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Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP. Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 2022; 88:1-33. [PMID: 35585929 PMCID: PMC8924126 DOI: 10.3897/mycokeys.88.77106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/25/2022] [Indexed: 12/17/2022] Open
Abstract
Full taxonomic characterisation of fungal communities is necessary for establishing ecological associations and early detection of pathogens and invasive species. Complex communities of fungi are regularly characterised by metabarcoding using the Internal Transcribed Spacer (ITS) and the Large-Subunit (LSU) gene of the rRNA locus, but reliance on a single short sequence fragment limits the confidence of identification. Here we link metabarcoding from the ITS2 and LSU D1-D2 regions to characterise fungal communities associated with bark beetles (Scolytinae), the likely vectors of several tree pathogens. Both markers revealed similar patterns of overall species richness and response to key variables (beetle species, forest type), but identification against the respective reference databases using various taxonomic classifiers revealed poor resolution towards lower taxonomic levels, especially the species level. Thus, Operational Taxonomic Units (OTUs) could not be linked via taxonomic classifiers across ITS and LSU fragments. However, using phylogenetic trees (focused on the epidemiologically important Sordariomycetes) we placed OTUs obtained with either marker relative to reference sequences of the entire rRNA cistron that includes both loci and demonstrated the largely similar phylogenetic distribution of ITS and LSU-derived OTUs. Sensitivity analysis of congruence in both markers suggested the biologically most defensible threshold values for OTU delimitation in Sordariomycetes to be 98% for ITS2 and 99% for LSU D1-D2. Studies of fungal communities using the canonical ITS barcode require corroboration across additional loci. Phylogenetic analysis of OTU sequences aligned to the full rRNA cistron shows higher success rate and greater accuracy of species identification compared to probabilistic taxonomic classifiers.
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2
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Paula DP. Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution. NEOTROPICAL ENTOMOLOGY 2021; 50:679-696. [PMID: 34374956 DOI: 10.1007/s13744-021-00895-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The advent of NGS-based methods has been profoundly transforming entomological research. Through continual development and improvement of different methods and sequencing platforms, NGS has promoted mass elucidation of partial or whole genetic materials associated with beneficial insects, pests (of agriculture, forestry and animal, and human health), and species of conservation concern, helping to unravel ecological and evolutionary mechanisms and characterizing survival, trophic interactions, and dispersal. It is shifting the scale of biodiversity and environmental analyses from individuals and biodiversity indicator species to the large-scale study of communities and ecosystems using bulk samples of species or a mixed "soup" of environmental DNA. As the NGS-based methods have become more affordable, complexity demystified, and specificity and sensitivity proven, their use in entomological research has spread widely. This article presents several examples on how NGS-based methods have been used in entomology to provide incentives to apply them when appropriate and to open our minds to the expected advances in entomology that are yet to come.
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Ban LP, Li JD, Yan M, Gao YH, Zhang JJ, Moural TW, Zhu F, Wang XM. Illumina Sequencing of 18S/16S rRNA Reveals Microbial Community Composition, Diversity, and Potential Pathogens in 17 Turfgrass Seeds. PLANT DISEASE 2021; 105:1328-1338. [PMID: 33084546 DOI: 10.1094/pdis-06-18-0946-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The increasing need for turfgrass seeds is coupled with the high risk of dangerous microbial pathogens being transmitted through the domestic and international trade of seeds. Concerns continue to be raised about seed safety and quality. Here, we show that next-generation sequencing (NGS) of DNA represents an effective and reliable tactic to monitor the microbial communities within turfgrass seeds. A comparison of DNA sequence data with reference databases revealed the presence of 26 different fungal orders. Among them, serious plant disease pathogens such as Bipolaris sorokiniana, Boeremia exigua, Claviceps purpurea, and Rhizoctonia zeae were detected. Seedborne bacteria, including Erwinia persicina and Acidovorax avenae, were identified from different bacterial orders. Our study indicated that the traditional culturing method and the NGS approach for pathogen identification complement each other. The reliability of culturing and NGS methods was further validated by PCR with specific primers. The combination of these different techniques ensures maximum sensitivity and specificity for turfgrass seed pathogen testing assay.
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Affiliation(s)
- Li-Ping Ban
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jin-Dong Li
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Min Yan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- National Animal Husbandry Station, Ministry of Agriculture, Beijing 100125, China
| | - Yu-Hao Gao
- The Affiliated High School of Peking University, Beijing 100190, China
| | - Jin-Jin Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Timothy W Moural
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Fang Zhu
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Xue-Min Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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4
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Hill R, Llewellyn T, Downes E, Oddy J, MacIntosh C, Kallow S, Panis B, Dickie JB, Gaya E. Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives. Front Microbiol 2021; 12:643731. [PMID: 33841366 PMCID: PMC8024981 DOI: 10.3389/fmicb.2021.643731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/19/2021] [Indexed: 01/19/2023] Open
Abstract
Seed banks were first established to conserve crop genetic diversity, but seed banking has more recently been extended to wild plants, particularly crop wild relatives (CWRs) (e.g., by the Millennium Seed Bank (MSB), Royal Botanic Gardens Kew). CWRs have been recognised as potential reservoirs of beneficial traits for our domesticated crops, and with mounting evidence of the importance of the microbiome to organismal health, it follows that the microbial communities of wild relatives could also be a valuable resource for crop resilience to environmental and pathogenic threats. Endophytic fungi reside asymptomatically inside all plant tissues and have been found to confer advantages to their plant host. Preserving the natural microbial diversity of plants could therefore represent an important secondary conservation role of seed banks. At the same time, species that are reported as endophytes may also be latent pathogens. We explored the potential of the MSB as an incidental fungal endophyte bank by assessing diversity of fungi inside stored seeds. Using banana CWRs in the genus Musa as a case-study, we sequenced an extended ITS-LSU fragment in order to delimit operational taxonomic units (OTUs) and used a similarity and phylogenetics approach for classification. Fungi were successfully detected inside just under one third of the seeds, with a few genera accounting for most of the OTUs-primarily Lasiodiplodia, Fusarium, and Aspergillus-while a large variety of rare OTUs from across the Ascomycota were isolated only once. Fusarium species were notably abundant-of significance in light of Fusarium wilt, a disease threatening global banana crops-and so were targeted for additional sequencing with the marker EF1α in order to delimit species and place them in a phylogeny of the genus. Endophyte community composition, diversity and abundance was significantly different across habitats, and we explored the relationship between community differences and seed germination/viability. Our results show that there is a previously neglected invisible fungal dimension to seed banking that could well have implications for the seed collection and storage procedures, and that collections such as the MSB are indeed a novel source of potentially useful fungal strains.
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Affiliation(s)
- Rowena Hill
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Biological and Chemical Sciences, Faculty of Science and Engineering, Queen Mary University of London, London, United Kingdom
| | - Theo Llewellyn
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Elizabeth Downes
- Department for Environment, Food and Rural Affairs, London, United Kingdom
| | - Joseph Oddy
- Department of Plant Science, Rothamsted Research, Harpenden, United Kingdom
| | - Catriona MacIntosh
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Simon Kallow
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
- Division of Crop Biotechnics, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven, Leuven, Belgium
| | - Bart Panis
- Bioversity International, Montpellier, France
| | - John B. Dickie
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
| | - Ester Gaya
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
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5
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Brentassi ME, Medina R, de la Fuente D, Franco ME, Toledo AV, Saparrat MC, Balatti PA. Endomycobiome associated with females of the planthopper Delphacodes kuscheli (Hemiptera: Delphacidae): A metabarcoding approach. Heliyon 2020; 6:e04634. [PMID: 32904272 PMCID: PMC7452442 DOI: 10.1016/j.heliyon.2020.e04634] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/09/2020] [Accepted: 08/03/2020] [Indexed: 12/22/2022] Open
Abstract
A metabarcoding approach was performed aimed at identifying fungi associated with Delphacodes kuscheli (Hemiptera: Delphacidae), the main vector of “Mal de Río Cuarto” disease in Argentina. A total of 91 fungal genera were found, and among them, 24 were previously identified for Delphacidae. The detection of fungi that are frequently associated with the phylloplane or are endophytes, as well as their presence in digestive tracts of other insects, suggest that feeding might be an important mechanism of their horizontal transfer in planthoppers. This study draws the baseline for future research regarding mutualistic associations present in D. kuscheli as well as their physiological role in the life cycle of this important pest that might lead to developing new management strategies to keep insects populations under control.
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Affiliation(s)
- María E Brentassi
- División Entomología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Buenos Aires, Argentina.,Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC), Buenos Aires, Argentina
| | - Rocío Medina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Centro de Investigaciones de Fitopatología (CIDEFI), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Daniela de la Fuente
- División Entomología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mario Ee Franco
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Centro de Investigaciones de Fitopatología (CIDEFI), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Andrea V Toledo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Centro de Investigaciones de Fitopatología (CIDEFI), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Mario Cn Saparrat
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Instituto de Fisiología Vegetal (INFIVE), Universidad Nacional de La Plata, Buenos Aires, Argentina.,Instituto de Botánica Carlos Spegazzini, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Buenos Aires, Argentina.,Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Pedro A Balatti
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC), Buenos Aires, Argentina.,Centro de Investigaciones de Fitopatología (CIDEFI), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, Buenos Aires, Argentina.,Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, Buenos Aires, Argentina
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6
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Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 2020; 11:14. [PMID: 32714773 PMCID: PMC7353689 DOI: 10.1186/s43008-020-00033-z] [Citation(s) in RCA: 178] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
| | - M. Catherine Aime
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| | - Andrew N. Miller
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970 USA
| | - Hiran A. Ariyawansa
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipe City, Taiwan
| | - Takayuki Aoki
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Agriculture and Food Research Organization, Genetic Resources Center, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Gianluigi Cardinali
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
| | - Pedro W. Crous
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Irina S. Druzhinina
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - David M. Geiser
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802 USA
| | - David L. Hawksworth
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ UK
- Jilin Agricultural University, Changchun, 130118 Jilin Province China
| | - Kevin D. Hyde
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- World Agroforestry Centre, East and Central Asia, Kunming, 650201 Yunnan China
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Rai, 50150 Thailand
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - Peter R. Johnston
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Manaaki Whenua – Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | | | - Elaine Malosso
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Avenida da Engenharia, s/n Cidade Universitária, Recife, PE 50.740-600 Brazil
| | - Tom W. May
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Maarja Öpik
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- University of Tartu, 40 Lai Street, 51 005 Tartu, Estonia
| | - Vincent Robert
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marc Stadler
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marco Thines
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60439 Frankfurt (Main); Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Andrey M. Yurkov
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
| | - Conrad L. Schoch
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
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7
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Ceriani-Nakamurakare E, Mc Cargo P, Gonzalez-Audino P, Ramos S, Carmarán C. New insights into fungal diversity associated with Megaplatypus mutatus: gut mycobiota. Symbiosis 2020. [DOI: 10.1007/s13199-020-00687-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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8
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Skelton J, Loyd A, Smith JA, Blanchette RA, Held BW, Hulcr J. Fungal symbionts of bark and ambrosia beetles can suppress decomposition of pine sapwood by competing with wood-decay fungi. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100926] [Citation(s) in RCA: 5] [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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9
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Epibiotic Fungal Communities of Three Tomicus spp. Infesting Pines in Southwestern China. Microorganisms 2019; 8:microorganisms8010015. [PMID: 31861833 PMCID: PMC7023379 DOI: 10.3390/microorganisms8010015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/14/2019] [Accepted: 12/16/2019] [Indexed: 01/13/2023] Open
Abstract
The association between insects and fungi has evolved over millions of years and is ubiquitous in nature. This symbiotic relationship holds critical implications for both partners, the insects and the associated microbes. Numerous fungi are externally allied with bark beetles and form a close symbiosis, but the community structures of these fungi are largely unknown. In Yunnan Province in southwestern China, the beetles Tomicus yunnanensis, T. minor, and T. brevipilosus are major forest pests that cause large losses of two indigenous pines, Pinus yunnanensis and P. kesiya. In this study, we used the Illumina MiSeq PE300 platform to process 48 samples of epibiotic fungal communities pooled from 1348 beetles; the beetles were collected during both the branch- and trunk-infection sections from five locations across Yunnan Province. Considerably greater species richness was detected using high-throughput sequencing of amplified internal transcribed spacer 1 (ITS1) ribosomal DNA (rDNA) libraries than previously documented by using culture-dependent methods. In total, 1,413,600 reads were generated, and a 97% sequence-similarity cutoff produced eight phyla, 31 classes, 83 orders, 181 families, 331 genera, 471 species, and 1157 operational taxonomic units (OTUs), with 659, 621, and 609 OTUs being confined to T. yunnanensis, T. minor, and T. brevipilosus, respectively. Tomicus yunnanensis, T. minor, and T. brevipilosus had the similar OTUs richness and evenness of fungal communities in Yunnan Province; nevertheless, the two fungal community compositions associated with T. yunnanensis and T. minor were structurally similar to each other but distinct from that associated with T. brevipilosus. Lastly, the results of principal co-ordinates analysis suggested that epibiotic fungal community structures of the three Tomicus spp. were conditioned strongly by the locations and pine hosts but weakly by beetle species and infection sections. Our findings provide baseline knowledge regarding the epibiotic fungal communities of three major Tomicus spp. in southwestern China.
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10
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Miller KE, Inward DJG, Gomez-Rodriguez C, Baselga A, Vogler AP. Predicting the unpredictable: How host specific is the mycobiota of bark and ambrosia beetles? FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Rassati D, Marini L, Malacrinò A. Acquisition of fungi from the environment modifies ambrosia beetle mycobiome during invasion. PeerJ 2019; 7:e8103. [PMID: 31763076 PMCID: PMC6870512 DOI: 10.7717/peerj.8103] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/25/2019] [Indexed: 01/05/2023] Open
Abstract
Microbial symbionts can play critical roles when their host attempts to colonize a new habitat. The lack of symbiont adaptation can in fact hinder the invasion process of their host. This scenario could change if the exotic species are able to acquire microorganisms from the invaded environment. Understanding the ecological factors that influence the take-up of new microorganisms is thus essential to clarify the mechanisms behind biological invasions. In this study, we tested whether different forest habitats influence the structure of the fungal communities associated with ambrosia beetles. We collected individuals of the most widespread exotic (Xylosandrus germanus) and native (Xyleborinus saxesenii) ambrosia beetle species in Europe in several old-growth and restored forests. We characterized the fungal communities associated with both species via metabarcoding. We showed that forest habitat shaped the community of fungi associated with both species, but the effect was stronger for the exotic X. germanus. Our results support the hypothesis that the direct contact with the mycobiome of the invaded environment might lead an exotic species to acquire native fungi. This process is likely favored by the occurrence of a bottleneck effect at the mycobiome level and/or the disruption of the mechanisms sustaining co-evolved insect-fungi symbiosis. Our study contributes to the understanding of the factors affecting insect-microbes interactions, helping to clarify the mechanisms behind biological invasions.
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Affiliation(s)
- Davide Rassati
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Padova, Italy
| | - Lorenzo Marini
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Padova, Italy
| | - Antonino Malacrinò
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH, United States of America
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12
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Skelton J, Jusino MA, Carlson PS, Smith K, Banik MT, Lindner DL, Palmer JM, Hulcr J. Relationships among wood‐boring beetles, fungi, and the decomposition of forest biomass. Mol Ecol 2019; 28:4971-4986. [DOI: 10.1111/mec.15263] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/20/2019] [Indexed: 01/29/2023]
Affiliation(s)
- James Skelton
- School of Forest Resources and Conservation University of Florida Gainesville FL USA
| | - Michelle A. Jusino
- Department of Plant Pathology University of Florida Gainesville FL USA
- United States Department of Agriculture, Forest Service Northern Research Station Center for Forest Mycology Research Madison WI USA
| | - Paige S. Carlson
- School of Forest Resources and Conservation University of Florida Gainesville FL USA
| | - Katherine Smith
- School of Forest Resources and Conservation University of Florida Gainesville FL USA
- United States Department of Agriculture, Forest Service Southern Research Station Southern Institute of Forest Genetics Saucier MS USA
| | - Mark T. Banik
- United States Department of Agriculture, Forest Service Northern Research Station Center for Forest Mycology Research Madison WI USA
| | - Daniel L. Lindner
- United States Department of Agriculture, Forest Service Northern Research Station Center for Forest Mycology Research Madison WI USA
| | - Jonathan M. Palmer
- United States Department of Agriculture, Forest Service Northern Research Station Center for Forest Mycology Research Madison WI USA
| | - Jiri Hulcr
- School of Forest Resources and Conservation University of Florida Gainesville FL USA
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Heeger F, Wurzbacher C, Bourne EC, Mazzoni CJ, Monaghan MT. Combining the 5.8S and ITS2 to improve classification of fungi. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13266] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Felix Heeger
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
| | - Christian Wurzbacher
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Chair of Urban Water Systems Engineering Technical University of Munich Garching Germany
| | - Elizabeth C. Bourne
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
| | - Camila J. Mazzoni
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Department of Evolutionary Genetics Leibniz Institute of Zoo‐ and Wildlife Research (IZW) Berlin Germany
| | - Michael T. Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Institut für Biologie Freie Universität Berlin Berlin Germany
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14
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Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ. Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. Gigascience 2019; 8:giz092. [PMID: 31363753 PMCID: PMC6667344 DOI: 10.1093/gigascience/giz092] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/25/2019] [Accepted: 07/09/2019] [Indexed: 12/21/2022] Open
Abstract
Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations. DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.
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Affiliation(s)
- Alexander M Piper
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Jana Batovska
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Noel O I Cogan
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - John Weiss
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - John Paul Cunningham
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Mark J Blacket
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
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15
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Ritter CD, Häggqvist S, Karlsson D, Sääksjärvi IE, Muasya AM, Nilsson RH, Antonelli A. Biodiversity assessments in the 21st century: the potential of insect traps to complement environmental samples for estimating eukaryotic and prokaryotic diversity using high-throughput DNA metabarcoding. Genome 2019; 62:147-159. [DOI: 10.1139/gen-2018-0096] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The rapid loss of biodiversity, coupled with difficulties in species identification, call for innovative approaches to assess biodiversity. Insects make up a substantial proportion of extant diversity and play fundamental roles in any given ecosystem. To complement morphological species identification, new techniques such as metabarcoding make it possible to quantify insect diversity and insect–ecosystem interactions through DNA sequencing. Here we examine the potential of bulk insect samples (i.e., containing many non-sorted specimens) to assess prokaryote and eukaryote biodiversity and to complement the taxonomic coverage of soil samples. We sampled 25 sites on three continents and in various ecosystems, collecting insects with SLAM traps (Brazil) and Malaise traps (South Africa and Sweden). We then compared our diversity estimates with the results obtained with biodiversity data from soil samples from the same localities. We found a largely different taxonomic composition between the soil and insect samples, testifying to the potential of bulk insect samples to complement soil samples. Finally, we found that non-destructive DNA extraction protocols, which preserve insect specimens for morphological studies, constitute a promising choice for cost-effective biodiversity assessments. We propose that the sampling and sequencing of insect samples should become a standard complement for biodiversity studies based on environmental DNA.
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Affiliation(s)
- Camila D. Ritter
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5 S05 R04 H83 D-45141 Essen, Germany
| | - Sibylle Häggqvist
- Swedish Museum of Natural History, Department of Zoology, Box 50007, 104 05 Stockholm, Sweden
| | - Dave Karlsson
- Station Linné, Skogsby 161, 386 94 Färjestaden, Sweden
| | | | - A. Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Rondebosch 7701, RSA
| | - R. Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, SE-41319 Göteborg, Sweden
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16
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Maqsood I, Bukhari SM, Ejaz R, Kausar S, Abbas MN, Ali B, Ke R. Biostatistical Options for Quantitative Diet Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5-12. [PMID: 30520629 DOI: 10.1021/acs.jafc.8b05156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sufficient statistics knowledge is crucial for the correct design of a research plan. The elucidations of results are interpretive only if appropriate statistical methods are applied. Statistical strategies are a particular approach to demonstrate complicated information in broad and explicable conclusions. The emergence of biostatistical approaches for diet evaluation has improved the accuracy of diet estimation, and different methodologies of data integration promise to magnify our understanding of ecological communities. The present study aimed to compile multiple statistical methods used for diet analysis. More specifically, the significant analysis used in diet assessment, central expectations, and preferences related to each measure was conceptualized. In addition, the ability of each test to evaluate diversity, richness, differentiation, fluctuation, similarity, and quantification of multiple diet items was summarized. Moreover, different options were proposed for researchers to select the appropriate statistical tests. This study covers a framework, aim, and understanding of the statistical test methods of diet analysis.
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Affiliation(s)
- Iram Maqsood
- College of Wildlife Resources , Northeast Forestry University , Hexing Road 59 Street , Xiang Fang District, Harbin City 150040 , China
- Department of Zoology , Shaheed Benazir Bhutto Women University Peshawar , Peshawar 25000 , Pakistan
| | - Syed Moshin Bukhari
- College of Wildlife and Ecology , University of Veterinary and Animal Sciences , Lahore 54500 , Pakistan
| | - Rabea Ejaz
- Department of Zoology , Shaheed Benazir Bhutto Women University Peshawar , Peshawar 25000 , Pakistan
| | - Saima Kausar
- College of Life Sciences . Anhui Agricultural University , Hefei 230036 , China
| | | | - Bahar Ali
- College of Plant Sciences and Technology, Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory , Huazhong Agriculture University , Wuhan , Hubei 430070 , China
| | - Rong Ke
- College of Wildlife Resources , Northeast Forestry University , Hexing Road 59 Street , Xiang Fang District, Harbin City 150040 , China
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Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00547] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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18
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Makiola A, Dickie IA, Holdaway RJ, Wood JR, Orwin KH, Lee CK, Glare TR. Biases in the metabarcoding of plant pathogens using rust fungi as a model system. Microbiologyopen 2018; 8:e00780. [PMID: 30585441 PMCID: PMC6612544 DOI: 10.1002/mbo3.780] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 01/24/2023] Open
Abstract
Plant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. This means there is a critical need to reliably and cost-effectively detect, identify, and monitor these fungi at large scales. We investigated and analyzed the causes of differences between next-generation sequencing (NGS) metabarcoding approaches and traditional DNA cloning in the detection and quantification of recognized species of rust fungi from environmental samples. We found significant differences between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) among different methods. However, there was no significant difference in relative abundance of OTUs that all methods were capable of detecting. Differences among the methods were mainly driven by the method's ability to detect specific OTUs, likely caused by mismatches with the NGS metabarcoding primers to some Puccinia species. Furthermore, detection ability did not seem to be influenced by differences in sequence lengths among methods, the most appropriate bioinformatic pipeline used for each method, or the ability to detect rare species. Our findings are important to future metabarcoding studies, because they highlight the main sources of difference among methods, and rule out several mechanisms that could drive these differences. Furthermore, strong congruity among three fundamentally different and independent methods demonstrates the promising potential of NGS metabarcoding for tracking important taxa such as rust fungi from within larger NGS metabarcoding communities. Our results support the use of NGS metabarcoding for the large-scale detection and quantification of rust fungi, but not for confirming the absence of species.
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Affiliation(s)
- Andreas Makiola
- Agroécologie, AgroSup Dijon, INRAUniversité Bourgogne, Université Bourgogne Franche‐ComtéDijonFrance,Bio‐Protection Research CentreLincoln UniversityLincolnNew Zealand
| | - Ian A. Dickie
- Bio‐Protection Research Centre, School of Biological SciencesUniversity of CanterburyNew Zealand
| | | | - Jamie R. Wood
- Manaaki Whenua – Landcare ResearchLincolnNew Zealand
| | - Kate H. Orwin
- Manaaki Whenua – Landcare ResearchLincolnNew Zealand
| | - Charles K. Lee
- Waikato DNA Sequencing Facility, School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | - Travis R. Glare
- Bio‐Protection Research CentreLincoln UniversityLincolnNew Zealand
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19
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Tremblay ÉD, Duceppe MO, Bérubé JA, Kimoto T, Lemieux C, Bilodeau GJ. Screening for Exotic Forest Pathogens to Increase Survey Capacity Using Metagenomics. PHYTOPATHOLOGY 2018; 108:1509-1521. [PMID: 29923801 DOI: 10.1094/phyto-02-18-0028-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Anthropogenic activities have a major impact on the global environment. Canada's natural resources are threatened by the spread of fungal pathogens, which is facilitated by agricultural practices and international trade. Fungi are introduced to new environments and sometimes become established, in which case they can cause disease outbreaks resulting in extensive forest decline. Here, we describe how a nationwide sample collection strategy coupled to next-generation sequencing (NGS) (i.e., metagenomics) can achieve fast and comprehensive screening for exotic invasive species. This methodology can help provide guidance to phytopathology stakeholders such as regulatory agencies. Several regulated invasive species were monitored by processing field samples collected over 3 years (2013 to 2015) near high-risk areas across Canada. Fifteen sequencing runs were required on the Ion Torrent platform to process 398 samples that yielded 45 million reads. High-throughput screening of fungal and oomycete operational taxonomic units using customized fungi-specific ribosomal internal transcribed spacer 1 barcoded primers was performed. Likewise, Phytophthora-specific barcoded primers were used to amplify the adenosine triphosphate synthase subunit 9-nicotinamide adenine dinucleotide dehydrogenase subunit 9 spacer. Several Phytophthora spp. were detected by NGS and confirmed by species-specific quantitative polymerase chain reaction (qPCR) assays. The target species Heterobasidion annosum sensu stricto could be detected only through metagenomics. We demonstrated that screening target species using a variety of sampling techniques and NGS-the results of which were validated by qPCR-has the potential to increase survey capacity and detection sensitivity, reduce hands-on time and costs, and assist regulatory agencies to identify ports of entry. Considering that early detection and prevention are the keys in mitigating invasive species damage, our method represents a substantial asset in plant pathology management.
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Affiliation(s)
- Émilie D Tremblay
- First, second, and sixth authors: Canadian Food Inspection Agency (CFIA), 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9, Canada; third author: Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380 Québec, Québec, G1V 4C7, Canada; fourth author: CFIA, 4321 Still Creek Dr, Burnaby, British Columbia, V5C 6S7, Canada; and fifth author: Institut de biologie intégrative et des systèmes, 1030 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Marc-Olivier Duceppe
- First, second, and sixth authors: Canadian Food Inspection Agency (CFIA), 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9, Canada; third author: Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380 Québec, Québec, G1V 4C7, Canada; fourth author: CFIA, 4321 Still Creek Dr, Burnaby, British Columbia, V5C 6S7, Canada; and fifth author: Institut de biologie intégrative et des systèmes, 1030 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Jean A Bérubé
- First, second, and sixth authors: Canadian Food Inspection Agency (CFIA), 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9, Canada; third author: Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380 Québec, Québec, G1V 4C7, Canada; fourth author: CFIA, 4321 Still Creek Dr, Burnaby, British Columbia, V5C 6S7, Canada; and fifth author: Institut de biologie intégrative et des systèmes, 1030 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Troy Kimoto
- First, second, and sixth authors: Canadian Food Inspection Agency (CFIA), 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9, Canada; third author: Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380 Québec, Québec, G1V 4C7, Canada; fourth author: CFIA, 4321 Still Creek Dr, Burnaby, British Columbia, V5C 6S7, Canada; and fifth author: Institut de biologie intégrative et des systèmes, 1030 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Claude Lemieux
- First, second, and sixth authors: Canadian Food Inspection Agency (CFIA), 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9, Canada; third author: Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380 Québec, Québec, G1V 4C7, Canada; fourth author: CFIA, 4321 Still Creek Dr, Burnaby, British Columbia, V5C 6S7, Canada; and fifth author: Institut de biologie intégrative et des systèmes, 1030 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Guillaume J Bilodeau
- First, second, and sixth authors: Canadian Food Inspection Agency (CFIA), 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9, Canada; third author: Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380 Québec, Québec, G1V 4C7, Canada; fourth author: CFIA, 4321 Still Creek Dr, Burnaby, British Columbia, V5C 6S7, Canada; and fifth author: Institut de biologie intégrative et des systèmes, 1030 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
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20
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Meta-Omics Tools in the World of Insect-Microorganism Interactions. BIOLOGY 2018; 7:biology7040050. [PMID: 30486337 PMCID: PMC6316257 DOI: 10.3390/biology7040050] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/16/2018] [Accepted: 11/22/2018] [Indexed: 02/07/2023]
Abstract
Microorganisms are able to influence several aspects of insects’ life, and this statement is gaining increasing strength, as research demonstrates it daily. At the same time, new sequencing technologies are now available at a lower cost per base, and bioinformatic procedures are becoming more user-friendly. This is triggering a huge effort in studying the microbial diversity associated to insects, and especially to economically important insect pests. The importance of the microbiome has been widely acknowledged for a wide range of animals, and also for insects this topic is gaining considerable importance. In addition to bacterial-associates, the insect-associated fungal communities are also gaining attention, especially those including plant pathogens. The use of meta-omics tools is not restricted to the description of the microbial world, but it can be also used in bio-surveillance, food safety assessment, or even to bring novelties to the industry. This mini-review aims to give a wide overview of how meta-omics tools are fostering advances in research on insect-microorganism interactions.
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21
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Linard B, Crampton-Platt A, Moriniere J, Timmermans MJ, Andújar C, Arribas P, Miller KE, Lipecki J, Favreau E, Hunter A, Gómez-Rodríguez C, Barton C, Nie R, Gillett CP, Breeschoten T, Bocak L, Vogler AP. The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera. Mol Phylogenet Evol 2018; 128:1-11. [DOI: 10.1016/j.ympev.2018.07.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 03/09/2018] [Indexed: 12/16/2022]
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22
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Skelton J, Jusino MA, Li Y, Bateman C, Thai PH, Wu C, Lindner DL, Hulcr J. Detecting Symbioses in Complex Communities: the Fungal Symbionts of Bark and Ambrosia Beetles Within Asian Pines. MICROBIAL ECOLOGY 2018; 76:839-850. [PMID: 29476344 DOI: 10.1007/s00248-018-1154-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/31/2018] [Indexed: 06/08/2023]
Abstract
Separating symbioses from incidental associations is a major obstacle in symbiosis research. In this survey of fungi associated with Asian bark and ambrosia beetles, we used quantitative culture and DNA barcode identification to characterize fungal communities associated with co-infesting beetle species in pines (Pinus) of China and Vietnam. To quantitatively discern likely symbioses from coincidental associations, we used multivariate analysis and multilevel pattern analysis (a type of indicator species analysis). Nearly half of the variation in fungal community composition in beetle galleries and on beetle bodies was explained by beetle species. We inferred a spectrum of ecological strategies among beetle-associated fungi: from generalist multispecies associates to highly specialized single-host symbionts that were consistently dominant within the mycangia of their hosts. Statistically significant fungal associates of ambrosia beetles were typically only found with one beetle species. In contrast, bark beetle-associated fungi were often associated with multiple beetle species. Ambrosia beetles and their galleries were frequently colonized by low-prevalence ambrosia fungi, suggesting that facultative ambrosial associations are commonplace, and ecological mechanisms such as specialization and competition may be important in these dynamic associations. The approach used here could effectively delimit symbiotic interactions in any system where symbioses are obscured by frequent incidental associations. It has multiple advantages including (1) powerful statistical tests for non-random associations among potential symbionts, (2) simultaneous evaluation of multiple co-occurring host and symbiont associations, and (3) identifying symbionts that are significantly associated with multiple host species.
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Affiliation(s)
- James Skelton
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32603, USA
| | - Michelle A Jusino
- United States Forest Service, Northern Research Station, Center for Forest Mycology Research, One Gifford Pinchot Drive, Madison, WI, 53726, USA
| | - You Li
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32603, USA
| | - Craig Bateman
- Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Pham Hong Thai
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Chengxu Wu
- Key Laboratory of Forest Protection of State Forest Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Daniel L Lindner
- United States Forest Service, Northern Research Station, Center for Forest Mycology Research, One Gifford Pinchot Drive, Madison, WI, 53726, USA
| | - Jiri Hulcr
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32603, USA.
- Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA.
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23
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Banchi E, Stankovic D, Fernández-Mendoza F, Gionechetti F, Pallavicini A, Muggia L. ITS2 metabarcoding analysis complements lichen mycobiome diversity data. Mycol Prog 2018; 17:1049-1066. [PMID: 30956650 PMCID: PMC6428334 DOI: 10.1007/s11557-018-1415-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/12/2018] [Accepted: 06/04/2018] [Indexed: 01/16/2023]
Abstract
Lichen thalli harbor complex fungal communities (mycobiomes) of species with divergent trophic and ecological strategies. The complexity and diversity of lichen mycobiomes are still largely unknown, despite surveys combining culture-based methods and high-throughput sequencing (HTS). The results of such surveys are strongly influenced by the barcode locus chosen, its sensitivity in discriminating taxa, and the depth to which public sequence repositories cover the phylogenetic spectrum of fungi. Here, we use HTS of the internal transcribed spacer 2 (ITS2) to assess the taxonomic composition and diversity of a well-characterized, alpine rock lichen community that includes thalli symptomatically infected by lichenicolous fungi as well as asymptomatic thalli. Taxa belonging to the order Chaetothyriales are the major components of the observed lichen mycobiomes. We predict sequences representative of lichenicolous fungi characterized morphologically and assess their asymptomatic presence in lichen thalli. We demonstrated the limitations of metabarcoding in fungi and show how the estimation of species diversity widely differs when ITS1 or ITS2 are used as barcode, and particularly biases the detection of Basidiomycota. The complementary analysis of both ITS1 and ITS2 loci is therefore required to reliably estimate the diversity of lichen mycobiomes.
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Affiliation(s)
- Elisa Banchi
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - David Stankovic
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
- National Institute of Biology, Marine Biology Station, Fornače 41, 6330 Piran, Slovenia
| | | | - Fabrizia Gionechetti
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
- Institute of Plant Sciences, Karl-Franzens University of Graz, Holteigasse 6, 8010 Graz, Austria
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24
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Aguayo J, Fourrier-Jeandel C, Husson C, Ioos R. Assessment of Passive Traps Combined with High-Throughput Sequencing To Study Airborne Fungal Communities. Appl Environ Microbiol 2018; 84:e02637-17. [PMID: 29572213 PMCID: PMC5960964 DOI: 10.1128/aem.02637-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/19/2018] [Indexed: 11/20/2022] Open
Abstract
Techniques based on high-throughput sequencing (HTS) of environmental DNA have provided a new way of studying fungal diversity. However, these techniques suffer from a number of methodological biases which may appear at any of the steps involved in a metabarcoding study. Air is one of the most important environments where fungi can be found, because it is the primary medium of dispersal for many species. Looking ahead to future developments, it was decided to test 20 protocols, including different passive spore traps, spore recovery procedures, DNA extraction kits, and barcode loci. HTS was performed with the Illumina MiSeq platform targeting two subloci of the fungal internal transcribed spacer. Multivariate analysis and generalized linear models showed that the type of passive spore trap, the spore recovery procedure, and the barcode all impact the description of fungal communities in terms of richness and diversity when assessed by HTS metabarcoding. In contrast, DNA extraction kits did not significantly impact these results. Although passive traps may be used to describe airborne fungal communities, a study using specific real-time PCR and a mock community showed that these kinds of traps are affected by environmental conditions that may induce losses of biological material, impacting diversity and community composition results.IMPORTANCE The advent of high-throughput sequencing (HTS) methods, such as those offered by next-generation sequencing (NGS) techniques, has opened a new era in the study of fungal diversity in different environmental substrates. In this study, we show that an assessment of the diversity of airborne fungal communities can reliably be achieved by the use of simple and robust passive spore traps. However, a comparison of sample processing protocols showed that several methodological biases may impact the results of fungal diversity when assessed by metabarcoding. Our data suggest that identifying these biases is of paramount importance to enable a correct identification and relative quantification of community members.
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Affiliation(s)
- Jaime Aguayo
- ANSES, Laboratoire de la Santé des Végétaux-LSV, Unité de Mycologie. Domaine de Pixérécourt, Malzéville, France
| | - Céline Fourrier-Jeandel
- ANSES, Laboratoire de la Santé des Végétaux-LSV, Unité de Mycologie. Domaine de Pixérécourt, Malzéville, France
| | - Claude Husson
- UMR IAM, INRA, Université de Lorraine, Nancy, France
| | - Renaud Ioos
- ANSES, Laboratoire de la Santé des Végétaux-LSV, Unité de Mycologie. Domaine de Pixérécourt, Malzéville, France
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25
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Thines M, Crous PW, Aime MC, Aoki T, Cai L, Hyde KD, Miller AN, Zhang N, Stadler M. Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon. IMA Fungus 2018; 9:177-183. [PMID: 30018878 PMCID: PMC6048572 DOI: 10.5598/imafungus.2018.09.01.11] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/23/2018] [Indexed: 11/08/2022] Open
Abstract
The large number of species still to be discovered in fungi, together with an exponentially growing number of environmental sequences that cannot be linked to known taxa, has fuelled the idea that it might be necessary to formally name fungi on the basis of sequence data only. Here we object to this idea due to several shortcomings of the approach, ranging from concerns regarding reproducibility and the violation of general scientific principles to ethical issues. We come to the conclusion that sequence-based nomenclature is potentially harmful for mycology as a discipline. Additionally, a classification based on sequences as types is not within reach anytime soon, because there is a lack of consensus regarding common standards due to the fast pace at which sequencing technologies develop.
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Affiliation(s)
- Marco Thines
- Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60483 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Pedro W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Takayuki Aoki
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Kevin D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, 59 Dudley Road, Foran Hall 201, New Brunswick, New Jersey 08901, USA
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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26
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Kohl KD. An Introductory "How-to" Guide for Incorporating Microbiome Research into Integrative and Comparative Biology. Integr Comp Biol 2018; 57:674-681. [PMID: 28985331 DOI: 10.1093/icb/icx013] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Research on host-associated microbial communities has grown rapidly. Despite the great body of work, inclusion of microbiota-related questions into integrative and comparative biology is still lagging behind other disciplines. The purpose of this paper is to offer an introduction into the basic tools and techniques of host-microbe research. Specifically, what considerations should be made before embarking on such projects (types of samples, types of controls)? How is microbiome data analyzed and integrated with data measured from the hosts? How can researchers experimentally manipulate the microbiome? With this information, integrative and comparative biologists should be able to include host-microbe studies into their research and push the boundaries of both fields.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
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27
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Hassan M, Essam T, Megahed S. Illumina sequencing and assessment of new cost-efficient protocol for metagenomic-DNA extraction from environmental water samples. Braz J Microbiol 2018; 49 Suppl 1:1-8. [PMID: 29631893 PMCID: PMC6328898 DOI: 10.1016/j.bjm.2018.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 03/14/2018] [Indexed: 10/24/2022] Open
Abstract
In this study, the development and assessment of a modified, efficient, and cost-efficient protocol for mDNA (metagenomic DNA) extraction from contaminated water samples was attempted. The efficiency of the developed protocol was investigated in comparison to a well-established commercial kit (Epicentre, Metagenomic DNA Isolation Kit for Water). The comparison was in terms of degree of shearing, yield, purity, duration, suitability for polymerase chain reaction and next-generation sequencing in addition to the quality of next-generation sequencing data. The DNA yield obtained from the developed protocol was 2.6 folds higher than that of the commercial kit. No significant difference in the alpha (Observed species, Chao1, Simpson and PD whole tree) and beta diversity was found between the DNA samples extracted by the commercial kit and the developed protocol. The number of high-quality sequences of the samples extracted by the developed method was 20% higher than those obtained by the samples processed by the kit. The developed economic protocol successfully yielded high-quality pure mDNA compatible with complex molecular applications. Thus we propose the developed protocol as a gold standard for future metagenomic studies investigating a large number of samples.
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Affiliation(s)
- Mariam Hassan
- Cairo University, Faculty of Pharmacy, Department of Microbiology and Immunology, Cairo, Egypt.
| | - Tamer Essam
- Cairo University, Faculty of Pharmacy, Department of Microbiology and Immunology, Cairo, Egypt
| | - Salwa Megahed
- Cairo University, Faculty of Pharmacy, Department of Microbiology and Immunology, Cairo, Egypt; October University for Modern Sciences and Arts (MSA), Faculty of Pharmacy, Department of Microbiology and Immunology, Cairo, Egypt
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28
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Kohl KD, Carey HV. A place for host-microbe symbiosis in the comparative physiologist's toolbox. ACTA ACUST UNITED AC 2017; 219:3496-3504. [PMID: 27852759 DOI: 10.1242/jeb.136325] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
Abstract
Although scientists have long appreciated that metazoans evolved in a microbial world, we are just beginning to appreciate the profound impact that host-associated microbes have on diverse aspects of animal biology. The enormous growth in our understanding of host-microbe symbioses is rapidly expanding the study of animal physiology, both technically and conceptually. Microbes associate functionally with various body surfaces of their hosts, although most reside in the gastrointestinal tract. Gut microbes convert dietary and host-derived substrates to metabolites such as short-chain fatty acids, thereby providing energy and nutrients to the host. Bacterial metabolites incorporated into the host metabolome can activate receptors on a variety of cell types and, in doing so, alter host physiology (including metabolism, organ function, biological rhythms, neural activity and behavior). Given that host-microbe interactions affect diverse aspects of host physiology, it is likely that they influence animal ecology and, if they confer fitness benefits, the evolutionary trajectory of a species. Multiple variables - including sampling regime, environmental parameters, host metadata and analytical methods - can influence experimental outcomes in host-microbiome studies, making careful experimental design and execution crucial to ensure reproducible and informative studies in the laboratory and field. Integration of microbiomes into comparative physiology and ecophysiological investigations can reveal the potential impacts of the microbiota on physiological responses to changing environments, and is likely to bring valuable insights to the study of host-microbiome interactions among a broad range of metazoans, including humans.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 53705, USA
| | - Hannah V Carey
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
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29
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30
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Hulcr J, Stelinski LL. The Ambrosia Symbiosis: From Evolutionary Ecology to Practical Management. ANNUAL REVIEW OF ENTOMOLOGY 2017; 62:285-303. [PMID: 27860522 DOI: 10.1146/annurev-ento-031616-035105] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The ambrosia beetle-fungus farming symbiosis is more heterogeneous than previously thought. There is not one but many ambrosia symbioses. Beetle-fungus specificity is clade dependent and ranges from strict to promiscuous. Each new origin has evolved a new mycangium. The most common relationship with host trees is colonization of freshly dead tissues, but there are also parasites of living trees, vectors of pathogenic fungi, and beetles living in rotten trees with a wood-decay symbiont. Most of these strategies are driven by fungal metabolism whereas beetle ecology is evolutionarily more flexible. The ambrosia lifestyle facilitated a radiation of social strategies, from fungus thieves to eusocial species to communities assembled by attraction to fungal scent. Although over 95% of the symbiotic pairs are economically harmless, there are also three types of pest damage: tree pathogen inoculation, mass accumulation on susceptible hosts, and structural damage. Beetles able to colonize live tree tissues are most likely to become invasive pests.
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Affiliation(s)
- Jiri Hulcr
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611;
- Entomology and Nematology Department, University of Florida, Gainesville, Florida 32611
| | - Lukasz L Stelinski
- Entomology and Nematology Department, University of Florida, Gainesville, Florida 32611
- Citrus Research and Education Center, University of Florida, Lake Alfred, Florida 33850;
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