Applications of DNA Bar Coding in Molecular Systematics of Fungi: a Review
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The Role and Use of Non-Saccharomyces Yeasts in Wine Production
The Role and Use of Non-Saccharomyces Yeasts in Wine Production N.P. Jolly1*, O.P.H. Augustyn1 and I.S. Pretorius2** (1) ARC Infruitec-Nietvoorbij***, Private Bag X5026, 7599 Stellenbosch, South Africa. (2) Institute for Wine Biotechnology, Department of Viticulture & Oenology, Stellenbosch University, Private Bag X1, 7602 Matieland (Stellenbosch), South Africa. Submitted for publication: September 2005 Accepted for publication: April 2006 Key words: Non-Saccharomyces, yeasts, vineyards, cellars, fermentation, wine. The contribution by the numerous grape-must-associated non-Saccharomyces yeasts to wine fermentation has been debated extensively. These yeasts, naturally present in all wine fermentations, are metabolically active and their metabolites can impact on wine quality. Although often seen as a source of microbial spoilage, there is substantial contrary evidence pointing to a positive contribution by these yeasts. The role of non-Saccharomyces yeasts in wine fermentation is therefore receiving increasing attention by wine microbiologists in Old and New World wine producing countries. Species that have been investigated for wine production thus far include those from the Candida, Kloeckera, Hanseniaspora, Zygosaccharomyces, Schizosaccharomyces, Torulaspora, Brettanomyces, Saccharomycodes, Pichia and Williopsis genera. In this review the use and role of non-Saccharomyces yeast in wine production is presented and research trends are discussed. INTRODUCTION roles of the numerous non-Saccharomyces yeasts normally asso- ciated with grape must and wine. These yeasts, naturally present Wine is the product of a complex biological and biochemical in all wine fermentations to a greater or lesser extent, are meta- interaction between grapes (grape juice) and different microor- bolically active and their metabolites can impact on wine quality. -
Evaluation of Seasonal Dynamics of Fungal DNA Assemblages in a Flow-Regulated Stream in a Restored Forest Using Edna Metabarcoding
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.10.420661; this version posted May 23, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding Shunsuke Matsuoka1, Yoriko Sugiyama2, Yoshito Shimono3, Masayuki Ushio4,5, Hideyuki Doi1 1. Graduate School of Simulation Studies, University of Hyogo 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, 650- 0047, Japan 2. Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan 3. Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan 4. Hakubi Center, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan 5. Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113, Japan Corresponding author: Shunsuke Matsuoka ([email protected]) Abstract Investigation of seasonal variations in fungal communities is essential for understanding biodiversity and ecosystem functions. However, the conventional sampling method, with substrate removal and high spatial heterogeneity of community compositions, makes surveying the seasonality of fungal communities challenging. Recently, water environmental DNA (eDNA) analysis has been explored for its utility in biodiversity surveys. In this study, we assessed whether the seasonality of fungal communities can be detected by monitoring eDNA in a forest stream. We conducted monthly water sampling in a forest stream over two years and used DNA metabarcoding to identify fungal eDNA. -
Environmental DNA for Wildlife Biology and Biodiversity Monitoring
Review Environmental DNA for wildlife biology and biodiversity monitoring 1,2* 3* 1,4 3 Kristine Bohmann , Alice Evans , M. Thomas P. Gilbert , Gary R. Carvalho , 3 3 5,6 3 Simon Creer , Michael Knapp , Douglas W. Yu , and Mark de Bruyn 1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5–7, 1350 Copenhagen K, Denmark 2 School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK 3 Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Deiniol Road, Bangor University, Bangor LL57 2UW, UK 4 Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6845, Australia 5 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Road, Kunming, Yunnan 650223, China 6 School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK Extraction and identification of DNA from an environ- technology. Today, science fiction is becoming reality as a mental sample has proven noteworthy recently in growing number of biologists are using eDNA for species detecting and monitoring not only common species, detection and biomonitoring, circumventing, or at least but also those that are endangered, invasive, or elusive. alleviating, the need to sight or sample living organisms. Particular attributes of so-called environmental DNA Such approaches are also accelerating the rate of discovery, (eDNA) analysis render it a potent tool for elucidating because no a priori information about the likely species mechanistic insights in ecological and evolutionary pro- found in a particular environment is required to identify cesses. -
DNA Barcoding of Fungi in the Forest Ecosystem of the Psunj and Papukissn Mountains 1847-6481 in Croatia Eissn 1849-0891
DNA Barcoding of Fungi in the Forest Ecosystem of the Psunj and PapukISSN Mountains 1847-6481 in Croatia eISSN 1849-0891 OrIGINAL SCIENtIFIC PAPEr DOI: https://doi.org/10.15177/seefor.20-17 DNA barcoding of Fungi in the Forest Ecosystem of the Psunj and Papuk Mountains in Croatia Nevenka Ćelepirović1,*, Sanja Novak Agbaba2, Monika Karija Vlahović3 (1) Croatian Forest Research Institute, Division of Genetics, Forest Tree Breeding and Citation: Ćelepirović N, Novak Agbaba S, Seed Science, Cvjetno naselje 41, HR-10450 Jastrebarsko, Croatia; (2) Croatian Forest Karija Vlahović M, 2020. DNA Barcoding Research Institute, Division of Forest Protection and Game Management, Cvjetno naselje of Fungi in the Forest Ecosystem of the 41, HR-10450 Jastrebarsko; (3) University of Zagreb, School of Medicine, Department of Psunj and Papuk Mountains in Croatia. forensic medicine and criminology, DNA Laboratory, HR-10000 Zagreb, Croatia. South-east Eur for 11(2): early view. https://doi.org/10.15177/seefor.20-17. * Correspondence: e-mail: [email protected] received: 21 Jul 2020; revised: 10 Nov 2020; Accepted: 18 Nov 2020; Published online: 7 Dec 2020 AbStract The saprotrophic, endophytic, and parasitic fungi were detected from the samples collected in the forest of the management unit East Psunj and Papuk Nature Park in Croatia. The disease symptoms, the morphology of fruiting bodies and fungal culture, and DNA barcoding were combined for determining the fungi at the genus or species level. DNA barcoding is a standardized and automated identification of species based on recognition of highly variable DNA sequences. DNA barcoding has a wide application in the diagnostic purpose of fungi in biological specimens. -
Environmental DNA for Improved Detection and Environmental Surveillance of Schistosomiasis
Environmental DNA for improved detection and environmental surveillance of schistosomiasis Mita E. Senguptaa,1, Micaela Hellströmb,c, Henry C. Kariukid, Annette Olsena, Philip F. Thomsenb,e, Helena Mejera, Eske Willerslevb,f,g,h, Mariam T. Mwanjei, Henry Madsena, Thomas K. Kristensena, Anna-Sofie Stensgaardj,2, and Birgitte J. Vennervalda,2 aDepartment of Veterinary and Animal Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark; bCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark; cAquabiota Water Research, SE-115 50, Sweden; dDepartment of Microbiology and Parasitology, Kenya Methodist University, 60200 Meru, Kenya; eDepartment of Bioscience, University of Aarhus, DK-8000 Aarhus C, Denmark; fDepartment of Zoology, University of Cambridge, CB2 3EJ Cambridge, United Kingdom; gHuman Genetics Programme, Wellcome Trust Sanger Institute, Hinxton, SB10 1SA Cambridge, United Kingdom; hDanish Institute for Advanced Study, University of Southern Denmark, DK-5230 Odense M, Denmark; iNeglected Tropical Diseases Unit, Division of Communicable Disease Prevention and Control, Ministry of Health, Nairobi, Kenya; and jCenter for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark Edited by Andrea Rinaldo, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland, and approved March 18, 2019 (received for review September 21, 2018) Schistosomiasis is a water-based, infectious disease with -
DNA Barcoding for Species Identification and Discovery in Diatoms
557_578_MANN.fm Page 557 Mercredi, 8. décembre 2010 8:58 08 Cryptogamie, Algologie, 2010, 31 (4): 557-577 © 2010 Adac. Tous droits réservés DNA barcoding for species identification and discovery in diatoms David G. MANN a* , Shinya SATO a, Rosa TROBAJO b, Pieter VANORMELINGEN c & Caroline SOUFFREAU c a Royal Botanic Garden Edinburgh, Inverleith Row, Edinburgh EH3 5LR, Scotland, UK b Aquatic Ecosystems, Institute for Food and Agricultural Research and Technology (IRTA), Ctra Poble Nou Km 5.5, Sant Carles de la Ràpita, Catalunya, E-43540, Spain c Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281-S8, B-9000 Gent, Belgium Abstract – Diatoms are the largest group of microalgae, play an enormous role in the biosphere, and have major significance as bioindicators. Traditional identification requires inter alia long training, considerable microscopical skill, and use of a vast and scattered literature. During the life cycle, diatom cells change in size and pattern, often also shape, but the full cycle is known in <1% of described species. Recent evidence shows that there are many pseudocryptic and cryptic species of diatoms, requiring molecular methods for discovery and recognition. These and other factors argue that DNA barcoding would be highly beneficial. It could be ‘strong’, resolving nearly all species, or ‘weak’, resolving mostly species already recognized from light microscopy. Attempts have already been made to identify suitable genes and we evaluate these on the basis of universality and practicality, and ability to discriminate between species in the very few ‘model’ systems offering likely examples of sister-species-pairs. No candidate marker is ideal but LSU rDNA and rbcL may be acceptable, though their discriminatory power is lower than that of some other markers. -
Intragenomic Variation in the ITS Rdna Region Obscures Phylogenetic Relationships and Inflates Estimates of Operational Taxonomic Units in Genus Laetiporus
Mycologia, 103(4), 2011, pp. 731–740. DOI: 10.3852/10-331 # 2011 by The Mycological Society of America, Lawrence, KS 66044-8897 Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus Daniel L. Lindner1 spacer region, intragenomic variation, molecular Mark T. Banik drive, sulfur shelf US Forest Service, Northern Research Station, Center for Forest Mycology Research, One Gifford Pinchot Drive, Madison, Wisconsin 53726 INTRODUCTION Genus Laetiporus Murrill (Basidiomycota, Polypo- rales) contains important polypore species with Abstract: Regions of rDNA are commonly used to worldwide distribution and the ability to produce infer phylogenetic relationships among fungal species cubical brown rot in living and dead wood of conifers and as DNA barcodes for identification. These and angiosperms. Ribosomal DNA sequences, includ- regions occur in large tandem arrays, and concerted ing sequences from the internal transcribed spacer evolution is believed to reduce intragenomic variation (ITS) and large subunit (LSU) regions, have been among copies within these arrays, although some used to define species and infer phylogenetic variation still might exist. Phylogenetic studies typi- relationships in Laetiporus and to confirm the cally use consensus sequencing, which effectively existence of cryptic species (Lindner and Banik conceals most intragenomic variation, but cloned 2008, Ota and Hattori 2008, Tomsovsky and Jankovsky sequences containing intragenomic variation are 2008, Ota et al. 2009, Vasaitis et al. 2009) described becoming prevalent in DNA databases. To under- with mating compatibility, ITS-RFLP, morphology stand effects of using cloned rDNA sequences in and host preference data (Banik et al. 1998, Banik phylogenetic analyses we amplified and cloned the and Burdsall 1999, Banik and Burdsall 2000, Burdsall ITS region from pure cultures of six Laetiporus and Banik 2001). -
Understanding Environmental DNA
bioRxiv preprint doi: https://doi.org/10.1101/660530; this version posted June 5, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Understanding Environmental DNA Ryan P. Kelly1,*, Andrew Olaf Shelton2, and Ramon´ Gallego1,2 1University of Washington, School of Marine and Environmental Affairs, Seattle, Washington USA 2Northwest Fisheries Science Center, NOAA Fisheries, Seattle, Washington USA *[email protected] ABSTRACT As environmental DNA (eDNA) studies have grown in popularity for use in ecological applications, it has become clear that their results differ in significant ways from those of traditional, non-PCR-based surveys. In general, eDNA studies that rely on amplicon sequencing may detect hundreds of species present in a sampled environment, but the resulting species composition can be idiosyncratic, reflecting species’ true biomass abundances poorly or not at all. Here, we use a set of simulations to develop a mechanistic understanding of the processes leading to eDNA results. In particular, we focus on the effects of PCR cycle number and primer amplification efficiency on the results of diversity metrics in sequencing studies. We then show that proportional indices of eDNA reads capture trends in taxon biomass with high accuracy, particularly where amplification efficiency is high (median correlation up to 0.97). Our results explain much of the observed behavior of eukaryotic eDNA studies, and lead to recommendations for best practices in the field. 1 Introduction Studies that survey the natural world by amplifying and sequencing DNA from environmental sources such as water, air, or soil – which we call metabarcoding or eDNA studies – have become a popular method for rapidly characterizing ecological communities [1, 2, 3, 4]. -
Using Environmental DNA for Marine Monitoring and Planning
Network of Conservation Educators & Practitioners What’s in the Water? Using environmental DNA for Marine Monitoring and Planning Author(s): Kristin E. Douglas, Patrick Shea, Ana Luz Porzecanski, and Eugenia Naro-Maciel Source: Lessons in Conservation, Vol. 10, Issue 1, pp. 29–48 Published by: Network of Conservation Educators and Practitioners, Center for Biodiversity and Conservation, American Museum of Natural History Stable URL: ncep.amnh.org/linc This article is featured in Lessons in Conservation, the official journal of the Network of Conservation Educators and Practitioners (NCEP). NCEP is a collaborative project of the American Museum of Natural History’s Center for Biodiversity and Conservation (CBC) and a number of institutions and individuals around the world. Lessons in Conservation is designed to introduce NCEP teaching and learning resources (or “modules”) to a broad audience. NCEP modules are designed for undergraduate and professional level education. These modules—and many more on a variety of conservation topics—are available for free download at our website, ncep.amnh.org. To learn more about NCEP, visit our website: ncep.amnh.org. All reproduction or distribution must provide full citation of the original work and provide a copyright notice as follows: “Copyright 2020, by the authors of the material and the Center for Biodiversity and Conservation of the American Museum of Natural History. All rights reserved.” Illustrations obtained from the American Museum of Natural History’s library: images.library.amnh.org/digital/ -
GRAS Notice for Pichia Kudriavzevii ASCUSDY21 for Use As a Direct Fed Microbial in Dairy Cattle
GRAS Notice for Pichia kudriavzevii ASCUSDY21 for Use as a Direct Fed Microbial in Dairy Cattle Prepared for: Division of Animal Feeds, (HFV-220) Center for Veterinary Medicine 7519 Standish Place Rockville, Maryland 20855 Submitted by: ASCUS Biosciences, Inc. 6450 Lusk Blvd Suite 209 San Diego, California 92121 GRAS Notice for Pichia kudriavzevii ASCUSDY21 for Use as a Direct Fed Microbial in Dairy Cattle TABLE OF CONTENTS PART 1 – SIGNED STATEMENTS AND CERTIFICATION ................................................................................... 9 1.1 Name and Address of Organization .............................................................................................. 9 1.2 Name of the Notified Substance ................................................................................................... 9 1.3 Intended Conditions of Use .......................................................................................................... 9 1.4 Statutory Basis for the Conclusion of GRAS Status ....................................................................... 9 1.5 Premarket Exception Status .......................................................................................................... 9 1.6 Availability of Information .......................................................................................................... 10 1.7 Freedom of Information Act, 5 U.S.C. 552 .................................................................................. 10 1.8 Certification ................................................................................................................................ -
Environmental DNA Monitoring of Species Presence During Aquatic Habitat Restoration
Environmental DNA monitoring of species presence during aquatic habitat restoration Gary M. Clark 1, Cameron R. Turner2,3, David M. Lodge2,3 1. Environmental DNA Solutions, Granger, IN 2. Center for Aquatic Conservation, University of Notre Dame, Notre Dame, IN 3. Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN Objectives 1. Environmental DNA overview 2. “eDNA” surveillance applications 3. Ozaukee County eDNA surveillance plan Myriad factors Stakeholder Success Aesthetics Economic Benefits Recreation Education Ecological Success Guiding image exists Learning Success Ecological improvement Scientific contribution Self-sustaining Management experience No lasting harm done Improve methods Assessment completed Stream Barrier Removal Palmer et al. 2005. Standards for ecologically successful river restoration. J. Appl. Ecol. How do you measure success? Fish passage & occupancy – a critical monitoring parameter Visual snorkel survey, ladder count, creel survey Electrofishing E-boat, backpack shocker Video Vaki RiverWatcher Mark & recapture Fin clip, external tag, CWT Telemetry Radio tag, acoustic tag, satellite tag Environmental DNA Genetic “fingerprints” in Water Column What is Environmental (e)DNA? • Require Direct Observation • “Non-invasive” genetic sampling How about aquatic eDNA? • Fish naturally shed DNA • Epithelial Cells • Feces, urine • Milt • Some cellular material will be carried in suspension and can be collected for analysis The eDNA methodology The presence of individual species can be detected by filtering -
Challenges of the Non-Conventional Yeast Wickerhamomyces Anomalus in Winemaking
fermentation Review Challenges of the Non-Conventional Yeast Wickerhamomyces anomalus in Winemaking Beatriz Padilla 1, Jose V. Gil 2,3 and Paloma Manzanares 2,* 1 INCLIVA Health Research Institute, 46010 Valencia, Spain; [email protected] 2 Department of Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, 46980 Valencia, Spain; [email protected] 3 Departamento de Medicina Preventiva y Salud Pública, Ciencias de la Alimentación, Toxicología y Medicina Legal, Facultad de Farmacia, Universitat de València, Burjassot, 46100 Valencia, Spain * Correspondence: [email protected]; Tel.: +34-96 390-0022 Received: 27 July 2018; Accepted: 18 August 2018; Published: 20 August 2018 Abstract: Nowadays it is widely accepted that non-Saccharomyces yeasts, which prevail during the early stages of alcoholic fermentation, contribute significantly to the character and quality of the final wine. Among these yeasts, Wickerhamomyces anomalus (formerly Pichia anomala, Hansenula anomala, Candida pelliculosa) has gained considerable importance for the wine industry since it exhibits interesting and potentially exploitable physiological and metabolic characteristics, although its growth along fermentation can still be seen as an uncontrollable risk. This species is widespread in nature and has been isolated from different environments including grapes and wines. Its use together with Saccharomyces cerevisiae in mixed culture fermentations has been proposed to increase wine particular characteristics. Here, we review the ability of W. anomalus to produce enzymes and metabolites of oenological relevance and we discuss its potential as a biocontrol agent in winemaking. Finally, biotechnological applications of W. anomalus beyond wine fermentation are briefly described. Keywords: non-Saccharomyces yeasts; Wickerhamomyces anomalus; Pichia anomala; enzymes; glycosidases; acetate esters; biocontrol; mixed starters; wine 1.