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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. -
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. -
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). -
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 -
The Mycetozoa of North America, Based Upon the Specimens in The
THE MYCETOZOA OF NORTH AMERICA HAGELSTEIN, MYCETOZOA PLATE 1 WOODLAND SCENES IZ THE MYCETOZOA OF NORTH AMERICA BASED UPON THE SPECIMENS IN THE HERBARIUM OF THE NEW YORK BOTANICAL GARDEN BY ROBERT HAGELSTEIN HONORARY CURATOR OF MYXOMYCETES ILLUSTRATED MINEOLA, NEW YORK PUBLISHED BY THE AUTHOR 1944 COPYRIGHT, 1944, BY ROBERT HAGELSTEIN LANCASTER PRESS, INC., LANCASTER, PA. PRINTED IN U. S. A. To (^My CJriend JOSEPH HENRI RISPAUD CONTENTS PAGES Preface 1-2 The Mycetozoa (introduction to life history) .... 3-6 Glossary 7-8 Classification with families and genera 9-12 Descriptions of genera and species 13-271 Conclusion 273-274 Literature cited or consulted 275-289 Index to genera and species 291-299 Explanation of plates 301-306 PLATES Plate 1 (frontispiece) facing title page 2 (colored) facing page 62 3 (colored) facing page 160 4 (colored) facing page 172 5 (colored) facing page 218 Plates 6-16 (half-tone) at end ^^^56^^^ f^^ PREFACE In the Herbarium of the New York Botanical Garden are the large private collections of Mycetozoa made by the late J. B. Ellis, and the late Dr. W. C. Sturgis. These include many speci- mens collected by the earlier American students, Bilgram, Farlow, Fullmer, Harkness, Harvey, Langlois, Macbride, Morgan, Peck, Ravenel, Rex, Thaxter, Wingate, and others. There is much type and authentic material. There are also several thousand specimens received from later collectors, and found in many parts of the world. During the past twenty years my associates and I have collected and studied in the field more than ten thousand developments in eastern North America. -
Morphological and Molecular Evidence of Arbuscular Mycorrhizal Fungal Associations in Costa Rican Epiphytic Bromeliads1
BIOTROPICA 37(2): 245–250 2005 10.1111/j.1744-7429.2005.00033.x Morphological and Molecular Evidence of Arbuscular Mycorrhizal Fungal Associations in Costa Rican Epiphytic Bromeliads1 Annette R. Rowe2 and Anne Pringle Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, California 94720-3102, U.S.A. ABSTRACT Arbuscular mycorrhizal fungi influence the growth, morphology, and fitness of a variety of plant species, but little is known of the arbuscular mycorrhizal (AM) fungal associations of plant species in forest canopies. Plant species’ associations with AM fungi are most often elucidated by examining the roots for fungal structures; however, morphological data may provide a limited resolution on a plant’s mycorrhizal status. We combined a traditional staining technique with a molecular marker (the 18S ribosomal gene) to determine whether or not a variety of epiphytic bromeliads form arbuscular mycorrhizal fungal associations. Using these methods we show that the epiphytic bromeliad Vriesea werkleana forms arbuscular mycorrhizal fungal associations with members of the genus Glomus. AM fungal sequences of this plant species formed three distinct clades nested within a larger Glomus clade; two of the clades did not group with any previously sequenced lineage of Glomus. Novel clades may represent novel species. Although Vriesea werkleana is associated with multiple AM fungal species, each individual plant is colonized by a single lineage. The combination of morphological and molecular methods provides a practical approach to the characterization of the mycorrhizal status of epiphytic bromeliads, and perhaps other tropical epiphytes. Key words: cloud forest; Costa Rica; Monteverde; symbiosis; tropical mycorrhizae; VAM fungi. -
Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
University of Rhode Island DigitalCommons@URI Biological Sciences Faculty Publications Biological Sciences 9-26-2018 Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes Christopher E. Lane Et Al Follow this and additional works at: https://digitalcommons.uri.edu/bio_facpubs Journal of Eukaryotic Microbiology ISSN 1066-5234 ORIGINAL ARTICLE Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes Sina M. Adla,* , David Bassb,c , Christopher E. Laned, Julius Lukese,f , Conrad L. Schochg, Alexey Smirnovh, Sabine Agathai, Cedric Berneyj , Matthew W. Brownk,l, Fabien Burkim,PacoCardenas n , Ivan Cepi cka o, Lyudmila Chistyakovap, Javier del Campoq, Micah Dunthornr,s , Bente Edvardsent , Yana Eglitu, Laure Guillouv, Vladimır Hamplw, Aaron A. Heissx, Mona Hoppenrathy, Timothy Y. Jamesz, Anna Karn- kowskaaa, Sergey Karpovh,ab, Eunsoo Kimx, Martin Koliskoe, Alexander Kudryavtsevh,ab, Daniel J.G. Lahrac, Enrique Laraad,ae , Line Le Gallaf , Denis H. Lynnag,ah , David G. Mannai,aj, Ramon Massanaq, Edward A.D. Mitchellad,ak , Christine Morrowal, Jong Soo Parkam , Jan W. Pawlowskian, Martha J. Powellao, Daniel J. Richterap, Sonja Rueckertaq, Lora Shadwickar, Satoshi Shimanoas, Frederick W. Spiegelar, Guifre Torruellaat , Noha Youssefau, Vasily Zlatogurskyh,av & Qianqian Zhangaw a Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, S7N 5A8, SK, Canada b Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom -
Phytoremediation with Geosiphon-Like Symbiosis?
Environ Sci Pollut Res (2016) 23:5992–5994 DOI 10.1007/s11356-016-6135-1 LETTER TO THE EDITOR Phytoremediation with Geosiphon-like symbiosis? Grzegorz Wojtczak1 & Paulina Janik2 Received: 19 September 2015 /Accepted: 19 January 2016 /Published online: 29 January 2016 # The Author(s) 2016. This article is published with open access at Springerlink.com Dear Editor, evolution of animals’ gut (as argued by Margaret McFall-Ngai In their recent article published in Environmental Science and in Velasquez-Manoff 2015). The comparison between root and Pollution Research, Anna Ogar et al. (2015) have shown, gut is not a simple analogy, as in both cases symbiotic microbes thanks to a careful experimental design, that the addition of significantly contribute to nutrition and protection of their hosts, diazotrophic bacteria together with mycorrhizal fungi signifi- and several developmental processes are mirrored in those cantly improves plant growth and performance. Strikingly, the seemingly different organs making their mode of evolution addition of inoculum containing only diazotrophs but not my- follow the same pattern (Selosse et al. 2014). Rhizophagus corrhizal fungi had contrary effect and led to the reduced irregularis (syn. Glomus intraradices), an arbuscular mycorrhi- shoots and roots biomass and lower photosynthesis efficiency zal fungus (phylum Glomeromycota), was used by Ogar and her of Medicago sativa and Hieracium pilosella,ascomparedto co-workers. Glomus sensu lato descended from the hypotheti- experimental plants co-inoculated with mycorrhizal fungi and cal, primordial-plant mycorrhizal symbionts and as all members nitrogen-fixing bacteria. The authors gave their credit to many of this group are unable to synthesize simple sugars, nor to take features of microbes used in the study that might have resulted them up from the environment. -
Abstract Phylogenetic Analysis of the Symbiotic
ABSTRACT PHYLOGENETIC ANALYSIS OF THE SYMBIOTIC NOSTOC CYANOBACTERIA AS ASSESSED BY THE NITROGEN FIXATION (NIFD) GENE by Hassan S. Salem Members of the genus Nostoc are the most commonly encountered cyanobacterial partners in terrestrial symbiotic systems. The objective of this study was to determine the taxonomic position of the various symbionts within the genus Nostoc, in addition to examining the evolutionary relationships between symbiont and free-living strains within the genus by analyzing the complete sequences of the nitrogen fixation (nif) genes. NifD was sequenced from thirty-two representative strains, and phylogenetically analyzed using the Maximum likelihood and Bayesian criteria. Such analyses indicate at least three well-supported clusters exist within the genus, with moderate bootstrap support for the differentiation between symbiont and free-living strains. Our analysis suggests 2 major patterns for the evolution of symbiosis within the genus Nostoc. The first resulting in the symbiosis with a broad range of plant groups, while the second exclusively leads to a symbiotic relationship with the aquatic water fern, Azolla. PHYLOGENETIC ANALYSIS OF THE SYMBIOTIC NOSTOC CYANOBACTERIA AS ASSESSED BY THE NITROGEN FIXATION (NIFD) GENE A Thesis Submitted to the Faculty of Miami University in partial fulfillment of the requirements for the degree of Master of Science Department of Botany by Hassan S. Salem Miami University Oxford, Ohio 2010 Advisor________________________ (Susan Barnum) Reader_________________________ (Nancy Smith-Huerta) -
Cyanobacteria in Terrestrial Symbiotic Systems
Cyanobacteria in Terrestrial Symbiotic Systems Jouko Rikkinen Abstract Filamentous cyanobacteria are important primary producers and N2 fixers in many terrestrial environments. As reduced nitrogen is often limiting, some thalloid liverworts (Marchantiophyta), hornworts (Anthocerophyta), the water fern Azolla (Salviniales), cycads (Cycadophyta), and the angiosperm Gunnera (Gunnerales) have evolved the ability to establish stable and structurally well-defined symbioses with N2-fixing cyanobacteria. Also a wide diversity of lichen-forming fungi have cyanobacteria as photosynthetic symbionts or as N2-fixing symbionts. Cyanolichen symbioses have evolved independently in different fungal lineages, and evolution has often resulted in convergent morphologies in distantly related groups. DNA techniques have provided a wealth of new information on the diversity of symbiotic cyanobacteria and their hosts. The fact that many plants and fungi engage in many different symbioses simultaneously underlines the probable significance of diffuse evolutionary relationships between different symbiotic systems, including cyanobacterial and mycorrhizal associations. This review introduces the reader to recent research on symbiotic cyanobacteria in terrestrial ecosystems and shortly describes the astonishing range of diversity in these ecologically important associations. Introduction Mutually beneficial symbiotic interactions are an inherent feature of most ecological communities. Nitrogen is essential for growth of land plants, but the availability of reduced nitrogen in the soil is often limiting. Diazotrophic bacteria are able to convert atmospheric dinitrogen (N2) to ammonia (NH3) that can be utilized by plants, and consequently, numerous land plants form an association with N2-fixing bacteria. These interactions include the morphologically and physiologically highly coevolved symbioses between legumes and rhizobia, between actinorhizal plants and Frankia, and a plethora of more casual associations between plants and prokaryotic diazotrophs (Bothe et al.