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Protozoologica Special Issue: Protists in Soil Processes
Acta Protozool. (2012) 51: 201–208 http://www.eko.uj.edu.pl/ap ActA doi:10.4467/16890027AP.12.016.0762 Protozoologica Special issue: Protists in Soil Processes Review paper Ecology of Soil Eumycetozoans Steven L. STEPHENSON1 and Alan FEEST2 1Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA; 2Institute of Advanced Studies, University of Bristol and Ecosulis ltd., Newton St Loe, Bath, United Kingdom Abstract. Eumycetozoans, commonly referred to as slime moulds, are common to abundant organisms in soils. Three groups of slime moulds (myxogastrids, dictyostelids and protostelids) are recognized, and the first two of these are among the most important bacterivores in the soil microhabitat. The purpose of this paper is first to provide a brief description of all three groups and then to review what is known about their distribution and ecology in soils. Key words: Amoebae, bacterivores, dictyostelids, myxogastrids, protostelids. INTRODUCTION that they are amoebozoans and not fungi (Bapteste et al. 2002, Yoon et al. 2008, Baudalf 2008). Three groups of slime moulds (myxogastrids, dic- One of the idiosyncratic branches of the eukary- tyostelids and protostelids) are recognized (Olive 1970, otic tree of life consists of an assemblage of amoe- 1975). Members of the three groups exhibit consider- boid protists referred to as the supergroup Amoebozoa able diversity in the type of aerial spore-bearing struc- (Fiore-Donno et al. 2010). The most diverse members tures produced, which can range from exceedingly of the Amoebozoa are the eumycetozoans, common- small examples (most protostelids) with only a single ly referred to as slime moulds. Since their discovery, spore to the very largest examples (certain myxogas- slime moulds have been variously classified as plants, trids) that contain many millions of spores. -
Public Description of Physarum Polycephalum Schwein. Public Description of Physarum Polycephalum Schwein
4/27/2017 Mushroom Observer: Public Description of Physarum polycephalum Schwein. Public Description of Physarum polycephalum Schwein. Title: Public Description (Default) Descriptions: Create Name: Physarum polycephalum Schwein. (/name/create_name_description/30400) View: public Public Description (Default) Edit: public (/name/show_name_description/1634) [Edit Version: 2 (/name/edit_name_description/1634)] Previous Version (/name/show_past_name_description/1634? version=1) Description status: Unreviewed Taxonomic Classification: Kingdom: Amoebozoa (http://mushroomobserver.org/observer/lookup_name/Amoebozoa) Phylum: Mycetozoa (http://mushroomobserver.org/observer/lookup_name/Mycetozoa) Class: Myxogastria (http://mushroomobserver.org/observer/lookup_name/Myxogastria) Order: Physarida (http://mushroomobserver.org/observer/lookup_name/Physarida) Family: Physaridae (http://mushroomobserver.org/observer/lookup_name/Physaridae) Genus: Physarum (http://mushroomobserver.org/observer/lookup_name/Physarum) General Description: Physarium polycephalum is one of the most widely recognized and cultivated plasmodia. P. polycephalum undergoes distinctive transformations from spore, to amoeboid, to plasmoid and sporangium. To the naked eye, the spores appear as a reddish or purplish brown mass; amoebas and myxoflagellates can only be seen under microscope; the plasmodium will be a bright yellow, highly reticulate network and have a much finer, denser, distinctive “fan” shape in the direction of movement. Sporangia are dark orange to brown and consist of gregarious lobes connected to a shriveled, thin stipe. Spores are uninucleate, globose, minutely spinose, 8 to 11 microns in diameter, brownish yellow individually, appear reddish to purplish brown in mass, and require 15 to 48 hours for incubation, defined as the time when seeds are sowed to the splitting of the spore walls. Incubation duration is constant whether a spore is fresh or 18 months old. Cultures are readily started on water drops on the surface of slides. -
Zygote Gene Expression and Plasmodial Development in Didymium Iridis
DePaul University Via Sapientiae College of Science and Health Theses and Dissertations College of Science and Health Summer 8-25-2019 Zygote gene expression and plasmodial development in Didymium iridis Sean Schaefer DePaul University, [email protected] Follow this and additional works at: https://via.library.depaul.edu/csh_etd Part of the Biology Commons Recommended Citation Schaefer, Sean, "Zygote gene expression and plasmodial development in Didymium iridis" (2019). College of Science and Health Theses and Dissertations. 322. https://via.library.depaul.edu/csh_etd/322 This Thesis is brought to you for free and open access by the College of Science and Health at Via Sapientiae. It has been accepted for inclusion in College of Science and Health Theses and Dissertations by an authorized administrator of Via Sapientiae. For more information, please contact [email protected]. Zygote gene expression and plasmodial development in Didymium iridis A Thesis presented in Partial fulfillment of the Requirements for the Degree of Master of Biology By Sean Schaefer 2019 Advisor: Dr. Margaret Silliker Department of Biological Sciences College of Liberal Arts and Sciences DePaul University Chicago, IL Abstract: Didymium iridis is a cosmopolitan species of plasmodial slime mold consisting of two distinct life stages. Haploid amoebae and diploid plasmodia feed on microscopic organisms such as bacteria and fungi through phagocytosis. Sexually compatible haploid amoebae act as gametes which when fused embark on an irreversible developmental change resulting in a diploid zygote. The zygote can undergo closed mitosis resulting in a multinucleated plasmodium. Little is known about changes in gene expression during this developmental transition. Our principal goal in this study was to provide a comprehensive list of genes likely to be involved in plasmodial development. -
Old Woman Creek National Estuarine Research Reserve Management Plan 2011-2016
Old Woman Creek National Estuarine Research Reserve Management Plan 2011-2016 April 1981 Revised, May 1982 2nd revision, April 1983 3rd revision, December 1999 4th revision, May 2011 Prepared for U.S. Department of Commerce Ohio Department of Natural Resources National Oceanic and Atmospheric Administration Division of Wildlife Office of Ocean and Coastal Resource Management 2045 Morse Road, Bldg. G Estuarine Reserves Division Columbus, Ohio 1305 East West Highway 43229-6693 Silver Spring, MD 20910 This management plan has been developed in accordance with NOAA regulations, including all provisions for public involvement. It is consistent with the congressional intent of Section 315 of the Coastal Zone Management Act of 1972, as amended, and the provisions of the Ohio Coastal Management Program. OWC NERR Management Plan, 2011 - 2016 Acknowledgements This management plan was prepared by the staff and Advisory Council of the Old Woman Creek National Estuarine Research Reserve (OWC NERR), in collaboration with the Ohio Department of Natural Resources-Division of Wildlife. Participants in the planning process included: Manager, Frank Lopez; Research Coordinator, Dr. David Klarer; Coastal Training Program Coordinator, Heather Elmer; Education Coordinator, Ann Keefe; Education Specialist Phoebe Van Zoest; and Office Assistant, Gloria Pasterak. Other Reserve staff including Dick Boyer and Marje Bernhardt contributed their expertise to numerous planning meetings. The Reserve is grateful for the input and recommendations provided by members of the Old Woman Creek NERR Advisory Council. The Reserve is appreciative of the review, guidance, and council of Division of Wildlife Executive Administrator Dave Scott and the mapping expertise of Keith Lott and the late Steve Barry. -
The Ascomycota
Papers and Proceedings of the Royal Society of Tasmania, Volume 139, 2005 49 A PRELIMINARY CENSUS OF THE MACROFUNGI OF MT WELLINGTON, TASMANIA – THE ASCOMYCOTA by Genevieve M. Gates and David A. Ratkowsky (with one appendix) Gates, G. M. & Ratkowsky, D. A. 2005 (16:xii): A preliminary census of the macrofungi of Mt Wellington, Tasmania – the Ascomycota. Papers and Proceedings of the Royal Society of Tasmania 139: 49–52. ISSN 0080-4703. School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia (GMG*); School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001, Australia (DAR). *Author for correspondence. This work continues the process of documenting the macrofungi of Mt Wellington. Two earlier publications were concerned with the gilled and non-gilled Basidiomycota, respectively, excluding the sequestrate species. The present work deals with the non-sequestrate Ascomycota, of which 42 species were found on Mt Wellington. Key Words: Macrofungi, Mt Wellington (Tasmania), Ascomycota, cup fungi, disc fungi. INTRODUCTION For the purposes of this survey, all Ascomycota having a conspicuous fruiting body were considered, excluding Two earlier papers in the preliminary documentation of the endophytes. Material collected during forays was described macrofungi of Mt Wellington, Tasmania, were confined macroscopically shortly after collection, and examined to the ‘agarics’ (gilled fungi) and the non-gilled species, microscopically to obtain details such as the size of the -
A Novel Structure Learning Algorithm for Bayesian Networks Inspired by Physarum Polycephalum
Physarum Learner: A Novel Structure Learning Algorithm for Bayesian Networks inspired by Physarum Polycephalum DISSERTATION ZUR ERLANGUNG DES DOKTORGRADES DER NATURWISSENSCHAFTEN (DR. RER. NAT.) DER FAKULTAT¨ FUR¨ BIOLOGIE UND VORKLINISCHE MEDIZIN DER UNIVERSITAT¨ REGENSBURG vorgelegt von Torsten Schon¨ aus Wassertrudingen¨ im Jahr 2013 Der Promotionsgesuch wurde eingereicht am: 21.05.2013 Die Arbeit wurde angeleitet von: Prof. Dr. Elmar W. Lang Unterschrift: Torsten Schon¨ ii iii Abstract Two novel algorithms for learning Bayesian network structure from data based on the true slime mold Physarum polycephalum are introduced. The first algorithm called C- PhyL calculates pairwise correlation coefficients in the dataset. Within an initially fully connected Physarum-Maze, the length of the connections is given by the inverse correla- tion coefficient between the connected nodes. Then, the shortest indirect path between each two nodes is determined using the Physarum Solver. In each iteration, a score of the surviving edges is increased. Based on that score, the highest ranked connections are combined to form a Bayesian network. The novel C-PhyL method is evaluated with different configurations and compared to the LAGD Hill Climber, Tabu Search and Simu- lated Annealing on a set of artificially generated and real benchmark networks of different characteristics, showing comparable performance regarding quality of training results and increased time efficiency for large datasets. The second novel algorithm called SO-PhyL is introduced and shown to be able to out- perform common score based structure learning algorithms for some benchmark datasets. SO-PhyL first initializes a fully connected Physarum-Maze with constant length and ran- dom conductivities. In each Physarum Solver iteration, the source and sink nodes are changed randomly and the conductivities are updated. -
A Revised Classification of Naked Lobose Amoebae (Amoebozoa
Protist, Vol. 162, 545–570, October 2011 http://www.elsevier.de/protis Published online date 28 July 2011 PROTIST NEWS A Revised Classification of Naked Lobose Amoebae (Amoebozoa: Lobosa) Introduction together constitute the amoebozoan subphy- lum Lobosa, which never have cilia or flagella, Molecular evidence and an associated reevaluation whereas Variosea (as here revised) together with of morphology have recently considerably revised Mycetozoa and Archamoebea are now grouped our views on relationships among the higher-level as the subphylum Conosa, whose constituent groups of amoebae. First of all, establishing the lineages either have cilia or flagella or have lost phylum Amoebozoa grouped all lobose amoe- them secondarily (Cavalier-Smith 1998, 2009). boid protists, whether naked or testate, aerobic Figure 1 is a schematic tree showing amoebozoan or anaerobic, with the Mycetozoa and Archamoe- relationships deduced from both morphology and bea (Cavalier-Smith 1998), and separated them DNA sequences. from both the heterolobosean amoebae (Page and The first attempt to construct a congruent molec- Blanton 1985), now belonging in the phylum Per- ular and morphological system of Amoebozoa by colozoa - Cavalier-Smith and Nikolaev (2008), and Cavalier-Smith et al. (2004) was limited by the the filose amoebae that belong in other phyla lack of molecular data for many amoeboid taxa, (notably Cercozoa: Bass et al. 2009a; Howe et al. which were therefore classified solely on morpho- 2011). logical evidence. Smirnov et al. (2005) suggested The phylum Amoebozoa consists of naked and another system for naked lobose amoebae only; testate lobose amoebae (e.g. Amoeba, Vannella, this left taxa with no molecular data incertae sedis, Hartmannella, Acanthamoeba, Arcella, Difflugia), which limited its utility. -
Preliminary Classification of Leotiomycetes
Mycosphere 10(1): 310–489 (2019) www.mycosphere.org ISSN 2077 7019 Article Doi 10.5943/mycosphere/10/1/7 Preliminary classification of Leotiomycetes Ekanayaka AH1,2, Hyde KD1,2, Gentekaki E2,3, McKenzie EHC4, Zhao Q1,*, Bulgakov TS5, Camporesi E6,7 1Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China 2Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand 3School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand 4Landcare Research Manaaki Whenua, Private Bag 92170, Auckland, New Zealand 5Russian Research Institute of Floriculture and Subtropical Crops, 2/28 Yana Fabritsiusa Street, Sochi 354002, Krasnodar region, Russia 6A.M.B. Gruppo Micologico Forlivese “Antonio Cicognani”, Via Roma 18, Forlì, Italy. 7A.M.B. Circolo Micologico “Giovanni Carini”, C.P. 314 Brescia, Italy. Ekanayaka AH, Hyde KD, Gentekaki E, McKenzie EHC, Zhao Q, Bulgakov TS, Camporesi E 2019 – Preliminary classification of Leotiomycetes. Mycosphere 10(1), 310–489, Doi 10.5943/mycosphere/10/1/7 Abstract Leotiomycetes is regarded as the inoperculate class of discomycetes within the phylum Ascomycota. Taxa are mainly characterized by asci with a simple pore blueing in Melzer’s reagent, although some taxa have lost this character. The monophyly of this class has been verified in several recent molecular studies. However, circumscription of the orders, families and generic level delimitation are still unsettled. This paper provides a modified backbone tree for the class Leotiomycetes based on phylogenetic analysis of combined ITS, LSU, SSU, TEF, and RPB2 loci. In the phylogenetic analysis, Leotiomycetes separates into 19 clades, which can be recognized as orders and order-level clades. -
Slime Moulds
Queen’s University Biological Station Species List: Slime Molds The current list has been compiled by Richard Aaron, a naturalist and educator from Toronto, who has been running the Fabulous Fall Fungi workshop at QUBS between 2009 and 2019. Dr. Ivy Schoepf, QUBS Research Coordinator, edited the list in 2020 to include full taxonomy and information regarding species’ status using resources from The Natural Heritage Information Centre (April 2018) and The IUCN Red List of Threatened Species (February 2018); iNaturalist and GBIF. Contact Ivy to report any errors, omissions and/or new sightings. Based on the aforementioned criteria we can expect to find a total of 33 species of slime molds (kingdom: Protozoa, phylum: Mycetozoa) present at QUBS. Species are Figure 1. One of the most commonly encountered reported using their full taxonomy; common slime mold at QUBS is the Dog Vomit Slime Mold (Fuligo septica). Slime molds are unique in the way name and status, based on whether the species is that they do not have cell walls. Unlike fungi, they of global or provincial concern (see Table 1 for also phagocytose their food before they digest it. details). All species are considered QUBS Photo courtesy of Mark Conboy. residents unless otherwise stated. Table 1. Status classification reported for the amphibians of QUBS. Global status based on IUCN Red List of Threatened Species rankings. Provincial status based on Ontario Natural Heritage Information Centre SRank. Global Status Provincial Status Extinct (EX) Presumed Extirpated (SX) Extinct in the -
Biodiversity of Plasmodial Slime Moulds (Myxogastria): Measurement and Interpretation
Protistology 1 (4), 161–178 (2000) Protistology August, 2000 Biodiversity of plasmodial slime moulds (Myxogastria): measurement and interpretation Yuri K. Novozhilova, Martin Schnittlerb, InnaV. Zemlianskaiac and Konstantin A. Fefelovd a V.L.Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia, b Fairmont State College, Fairmont, West Virginia, U.S.A., c Volgograd Medical Academy, Department of Pharmacology and Botany, Volgograd, Russia, d Ural State University, Department of Botany, Yekaterinburg, Russia Summary For myxomycetes the understanding of their diversity and of their ecological function remains underdeveloped. Various problems in recording myxomycetes and analysis of their diversity are discussed by the examples taken from tundra, boreal, and arid areas of Russia and Kazakhstan. Recent advances in inventory of some regions of these areas are summarised. A rapid technique of moist chamber cultures can be used to obtain quantitative estimates of myxomycete species diversity and species abundance. Substrate sampling and species isolation by the moist chamber technique are indispensable for myxomycete inventory, measurement of species richness, and species abundance. General principles for the analysis of myxomycete diversity are discussed. Key words: slime moulds, Mycetozoa, Myxomycetes, biodiversity, ecology, distribu- tion, habitats Introduction decay (Madelin, 1984). The life cycle of myxomycetes includes two trophic stages: uninucleate myxoflagellates General patterns of community structure of terrestrial or amoebae, and a multi-nucleate plasmodium (Fig. 1). macro-organisms (plants, animals, and macrofungi) are The entire plasmodium turns almost all into fruit bodies, well known. Some mathematics methods are used for their called sporocarps (sporangia, aethalia, pseudoaethalia, or studying, from which the most popular are the quantita- plasmodiocarps). -
9B Taxonomy to Genus
Fungus and Lichen Genera in the NEMF Database Taxonomic hierarchy: phyllum > class (-etes) > order (-ales) > family (-ceae) > genus. Total number of genera in the database: 526 Anamorphic fungi (see p. 4), which are disseminated by propagules not formed from cells where meiosis has occurred, are presently not grouped by class, order, etc. Most propagules can be referred to as "conidia," but some are derived from unspecialized vegetative mycelium. A significant number are correlated with fungal states that produce spores derived from cells where meiosis has, or is assumed to have, occurred. These are, where known, members of the ascomycetes or basidiomycetes. However, in many cases, they are still undescribed, unrecognized or poorly known. (Explanation paraphrased from "Dictionary of the Fungi, 9th Edition.") Principal authority for this taxonomy is the Dictionary of the Fungi and its online database, www.indexfungorum.org. For lichens, see Lecanoromycetes on p. 3. Basidiomycota Aegerita Poria Macrolepiota Grandinia Poronidulus Melanophyllum Agaricomycetes Hyphoderma Postia Amanitaceae Cantharellales Meripilaceae Pycnoporellus Amanita Cantharellaceae Abortiporus Skeletocutis Bolbitiaceae Cantharellus Antrodia Trichaptum Agrocybe Craterellus Grifola Tyromyces Bolbitius Clavulinaceae Meripilus Sistotremataceae Conocybe Clavulina Physisporinus Trechispora Hebeloma Hydnaceae Meruliaceae Sparassidaceae Panaeolina Hydnum Climacodon Sparassis Clavariaceae Polyporales Gloeoporus Steccherinaceae Clavaria Albatrellaceae Hyphodermopsis Antrodiella -
Slime Molds: Biology and Diversity
Glime, J. M. 2019. Slime Molds: Biology and Diversity. Chapt. 3-1. In: Glime, J. M. Bryophyte Ecology. Volume 2. Bryological 3-1-1 Interaction. Ebook sponsored by Michigan Technological University and the International Association of Bryologists. Last updated 18 July 2020 and available at <https://digitalcommons.mtu.edu/bryophyte-ecology/>. CHAPTER 3-1 SLIME MOLDS: BIOLOGY AND DIVERSITY TABLE OF CONTENTS What are Slime Molds? ....................................................................................................................................... 3-1-2 Identification Difficulties ...................................................................................................................................... 3-1- Reproduction and Colonization ........................................................................................................................... 3-1-5 General Life Cycle ....................................................................................................................................... 3-1-6 Seasonal Changes ......................................................................................................................................... 3-1-7 Environmental Stimuli ............................................................................................................................... 3-1-13 Light .................................................................................................................................................... 3-1-13 pH and Volatile Substances