Reich
- Molecular Ecology Group, University of Bremen, FB2, Bremen, Germany
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Sen K, Bai M, Sen B, Wang G. Disentangling the structure and function of mycoplankton communities in the context of marine environmental heterogeneity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:142635. [PMID: 33071110 DOI: 10.1016/j.scitotenv.2020.142635] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Mycoplankton are a diverse and ubiquitous component of marine environments with a suggested role in ocean biogeochemical cycling. Thus far, the patterns of their abundance, structure, and function against spatial environmental heterogeneity remains poorly understood. Based on in silico and experimental evaluation of multiple markers, we adopted the ITS1 region to determine the composition, guilds, and metabolic potential of mycoplankton communities in contrasting marine environments. The trophic status of estuarine (SB1 and SB2) and coastal (DB1 and DB2) sites, but not oceanic (OS) site, was the major factor that determined their abundances. While ascomycetous fungi dominated the estuarine and coastal sites, basidiomycetous fungi were found to dominate the oceanic site. The zoosporic fungi were relatively more abundant in SB1 and DB2 sites compared to the other sites. The relative abundances of the core fungi, namely Cystobasidium, Phlebia, Rhodotorula, Trichoderma, Alternaria, Penicillium, Malassezia, and Aspergillus varied widely across the sites. Additionally, several fungal genera unique to each site were also identified. DB2 site exhibited the lowest fungal richness while the OS site the highest. Conversely, the diversity and evenness were the lowest for the OS site but highest for the SB1 site. Temperature, pH, and chlorophyll-a were strongly associated with spatial diversity patterns. Of the 11 assigned guilds, some guilds particularly were not detected, including plant pathogen-wood saprotroph in DB2, the endophyte-plant pathogen in OS, the animal pathogen in SB1, and fungal parasite in DB1 and SB2. Within core functions-metabolism of amino acids, carbohydrates and energy, fatty acids and lipids, nitrogen, sulfur, and other compounds-several pathways showed spatial variations. Overall, this study not just broadens the taxonomic and metabolic repertoire of marine mycoplankton but also provides the first evidence of how these are shaped by site-scale environmental heterogeneity.
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Affiliation(s)
- Kalyani Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Mohan Bai
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Biswarup Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Qingdao Institute Ocean Engineering of Tianjin University, Qingdao 266237, China.
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11
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Marine Fungal Communities: Metabolic Engineering for Secondary Metabolites and Their Industrial Applications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-68260-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Moussa AY, Sobhy HA, Eldahshan OA, Singab ANB. Caspicaiene: a new kaurene diterpene with anti-tubercular activity from an Aspergillus endophytic isolate in Gleditsia caspia desf. Nat Prod Res 2020; 35:5653-5664. [PMID: 32954811 DOI: 10.1080/14786419.2020.1824222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A new kaurene derivative with a new 6/6/6/5/6 ring system structure, given the trivial name caspicaiene, was isolated from the fungal culture of the Aspergillus N830 isolate identified by ITS region DNA sequencing. The compound was characterized by 1, 2 D NMR, and HR-ESI-MS-MS and revealed a promising anti-tubercular effect using the Alamar Blue Assay (MABA), in a dose dependent manner, with MIC value of 124.5 µM. Furthermore, six known compounds were isolated and showed significant MIC values against Mycobacterium tuberculosis, ranging between 15.63 µg/mL (26.5 µM) to 125 µg/mL (500 µM), compared to the positive control isoniazid whose MIC value was 0.24 µg/mL (1.75 µM), which sets them forth as potentially natural anti-tubercular agents. To gain further insight of the underlying mechanism, in-silico molecular docking, using the C-Docker protocol, was conducted and demonstrated various interactions between the isolated compounds and three key mycobacterial enzymes. Additionally, the cytotoxic activity was reported and showed the safety of these molecules according to the calculated safety index in the human hepatic cancer cell line (HepG2) and Vero cell lines.
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Affiliation(s)
- Ashaimaa Y Moussa
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Hagar A Sobhy
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Omayma A Eldahshan
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.,Center for Drug Discovery Research and Development, Ain Shams University, Cairo, Egypt
| | - Abdel Nasser B Singab
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.,Center for Drug Discovery Research and Development, Ain Shams University, Cairo, Egypt
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Abstract
Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.
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14
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Hagestad OC, Andersen JH, Altermark B, Hansen E, Rämä T. Cultivable marine fungi from the Arctic Archipelago of Svalbard and their antibacterial activity. Mycology 2019; 11:230-242. [PMID: 33062384 PMCID: PMC7534220 DOI: 10.1080/21501203.2019.1708492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/01/2019] [Indexed: 11/01/2022] Open
Abstract
During a research cruise in 2016, we isolated fungi from sediments, seawater, driftwood, fruiting bodies, and macroalgae using three different media to assess species richness and potential bioactivity of cultivable marine fungi in the High Arctic region. Ten stations from the Svalbard archipelago (73-80 °N, 18-31 °E) were investigated and 33 fungal isolates were obtained. These grouped into 22 operational taxonomic units (OTUs) using nuc rDNA internal transcribed spacer regions (ITS1-5.8S-ITS2 = ITS) with acut-off set at 98% similarity. The taxonomic analysis showed that 17 OTUs belonged to Ascomycota, one to Basidiomycota, two to Mucoromycota and two were fungal-like organisms. The nuc rDNA V1-V5 regions of 18S (18S) and D1-D3 regions of 28S (28S) were sequenced from representative isolates of each OTU for comparison to GenBank sequences. Isolates of Lulworthiales and Eurotiales were the most abundant, with seven isolates each. Among the 22 OTUs, nine represent potentially undescribed species based on low similarity to GenBank sequences and 10 isolates showed inhibitory activity against Gram-positive bacteria in an agar diffusion plug assay. These results show promise for the Arctic region as asource of novel marine fungi with the ability to produce bioactive secondary metabolites with antibacterial properties.
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Affiliation(s)
- Ole Christian Hagestad
- Marbio, The Norwegian College of Fishery Science, Department at Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jeanette H. Andersen
- Marbio, The Norwegian College of Fishery Science, Department at Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Bjørn Altermark
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Espen Hansen
- Marbio, The Norwegian College of Fishery Science, Department at Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Teppo Rämä
- Marbio, The Norwegian College of Fishery Science, Department at Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
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15
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Bovio E, Sfecci E, Poli A, Gnavi G, Prigione V, Lacour T, Mehiri M, Varese GC. The culturable mycobiota associated with the Mediterranean sponges Aplysina cavernicola, Crambe crambe and Phorbas tenacior. FEMS Microbiol Lett 2019; 366:5710934. [PMID: 31960895 DOI: 10.1093/femsle/fnaa014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 01/20/2020] [Indexed: 01/15/2023] Open
Abstract
Marine fungi are part of the huge and understudied biodiversity hosted in the sea. To broaden the knowledge on fungi inhabiting the Mediterranean Sea and their role in sponge holobiont, three sponges namely Aplysina cavernicola, Crambe crambe and Phorbas tenacior were collected in Villefranche sur Mer, (France) at about 25 m depth. The fungal communities associated with the sponges were isolated using different techniques to increase the numbers of fungi isolated. All fungi were identified to species level giving rise to 19, 13 and 3 species for P. tenacior, A. cavernicola and C. crambe, respectively. Of note, 35.7% and 50.0% of the species detected were either reported for the first time in the marine environment or in association with sponges. The mini-satellite analysis confirmed the uniqueness of the mycobiota of each sponge, leading to think that the sponge, with its metabolome, may shape the microbial community.
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Affiliation(s)
- Elena Bovio
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Turin, Viale Mattioli 25, 10125 Turin, Italy.,University Nice Côte d'Azur, CNRS, Nice Institute of Chemistry, UMR 7272, Marine Natural Products Team, Nice 60103, France
| | - Estelle Sfecci
- University Nice Côte d'Azur, CNRS, Nice Institute of Chemistry, UMR 7272, Marine Natural Products Team, Nice 60103, France
| | - Anna Poli
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | - Giorgio Gnavi
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | - Valeria Prigione
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | | | - Mohamed Mehiri
- University Nice Côte d'Azur, CNRS, Nice Institute of Chemistry, UMR 7272, Marine Natural Products Team, Nice 60103, France
| | - Giovanna Cristina Varese
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Turin, Viale Mattioli 25, 10125 Turin, Italy
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16
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Marine Fungi: Biotechnological Perspectives from Deep-Hypersaline Anoxic Basins. DIVERSITY 2019. [DOI: 10.3390/d11070113] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Deep-sea hypersaline anoxic basins (DHABs) are one of the most hostile environments on Earth. Even though DHABs have hypersaline conditions, anoxia and high hydrostatic pressure, they host incredible microbial biodiversity. Among eukaryotes inhabiting these systems, recent studies demonstrated that fungi are a quantitatively relevant component. Here, fungi can benefit from the accumulation of large amounts of organic material. Marine fungi are also known to produce bioactive molecules. In particular, halophilic and halotolerant fungi are a reservoir of enzymes and secondary metabolites with valuable applications in industrial, pharmaceutical, and environmental biotechnology. Here we report that among the fungal taxa identified from the Mediterranean and Red Sea DHABs, halotolerant halophilic species belonging to the genera Aspergillus and Penicillium can be used or screened for enzymes and bioactive molecules. Fungi living in DHABs can extend our knowledge about the limits of life, and the discovery of new species and molecules from these environments can have high biotechnological potential.
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17
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Bovio E, Garzoli L, Poli A, Luganini A, Villa P, Musumeci R, McCormack GP, Cocuzza CE, Gribaudo G, Mehiri M, Varese GC. Marine Fungi from the Sponge Grantia compressa: Biodiversity, Chemodiversity, and Biotechnological Potential. Mar Drugs 2019; 17:E220. [PMID: 30978942 PMCID: PMC6520677 DOI: 10.3390/md17040220] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 04/01/2019] [Accepted: 04/08/2019] [Indexed: 11/21/2022] Open
Abstract
The emergence of antibiotic resistance and viruses with high epidemic potential made unexplored marine environments an appealing target source for new metabolites. Marine fungi represent one of the most suitable sources for the discovery of new compounds. Thus, the aim of this work was (i) to isolate and identify fungi associated with the Atlantic sponge Grantia compressa; (ii) to study the fungal metabolites by applying the OSMAC approach (one strain; many compounds); (iii) to test fungal compounds for their antimicrobial activities. Twenty-one fungal strains (17 taxa) were isolated from G. compressa. The OSMAC approach revealed an astonishing metabolic diversity in the marine fungus Eurotium chevalieri MUT 2316, from which 10 compounds were extracted, isolated, and characterized. All metabolites were tested against viruses and bacteria (reference and multidrug-resistant strains). Dihydroauroglaucin completely inhibited the replication of influenza A virus; as for herpes simplex virus 1, total inhibition of replication was observed for both physcion and neoechinulin D. Six out of 10 compounds were active against Gram-positive bacteria with isodihydroauroglaucin being the most promising compound (minimal inhibitory concentration (MIC) 4-64 µg/mL) with bactericidal activity. Overall, G. compressa proved to be an outstanding source of fungal diversity. Marine fungi were capable of producing different metabolites; in particular, the compounds isolated from E. chevalieri showed promising bioactivity against well-known and emerging pathogens.
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Affiliation(s)
- Elena Bovio
- Mycotheca Universitatis Taurinensis, Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy.
- University Nice Côte d'Azur, CNRS, Nice Institute of Chemistry, UMR 7272, Marine Natural Products Team, 60103 Nice, France.
| | - Laura Garzoli
- Mycotheca Universitatis Taurinensis, Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy.
| | - Anna Poli
- Mycotheca Universitatis Taurinensis, Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy.
| | - Anna Luganini
- Laboratory of Microbiology and Virology, Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy.
| | - Pietro Villa
- Laboratory of Clinical Microbiology and Virology, Department of Medicine, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Italy.
| | - Rosario Musumeci
- Laboratory of Clinical Microbiology and Virology, Department of Medicine, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Italy.
| | - Grace P McCormack
- Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland.
| | - Clementina E Cocuzza
- Laboratory of Clinical Microbiology and Virology, Department of Medicine, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Italy.
| | - Giorgio Gribaudo
- Laboratory of Microbiology and Virology, Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy.
| | - Mohamed Mehiri
- University Nice Côte d'Azur, CNRS, Nice Institute of Chemistry, UMR 7272, Marine Natural Products Team, 60103 Nice, France.
| | - Giovanna C Varese
- Mycotheca Universitatis Taurinensis, Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy.
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19
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Banos S, Lentendu G, Kopf A, Wubet T, Glöckner FO, Reich M. A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms. BMC Microbiol 2018; 18:190. [PMID: 30458701 PMCID: PMC6247509 DOI: 10.1186/s12866-018-1331-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several fungi-specific primers target the 18S rRNA gene sequence, one of the prominent markers for fungal classification. The design of most primers goes back to the last decades. Since then, the number of sequences in public databases increased leading to the discovery of new fungal groups and changes in fungal taxonomy. However, no reevaluation of primers was carried out and relevant information on most primers is missing. With this study, we aimed to develop an 18S rRNA gene sequence primer toolkit allowing an easy selection of the best primer pair appropriate for different sequencing platforms, research aims (biodiversity assessment versus isolate classification) and target groups. RESULTS We performed an intensive literature research, reshuffled existing primers into new pairs, designed new Illumina-primers, and annealing blocking oligonucleotides. A final number of 439 primer pairs were subjected to in silico PCRs. Best primer pairs were selected and experimentally tested. The most promising primer pair with a small amplicon size, nu-SSU-1333-5'/nu-SSU-1647-3' (FF390/FR-1), was successful in describing fungal communities by Illumina sequencing. Results were confirmed by a simultaneous metagenomics and eukaryote-specific primer approach. Co-amplification occurred in all sample types but was effectively reduced by blocking oligonucleotides. CONCLUSIONS The compiled data revealed the presence of an enormous diversity of fungal 18S rRNA gene primer pairs in terms of fungal coverage, phylum spectrum and co-amplification. Therefore, the primer pair has to be carefully selected to fulfill the requirements of the individual research projects. The presented primer toolkit offers comprehensive lists of 164 primers, 439 primer combinations, 4 blocking oligonucleotides, and top primer pairs holding all relevant information including primer's characteristics and performance to facilitate primer pair selection.
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Affiliation(s)
- Stefanos Banos
- Molecular Ecology, Institute of Ecology, FB02, University of Bremen, Leobener Str. 2, 28359, Bremen, Germany
| | - Guillaume Lentendu
- Department of Soil Ecology, Helmholtz Centre for Environmental Research GmbH - UFZ, Halle-Saale, Germany.,Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Anna Kopf
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, Helmholtz Centre for Environmental Research GmbH - UFZ, Halle-Saale, Germany.,Present address: Department of Community Ecology, Helmholtz Centre for Environmental Research GmbH - UFZ, Halle-Saale, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Frank Oliver Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
| | - Marlis Reich
- Molecular Ecology, Institute of Ecology, FB02, University of Bremen, Leobener Str. 2, 28359, Bremen, Germany.
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20
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Balabanova L, Slepchenko L, Son O, Tekutyeva L. Biotechnology Potential of Marine Fungi Degrading Plant and Algae Polymeric Substrates. Front Microbiol 2018; 9:1527. [PMID: 30050513 PMCID: PMC6052901 DOI: 10.3389/fmicb.2018.01527] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022] Open
Abstract
Filamentous fungi possess the metabolic capacity to degrade environment organic matter, much of which is the plant and algae material enriched with the cell wall carbohydrates and polyphenol complexes that frequently can be assimilated by only marine fungi. As the most renewable energy feedstock on the Earth, the plant or algae polymeric substrates induce an expression of microbial extracellular enzymes that catalyze their cleaving up to the component sugars. However, the question of what the marine fungi contributes to the plant and algae material biotransformation processes has yet to be highlighted sufficiently. In this review, we summarized the potential of marine fungi alternatively to terrestrial fungi to produce the biotechnologically valuable extracellular enzymes in response to the plant and macroalgae polymeric substrates as sources of carbon for their bioconversion used for industries and bioremediation.
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Affiliation(s)
- Larissa Balabanova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- Innovative Technology Center, Far Eastern Federal University, Vladivostok, Russia
| | - Lubov Slepchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- Innovative Technology Center, Far Eastern Federal University, Vladivostok, Russia
| | - Oksana Son
- Innovative Technology Center, Far Eastern Federal University, Vladivostok, Russia
| | - Liudmila Tekutyeva
- Innovative Technology Center, Far Eastern Federal University, Vladivostok, Russia
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21
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Adnan M, Alshammari E, Patel M, Amir Ashraf S, Khan S, Hadi S. Significance and potential of marine microbial natural bioactive compounds against biofilms/biofouling: necessity for green chemistry. PeerJ 2018; 6:e5049. [PMID: 29967730 PMCID: PMC6026461 DOI: 10.7717/peerj.5049] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/01/2018] [Indexed: 12/17/2022] Open
Abstract
Natural products from the unique environments of sea water and oceans represent a largely unfamiliar source for isolation of new microbes, which are potent producers of secondary bioactive metabolites. These unique life-forms from the marine ecosphere have served as an important source of drugs since ancient times and still offer a valuable resource for novel findings by providing remedial treatments. Therefore, it can be expected that many naturally bioactive marine microbial compounds with novel structures and bioactivities against those from terrestrial environments may be found among marine metabolites. Biofilms in aquatic environment possess serious problems to naval forces and oceanic industries around the globe. Current anti-biofilm or anti-biofouling technology is based on the use of toxic substances that can be harmful to their surrounding natural locales. Comprehensive research has been done to examine the bioactive potential of marine microbes. Results are remarkably varied and dynamic, but there is an urgent need for bioactive compounds with environmentally friendly or "green" chemical activities. Marine microbes have the potential as upcoming and promising source of non-toxic compounds with sustainable anti-biofouling/anti-biofilm properties as they can produce substances that can inhibit not only the chemical components required for biofilm production but also the attachment, microorganism growth, and/or cell-cell communication.
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Affiliation(s)
- Mohd Adnan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Eyad Alshammari
- Department of Clinical Nutrition, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Mitesh Patel
- Department of Biosciences, Bapalal Vaidhya Botanical Research Centre, Veer Narmad South Gujarat University, Surat, India
| | - Syed Amir Ashraf
- Department of Clinical Nutrition, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Saif Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Sibte Hadi
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, UK
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22
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Yarza P, Yilmaz P, Panzer K, Glöckner FO, Reich M. A phylogenetic framework for the kingdom Fungi based on 18S rRNA gene sequences. Mar Genomics 2017; 36:33-39. [PMID: 28578827 DOI: 10.1016/j.margen.2017.05.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/28/2017] [Accepted: 05/15/2017] [Indexed: 11/27/2022]
Abstract
The usage of molecular phylogenetic approaches is critical to advance the understanding of systematics and community processes in the kingdom Fungi. Among the possible phylogenetic markers (or combinations of them), the 18S rRNA gene appears currently as the most prominent candidate due to its large availability in public databases and informative content. The purpose of this work was the creation of a reference phylogenetic framework that can serve as ready-to-use package for its application on fungal classification and community analysis. The current database contains 9329 representative 18S rRNA gene sequences covering the whole fungal kingdom, a manually curated alignment, an annotated and revised phylogenetic tree with all the sequence entries, updated information on current taxonomy, and recommendations of use. Out of 201 total fungal taxa with more than two sequences in the dataset, 179 were monophyletic. From another perspective, 66% of the entries had a tree-derived classification identical to that obtained from the NCBI taxonomy, whereas 34% differed in one or the other rank. Most of the differences were associated to missing taxonomic assignments in NCBI taxonomy, or the unexpected position of sequences that positioned out of their theoretically corresponding clades. The strong correlation observed with current fungal taxonomy evidences that 18S rRNA gene sequence-based phylogenies are adequate to reflect genealogy of Fungi at the levels of order and above, and justify their further usage and exploration.
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Affiliation(s)
- Pablo Yarza
- Ribocon GmbH, Fahrenheitstrasse 1, 28359 Bremen, Germany.
| | - Pelin Yilmaz
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
| | - Katrin Panzer
- University of Bremen, Molecular Ecology, BreMarE, Leobener Str. 5, 28359 Bremen, Germany; Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Frank Oliver Glöckner
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany; Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Marlis Reich
- University of Bremen, Molecular Ecology, BreMarE, Leobener Str. 5, 28359 Bremen, Germany.
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