Browsing by Author "Powell, Martha J."

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    Characterization of Amoeboaphelidium protococcarum, an Algal Parasite New to the Cryptomycota Isolated from an Outdoor Algal Pond Used for the Production of Biofuel
    (PLOS, 2013) Letcher, Peter M.; Lopez, Salvador; Schmieder, Robert; Lee, Philip A.; Behnke, Craig; Powell, Martha J.; McBride, Robert C.; University of Alabama Tuscaloosa; San Diego State University
    Mass culture of algae for the production of biofuels is a developing technology designed to offset the depletion of fossil fuel reserves. However, large scale culture of algae in open ponds can be challenging because of incidences of infestation with algal parasites. Without knowledge of the identity of the specific parasite and how to control these pests, algal-based biofuel production will be limited. We have characterized a eukaryotic parasite of Scenedesmus dimorphus growing in outdoor ponds used for biofuel production. We demonstrated that as the genomic DNA of parasite FD01 increases, the concentration of S. dimorphus cells decreases; consequently, this is a highly destructive pathogen. Techniques for culture of the parasite and host were developed, and the endoparasite was identified as the Aphelidea, Amoeboaphelidium protococcarum. Phylogenetic analysis of ribosomal sequences revealed that parasite FD01 placed within the recently described Cryptomycota, a poorly known phylum based on two species of Rozella and environmental samples. Transmission electron microscopy demonstrated that aplanospores of the parasite produced filose pseudopodia, which contained fine fibers the diameter of actin microfilaments. Multiple lipid globules clustered and were associated with microbodies, mitochondria and a membrane cisternae, an arrangement characteristic of the microbody-lipid globule complex of chytrid zoospores. After encystment and attachment to the host cells, the parasite injected its protoplast into the host between the host cell wall and plasma membrane. At maturity the unwalled parasite occupied the entire host cell. After cleavage of the protoplast into aplanospores, a vacuole and lipids remained in the host cell. Amoeboaphelidium protococcarum isolate FD01 is characteristic of the original description of this species and is different from strain X-5 recently characterized. Our results help put a face on the Cryptomycota, revealing that the phylum is more diverse than previously understood and include some of the Aphelidea as well as Rozella species and potentially Microsporidia.
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    The Collection of Zoosporic Eufungi at the University of Michigan (CZEUM): introducing a new repository of barcodedChytridiomycetaandBlastocladiomycotacultures
    (BMC, 2020) Simmons, D. Rabern; Bonds, Anne E.; Castillo, Buck T.; Clemons, Rebecca A.; Glasco, Alex D.; Myers, Jillian M.; Thapa, Natasha; Letcher, Peter M.; Powell, Martha J.; Longcore, Joyce E.; James, Timothy Y.; University of Michigan; University of Alabama Tuscaloosa; University of Maine Orono
    We formed the Collection of Zoosporic Eufungi at the University of Michigan (CZEUM) in 2018 as a cryopreserved fungal collection consolidating the University of Maine Culture Collection (UMCC, or JEL), the University of Alabama Chytrid Culture Collection (UACCC), and additional zoosporic eufungal accessions. The CZEUM is established as a community resource containing 1045 cryopreserved cultures ofChytridiomycota,Monoblepharidomycota, andBlastocladiomycota, with 52 cultures being ex-type strains. We molecularly characterized 431 cultures by amplifying the majority of the rDNA operon in a single reaction, yielding an average fragment length of 4739 bp. We sequenced multiplexed samples with an Oxford Nanopore Technology MinION device and software, and demonstrate the method is accurate by producing sequences identical to published Sanger sequences. With these data, we generated a phylogeny of 882 zoosporic eufungi strains to produce the most comprehensive phylogeny of these taxa to date. The CZEUM is thus largely characterized by molecular data, which can guide instructors and researchers on future studies of these organisms. Cultures from the CZEUM can be purchased through an online portal.
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    Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
    (Oxford University Press, 2014) Schoch, Conrad L.; Robbertse, Barbara; Robert, Vincent; Duong Vu; Cardinali, Gianluigi; Irinyi, Laszlo; Meyer, Wieland; Nilsson, R. Henrik; Hughes, Karen; Miller, Andrew N.; Kirk, Paul M.; Abarenkov, Kessy; Aime, M. Catherine; Ariyawansa, Hiran A.; Bidartondo, Martin; Boekhout, Teun; Buyck, Bart; Cai, Qing; Chen, Jie; Crespo, Ana; Crous, Pedro W.; Damm, Ulrike; De Beer, Z. Wilhelm; Dentinger, Bryn T. M.; Divakar, Pradeep K.; Duenas, Margarita; Feau, Nicolas; Fliegerova, Katerina; Garcia, Miguel A.; Ge, Zai-Wei; Griffith, GarethW.; Groenewald, Johannes Z.; Groenewald, Marizeth; Grube, Martin; Gryzenhout, Marieka; Gueidan, Cecile; Guo, Liangdong; Hambleton, Sarah; Hamelin, Richard; Hansen, Karen; Hofstetter, Valerie; Hong, Seung-Beom; Houbraken, Jos; Hyde, Kevin D.; Inderbitzin, Patrik; Johnston, Peter R.; Karunarathna, Samantha C.; Koljalg, Urmas; Kovacs, Gabor M.; Kraichak, Ekaphan; Krizsan, Krisztina; Kurtzman, Cletus P.; Larsson, Karl-Henrik; Leavitt, Steven; Letcher, Peter M.; Liimatainen, Kare; Liu, Jian-Kui; Lodge, D. Jean; Luangsa-ard, Janet Jennifer; Lumbsch, H. Thorsten; Maharachchikumbura, Sajeewa S. N.; Manamgoda, Dimuthu; Martin, Maria P.; Minnis, Andrew M.; Moncalvo, Jean-Marc; Mule, Giuseppina; Nakasone, Karen K.; Niskanen, Tuula; Olariaga, Ibai; Papp, Tamas; Petkovits, Tamas; Pino-Bodas, Raquel; Powell, Martha J.; Raja, Huzefa A.; Redecker, Dirk; Sarmiento-Ramirez, J. M.; Seifert, Keith A.; Shrestha, Bhushan; Stenroos, Soili; Stielow, Benjamin; Suh, Sung-Oui; Tanaka, Kazuaki; Tedersoo, Leho; Teresa Telleria, M.; Udayanga, Dhanushka; Untereiner, Wendy A.; Dieguez Uribeondo, Javier; Subbarao, Krishna V.; Vagvoelgyi, Csaba; Visagie, Cobus; Voigt, Kerstin; Walker, Donald M.; Weir, Bevan S.; Weiss, Michael; Wijayawardene, Nalin N.; Wingfield, Michael J.; Xu, J. P.; Yang, Zhu L.; Zhang, Ning; Zhuang, Wen-Ying; Federhen, Scott; National Institutes of Health (NIH) - USA; NIH National Library of Medicine (NLM); Royal Netherlands Academy of Arts & Sciences; Westerdijk Fungal Biodiversity Institute (KNAW); University of Perugia; University of Sydney; Westmead Institute for Medical Research; University of Gothenburg; University of Tennessee Knoxville; Illinois Natural History Survey; University of Illinois Urbana-Champaign; Royal Botanic Gardens, Kew; University of Tartu; Purdue University West Lafayette Campus; Purdue University; Mae Fah Luang University; Imperial College London; UDICE-French Research Universities; Sorbonne Universite; Centre National de la Recherche Scientifique (CNRS); CNRS - Institute of Ecology & Environment (INEE); Museum National d'Histoire Naturelle (MNHN); Chinese Academy of Sciences; Kunming Institute of Botany, CAS; Complutense University of Madrid; Senckenberg Gesellschaft fur Naturforschung (SGN); University of Pretoria; Consejo Superior de Investigaciones Cientificas (CSIC); CSIC - Real Jardin Botanico de Madrid; University of British Columbia; Czech Academy of Sciences; Institute of Animal Physiology & Genetics of the Czech Academy of Sciences; University of Toronto; University Toronto Mississauga; Aberystwyth University; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC); Institute of Biological, Environmental, Rural & Sciences (IBERS); University of Graz; University of the Free State; Commonwealth Scientific & Industrial Research Organisation (CSIRO); Institute of Microbiology, CAS; Agriculture & Agri Food Canada; Swedish Museum of Natural History; Swiss Federal Research Station Agroscope; Rural Development Administration (RDA), Republic of Korea; University of California Davis; Landcare Research - New Zealand; Eotvos Lorand University; Eotvos Lorand Research Network; Hungarian Academy of Sciences; Hungarian Centre for Agricultural Research; Field Museum of Natural History (Chicago); Szeged University; United States Department of Agriculture (USDA); University of Alabama Tuscaloosa; University of Helsinki; United States Forest Service; National Science & Technology Development Agency - Thailand; National Center Genetic Engineering & Biotechnology (BIOTEC); University of Wisconsin Madison; Royal Ontario Museum; Consiglio Nazionale delle Ricerche (CNR); Istituto Scienze delle Produzioni Alimentari (ISPA-CNR); University of North Carolina; University of North Carolina Greensboro; Universite de Bourgogne; Institut Agro; AgroSup Dijon; Sungkyunkwan University (SKKU); Hirosaki University; Brandon University; Hans Knoll Institute (HKI); Friedrich Schiller University of Jena; University of Findlay; Eberhard Karls University of Tubingen; McMaster University; Rutgers State University New Brunswick
    DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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    Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
    (Wiley, 2019) Adl, Sina M.; Bass, David; Lane, Christopher E.; Lukes, Julius; Schoch, Conrad L.; Smirnov, Alexey; Agatha, Sabine; Berney, Cedric; Brown, Matthew W.; Burki, Fabien; Cardenas, Paco; Cepicka, Ivan; Chistyakova, Lyudmila; del Campo, Javier; Dunthorn, Micah; Edvardsen, Bente; Eglit, Yana; Guillou, Laure; Hampl, Vladimir; Heiss, Aaron A.; Hoppenrath, Mona; James, Timothy Y.; Karnkowska, Anna; Karpov, Sergey; Kim, Eunsoo; Kolisko, Martin; Kudryavtsev, Alexander; Lahr, Daniel J. G.; Lara, Enrique; Le Gall, Line; Lynn, Denis H.; Mann, David G.; Massana, Ramon; Mitchell, Edward A. D.; Morrow, Christine; Park, Jong Soo; Pawlowski, Jan W.; Powell, Martha J.; Richter, Daniel J.; Rueckert, Sonja; Shadwick, Lora; Shimano, Satoshi; Spiegel, Frederick W.; Torruella, Guifre; Youssef, Noha; Zlatogursky, Vasily; Zhang, Qianqian; University of Saskatchewan; Natural History Museum London; Centre for Environment Fisheries & Aquaculture Science; University of Rhode Island; Czech Academy of Sciences; Biology Centre of the Czech Academy of Sciences; University of South Bohemia Ceske Budejovice; National Institutes of Health (NIH) - USA; NIH National Library of Medicine (NLM); Saint Petersburg State University; Salzburg University; Centre National de la Recherche Scientifique (CNRS); CNRS - Institute of Ecology & Environment (INEE); UDICE-French Research Universities; Sorbonne Universite; Mississippi State University; Uppsala University; Charles University Prague; Consejo Superior de Investigaciones Cientificas (CSIC); CSIC - Centro Mediterraneo de Investigaciones Marinas y Ambientales (CMIMA); CSIC - Instituto de Ciencias del Mar (ICM); University of Kaiserslautern; University of Duisburg Essen; University of Oslo; Dalhousie University; American Museum of Natural History (AMNH); University of Michigan; University of Warsaw; Russian Academy of Sciences; Zoological Institute of the Russian Academy of Sciences; Universidade de Sao Paulo; University of Neuchatel; Museum National d'Histoire Naturelle (MNHN); University of Guelph; University of British Columbia; IRTA; Kyungpook National University; University of Geneva; University of Alabama Tuscaloosa; CSIC-UPF - Institut de Biologia Evolutiva (IBE); Pompeu Fabra University; Edinburgh Napier University; University of Arkansas Fayetteville; Hosei University; Universite Paris Saclay; Oklahoma State University - Stillwater; Chinese Academy of Sciences; Yantai Institute of Coastal Zone Research, CAS
    This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.
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    A taxonomic summary and revision of Rozella (Cryptomycota)
    (International Mycological Association, 2018) Letcher, Peter M.; Powell, Martha J.; University of Alabama Tuscaloosa
    Rozella is a genus of endoparasites of a broad range of hosts. Most species are known by their morphology and host specificity, while only three have been examined ultrastructurally and had portions of their genome sequenced. Determined in molecular phylogenies to be the earliest diverging lineage in kingdom Fungi, Rozella currently nests among an abundance of environmental sequences in phylum Cryptomycota, superphylum Opisthosporidia. Here we briefly summarize a history of Rozella, provide descriptions of all species, and include a key to the species of Rozella.
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    A taxonomic summary of Aphelidiaceae
    (BMC, 2019) Letcher, Peter M.; Powell, Martha J.; University of Alabama Tuscaloosa
    Aphelids are parasitoids of various algae and diatoms, and in a recent classification are contained in family Aphelidiaceae, phylum Aphelidiomycota, kingdom Fungi. Family Aphelidiaceae (the only family in the phylum) is composed of four genera: Aphelidium, Paraphelidium, Amoeboaphelidium, and Pseudaphelidium. All species are known morphologically, and most have been illustrated. Few have been examined ultrastructurally, and even fewer have been sequenced for molecular comparisons. Recent studies in molecular phylogenetics have revealed an abundance of related environmental sequences that indicate unrealized biodiversity within the group. Herein, we briefly summarize the history of aphelids and acknowledge the controversy of placement of the group with related organisms. With light microscopic images and transmission electron micrographs, we illustrate typical life cycle stages for aphelids, provide updated descriptions and taxonomy for all described species, and provide a key to the species.