Publications by authors named "Martha J Powell"

45 Publications

The Collection of Zoosporic Eufungi at the University of Michigan (CZEUM): introducing a new repository of barcoded and cultures.

IMA Fungus 2020 6;11:20. Epub 2020 Oct 6.

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA.

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 of , , and , 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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http://dx.doi.org/10.1186/s43008-020-00041-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7537106PMC
October 2020

A taxonomic summary of .

IMA Fungus 2019 7;10. Epub 2019 Jun 7.

Department of Biological Sciences, The University of Alabama, 1332 SEC, Box 870344, 300 Hackberry Lane, Tuscaloosa, AL 35487 USA.

Aphelids are parasitoids of various algae and diatoms, and in a recent classification are contained in family , phylum , kingdom . Family (the only family in the phylum) is composed of four genera: , , , and . 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.
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http://dx.doi.org/10.1186/s43008-019-0005-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325670PMC
June 2019

Ultrastructure of early stages of Rozella allomycis (Cryptomycota) infection of its host, Allomyces macrogynus (Blastocladiomycota).

Fungal Biol 2019 02 22;123(2):109-116. Epub 2018 Nov 22.

Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487, USA. Electronic address:

This study reconstructs early stages of Rozella allomycis endoparasitic infection of its host, Allomyces macrogynus. Young thalli of A. macrogynus were inoculated with suspensions of R. allomycis zoospores and allowed to develop for 120 h. Infected thalli at intervals were fixed for electron microscopy and observed. Zoospores were attracted to host thalli, encysted on their surfaces, and penetrated their walls with an infection tube. The parasite cyst discharged its protoplast through an infection tube, which invaginated the host plasma membrane. The host plasma membrane then surrounded the parasite protoplast and formed a compartment confining it inside host cytoplasm. The earliest host-parasite interface within host cytoplasm consisted of two membranes, the outer layer the host plasma membrane and the inner layer the parasite plasma membrane. At first a wide space separated the two membranes and no material was observed within this space. Later, as the endoparasite thallus expanded within the compartment, the two membranes became closely appressed. As the endoparasite thallus continued to enlarge, the interface developed into three membrane layers. Thus, host plasma membrane surrounded the parasite protoplast initially without the parasite having to pierce the host plasma membrane for entry. Significantly, host-derived membrane was at the interface throughout development.
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http://dx.doi.org/10.1016/j.funbio.2018.11.009DOI Listing
February 2019

A taxonomic summary and revision of ().

IMA Fungus 2018 Jul 16;9:383-399. Epub 2018 Nov 16.

Department of Biological Sciences, The University of Alabama, 1332 SEC, Box 870344, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA.

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 , currently nests among an abundance of environmental sequences in phylum , superphylum . Here we briefly summarize a history of , provide descriptions of all species, and include a key to the species of .
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http://dx.doi.org/10.5598/imafungus.2018.09.02.09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317583PMC
July 2018

Morphology, zoospore ultrastructure, and phylogenetic position of Polyphlyctis willoughbyi, a new species in Chytridiales (Chytridiomycota).

Fungal Biol 2018 12 24;122(12):1171-1183. Epub 2018 Aug 24.

Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA. Electronic address:

The purpose of our research is to investigate the morphology, zoospore ultrastructure, and molecular phylogenetic placement of a chytrid from Australia. From a survey of chytrid fungi in New South Wales, Australia, we isolated strain PL AUS 026 and putatively identified it as Polyphlyctis unispina. Light microscopic evaluation determined strain PL AUS 026 to be similar to two other strains of P. unispina characterized in the literature but to have a more complex thallus than that of the type. Molecular phylogenetic analyses placed our strain as sister of or basal to Chytridiaceae, Chytridiales. Ultrastructural analysis of the zoospore of strain PL AUS 026 revealed unique features. On the basis of our analyses we designate strain PL AUS 026 as a new species, Polyphlyctis willoughbyi. This research extends our concept of Chytridiaceae systematics and ultrastructural variation in the Chytridiales zoospore.
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http://dx.doi.org/10.1016/j.funbio.2018.08.003DOI Listing
December 2018

Morphology, zoospore ultrastructure, and molecular position of taxa in the Asterophlyctis lineage (Chytridiales, Chytridiomycota).

Fungal Biol 2018 11 17;122(11):1109-1123. Epub 2018 Sep 17.

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA. Electronic address:

The purpose of our research is to investigate morphology, zoospore ultrastructure, and molecular placement of six strains in the Asterophlyctis (Chytridiales) lineage. In previous molecular analyses strain JEL 186, putatively Asterophlyctis sarcoptoides, placed as basal in family Chytriomycetaceae. Recent sampling for chytrids resulted in isolation of five strains (WJD 209, MP 058, JEL 524, JEL 857, and JEL 885) molecularly related to strain JEL 186. Our morphological evaluations reveal that strains JEL 186 and WJD 209 are members of Asterophlyctis. Strain WJD 209 is considered representative of the type, A. sarcoptoides, and strain JEL 186 a new species, Asterophlyctis michiganensis. The four strains MP 058, JEL 524, JEL 857, and JEL 885 are distinct from Asterophlyctis, and we consider them as members of a new genus, Wheelerophlyctis, composed of two species, Wheelerophlyctis interior and Wheelerophlyctis interiexterior. Asterophlyctis and Wheelerophlyctis are sister taxa and we demarcate that lineage as Asterophlyctaceae. The two genera also have similar zoospore ultrastructure, which is unique among strains in Chytridiales. In consideration of their molecular position and zoospore ultrastructure, we hypothesize that Asterophlyctis and Wheelerophlyctis represent a bridge between Chytriomycetaceae and Chytridiaceae. This research expands our concepts of systematics and zoospore ultrastructural variation in Chytridiales.
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http://dx.doi.org/10.1016/j.funbio.2018.09.002DOI Listing
November 2018

Zopfochytrium is a new genus in the Chytridiales with distinct zoospore ultrastructure.

Fungal Biol 2018 11 29;122(11):1041-1049. Epub 2018 Aug 29.

Department of Biological Sciences, The University of Alabama, Tuscaloosa AL 35487, USA.

While surveying chytrid diversity in lakes and streams, we found on cellulosic bait a chytrid that had both monocentric and polycentric thallus forms. We brought this chytrid into axenic culture from three sites in eastern North America, studied its thallus development and zoospore ultrastructure, and compared its 28S rDNA sequence with those of other members of the Chytridiomycota. Thallus morphology matched that described for the rare chytrid, Cladochytrium polystomum Zopf. Sporangia were spherical and produced numerous long discharge tubes. After discharge, zoospores remained in spherical clusters at the tips of the inoperculate openings of discharge tubes. After 10-30 min zoospores either swam away or encysted in place. Zoospore ultrastructural features included a cell coat, flagellar plug, and paracrystalline inclusion, features typical of members of the Chytridiales. However, the flagellar apparatus structure and organellar organization differed from that of zoospores previously described. Based on its molecular phylogeny and its zoospore ultrastructural features, we classify C. polystomum as a member of the Chytridiaceae in the Chytridiales. Because its thallus development and its ribosomal DNA sequences diverged decidedly from those of Cladochytrium tenue Nowak, the type species of Cladochytrium, we erected Zopfochytrium as a new genus for this chytrid.
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http://dx.doi.org/10.1016/j.funbio.2018.08.005DOI Listing
November 2018

Inventory of chytrid diversity in two temporary forest ponds using a multiphasic approach.

Mycologia 2018 Sep-Oct;110(5):811-821. Epub 2018 Oct 1.

a Department of Biological Sciences , University of Alabama , Tuscaloosa , Alabama 35487.

Food webs in temporary forest ponds are driven by decomposition of terrestrial inputs. Chytrid fungi are important components of the fungal community, degrading leaf litter in streams reliant on terrestrial inputs and in lake ecosystems where they may stabilize the food web. However, little is known about chytrid fungi in temporary forest ponds. We inventoried the chytrid diversity present in two temporary forest ponds via light microscopy of baited samples and ion semiconductor (Ion Torrent) sequencing of environmental DNA. We quantified trends of chytrid alpha and beta diversity as a function of spatial and temporal factors. A total of 59 chytrid taxa were detected throughout the study. Beta diversity exhibited variation across the sampled months for both the entire fungal community as well as for chytrids alone. Shifts in community composition were also apparent, although diversity metrics and composition patterns did not meet adjusted P values. The results of this study highlight the diversity of chytrid fungi in temporary forest ponds and the need for further studies on the spatial and temporal dynamics of chytrid species.
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http://dx.doi.org/10.1080/00275514.2018.1510725DOI Listing
March 2019

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes.

J Eukaryot Microbiol 2019 01;66(1):4-119

Institut de Systématique, Évolution, Biodiversité, Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 39, Paris, 75005, France.

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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http://dx.doi.org/10.1111/jeu.12691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6492006PMC
January 2019

Cytochemical Localization of Polyphenol Oxidase Activity in K2-Bodies of Saprolegnia ferax Secondary Zoospores.

J Eukaryot Microbiol 2019 05 29;66(3):404-412. Epub 2018 Aug 29.

Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, 35487.

Zoospores of the oomycete Saprolegnia ferax release adhesive material from K-bodies at the onset of attachment to substrates. To understand more fully how K-bodies function in adhesion, enzyme activity was investigated cytochemically in secondary zoospores. Presence of catalase, a marker enzyme for microbodies, was explored in the diaminobenzidine (DAB) reaction. Although pH 9.2 DAB-staining characteristic of catalase activity was detected in the granular matrix regions of K-bodies, reaction controls indicated that the reaction was due to oxidative enzyme activity other than catalase. Because polyphenol oxidase (PPO) is another metal-containing enzyme capable of oxidizing DAB, activity of this enzyme was tested with a more specific substrate, dihydroxyphenylalanine (DOPA). In the DOPA procedure, reaction product was exclusively localized within K-bodies, indicating the presence of PPO. Results with three methods of reaction controls (elimination of substrate, addition of a PPO enzyme inhibitor, and heat-inactivation of enzymes) all supported the presence of PPO in K-bodies. This study highlights potential roles for K-body PPO in stabilization of adhesion bodies by: cross-linking matrix phenolic proteins or glycoproteins as K-bodies discharge adhesives onto substrates, or polymerizing phenolics protective against microbial attacks of the adhesion pad.
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http://dx.doi.org/10.1111/jeu.12682DOI Listing
May 2019

Morphology, Ultrastructure, and Molecular Phylogeny of Rozella multimorpha, a New Species in Cryptomycota.

J Eukaryot Microbiol 2018 03 17;65(2):180-190. Epub 2017 Aug 17.

Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, 35487, USA.

Increasing numbers of sequences of basal fungi from environmental DNA studies are being deposited in public databases. Many of these sequences remain unclassified below the phylum level because sequence information from identified species is sparse. Lack of basic biological knowledge due to a dearth of identified species is extreme in Cryptomycota, a new phylum widespread in the environment and phylogenetically basal within the fungal lineage. Consequently, we are attempting to fill gaps in the knowledge of Rozella, the best-known genus in this lineage. Rozella is a genus of unwalled, holocarpic, endobiotic parasites of hosts including Chytridiomycota, Blastocladiomycota, Oomycota, Basidiomycota, and a green alga, with most species descriptions based on morphology and host specificity. We found a Rozella parasitizing a Pythium host that was a saprobe on spruce pollen bait placed with an aquatic sample. We characterized the parasite with light microscopy, TEM of its zoospores and sporangia, and its 18S/28S rDNA. Comparison with other Rozella species indicates that the new isolate differs morphologically, ultrastructurally, and genetically from Rozella species for which we have data. Features of the zoospore also differ from those of previously studied species. Herein we describe the Rozella as a new species, R. multimorpha.
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http://dx.doi.org/10.1111/jeu.12452DOI Listing
March 2018

Ultrastructural characterization of the host-parasite interface between Allomyces anomalus (Blastocladiomycota) and Rozella allomycis (Cryptomycota).

Fungal Biol 2017 Jun - Jul;121(6-7):561-572. Epub 2017 Mar 21.

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

Rozella allomycis is an obligate endoparasite of the water mold Allomyces and a member of a clade (= Opisthosporidia) sister to the traditional Fungi. Gaining insights into Rozella's development as a phylogenetically pivotal endoparasite can aid our understanding of structural adaptations and evolution of the Opisthosporidia clade, especially within the context of genomic information. The purpose of this study is to characterize the interface between R. allomycis and Allomyces anomalus. Electron microscopy of developing plasmodia of R. allomycis in host hyphae shows that the interface consists of three-membrane layers, interpreted as the parasite's plasma membrane (inner one layer) and a host cisterna (outer two layers). As sporangial and resting spore plasmodia develop, host mitochondria typically cluster at the surface of the parasite and eventually align parallel to the three-membrane layered interface. The parasite's mitochondria have only a few cristae and the mitochondrial matrix is sparse, clearly distinguishing parasite mitochondria from those of the host. Consistent with the expected organellar topology if the parasite plasmodia phagocytize host cytoplasm, phagocytic vacuoles are at first bounded by three-membrane layers with host-type mitochondria lining the inner membrane. Thus, Rozella's nutrition, at least in part, is phagotrophic in contrast to osmotrophic nutrition of traditional fungi.
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http://dx.doi.org/10.1016/j.funbio.2017.03.002DOI Listing
February 2018

Molecular Phylogeny and Ultrastructure of Aphelidium desmodesmi, a New Species in Aphelida (Opisthosporidia).

J Eukaryot Microbiol 2017 09 10;64(5):655-667. Epub 2017 Mar 10.

Crop Protection Group, Sapphire Energy, Inc., Las Cruces, New Mexico, 88007.

Aphelids are a diverse group of intracellular parasitoids of algae and diatoms, and are sister to true fungi. Included in four genera, the 14 described species utilize phagocytosis as their mode of nutrition, and the life cycles of these taxa are remarkably similar. However, their putative specificity of host, morphological and ultrastructural features, and genetic divergence have been considered in taxon delineation. Here, we examine the host specificity, morphology, ultrastructure, and molecular 18S gene sequence of a new species in Aphelida, Aphelidium desmodesmi sp. nov. This taxon is in a well-supported clade with two other species of Aphelidium, and this lineage is sister to Amoeboaphelidium and Paraphelidium. Of interest, the mitochondrial structure of Aph. desmodesmi is more like that of Paraphelidium than that of Aphelidium aff. melosirae, the only other species of Aphelidium to have been examined ultrastructurally. This research examines and expands our understanding of host range, morphological diversity, and genetic divergence of the aphelids.
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http://dx.doi.org/10.1111/jeu.12401DOI Listing
September 2017

Morphological, molecular, and ultrastructural characterization of Rozella rhizoclosmatii, a new species in Cryptomycota.

Fungal Biol 2017 01 4;121(1):1-10. Epub 2016 Sep 4.

Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA. Electronic address:

Rozella is a genus of unwalled endoparasites of a variety of hosts including Oomycota (Stramenopiles), Blastocladiomycota and Chytridiomycota (Fungi), and one green alga (Coleochaete, Chlorophyceae). It currently includes more than 20 formally described species, and no new species of Rozella have been described since 1987. We discovered a new Rozella species parasitizing Rhizoclosmatium globosum (Chytridiales, Chytridiomycota) and investigated its morphology, ultrastructure, and phylogenetic position. Herein named as Rozella rhizoclosmatii sp. nov., the organism induces hypertrophy of the host. Its zoospore is ultrastructurally similar to that of Rozella allomycis, although it has a unique zoospore ultrastructural feature, a lattice of perpendicular rods about the nucleus. The 18S rDNA molecular sequence of R. rhizoclosmatii is similar to that of the previously sequenced 'Rozella ex Rhizoclosmatium'. This is the first study to inclusively characterize a new species of Rozella with morphological, ultrastructural and molecular data. As this is only the second Rozella species to be examined ultrastructurally, and because it is parasitic on a member of Chytridiomycota and not Blastocladiomycota, this research supports the conservative nature of zoospore ultrastructure to help define the genus.
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http://dx.doi.org/10.1016/j.funbio.2016.08.008DOI Listing
January 2017

Borealophlyctis nickersoniae, a new species in Rhizophlyctidales.

Mycologia 2016 Jul-Aug;108(4):744-52

Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487.

Zoospore ultrastructural characters combined with molecular phylogenetic hypotheses have been used to revise the taxonomy of zoosporic true fungi. An example is the reclassification of Rhizophlyctis rosea-like fungal strains into four new families and three new genera within the order Rhizophlyctidales. One genus was Borealophlyctis, which included a Canadian isolate, DAOMC 229843. A recent survey of chytrid diversity in Alabama (USA) yielded additional strains (WJD 170, WJD 171) in the Borealophlyctis lineage. With light and transmission-electron microscopy we examined strains DAOMC 229843, WJD 170 and WJD 171. We also analyzed partial nuc 28S rDNA D1-D3 domains (28S) and nuc rDNA region encompassing the internal transcribed spacers 1 and 2 and 5.8S (ITS) sequences to determine the phylogenetic placement of the strains within Rhizophlyctidales. Based on molecular divergence and morphological differences from the type Borealophlyctis paxensis, we recognize DAOMC 229843, WJD 170 and WJD 171 as representatives of the new species Borealophlyctis nickersoniae.
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http://dx.doi.org/10.3852/15-205DOI Listing
January 2018

Characterization of a new chytrid species parasitic on the dinoflagellate, Peridinium gatunense.

Mycologia 2016 Jul-Aug;108(4):731-43

Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research LTD, Migdal, Israel.

Only a few chytrid fungi have been reported as parasites of dinoflagellates. Among these reports, chytrids are periodically observed growing on the dinoflagellate, Peridinium gatunense, in Lake Kinneret (Sea of Galilee), Israel. Because of the distinctive roles of parasitic chytrid fungi in decreasing phytoplankton populations and in transforming inedible algae into chytrid biomass which zooplankton grazers can eat, characterizing dinoflagellate parasites contributes to our understanding of the sustainability of this important water resource. An undescribed chytrid parasite of P. gatunense from Lake Kinneret has recently been brought into pure culture (KLL_TL-060613), facilitating exploration of its infection process. To evaluate the ability of this chytrid to affect host populations, we determined the effect of: (1) temperature and light (or dark) on prevalence of infection and (2) host growth phase and parasite:host ratio on percentage of infection. The greatest amplification in host infection occurred in cultures grown in the dark at 25 C. The percentage of host cells infected increased as the availability of host cells compared to parasite cells increased. These results demonstrate that environmental factors influence the chytrid's potential to affect Peridinium gatunense populations. Because this chytrid had not been described taxonomically, we characterized its thallus morphology, development, zoospore ultrastructure and phylogenetic relationships. Zoospore ultrastructure was compatible with the Group II type zoospore characteristic of the family Chytridiaceae in the Chytridiales. Consistent with this observation, phylogenetic analyses of nuc 28S rDNA D1-D3 domains (28S) placed the chytrid in a clade among described taxa in the Chytridiaceae. Because thallus morphology was distinct from these other taxa, as well as other described parasites of dinoflagellates, this chytrid is described as a new genus and species, Dinochytrium kinnereticum.
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http://dx.doi.org/10.3852/15-197DOI Listing
January 2018

An ultrastructural study of Paraphysoderma sedebokerense (Blastocladiomycota), an epibiotic parasite of microalgae.

Fungal Biol 2016 Mar 1;120(3):324-37. Epub 2015 Dec 1.

Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA.

Successful algal cultivation for biofuel production is one path in the transition to a renewable energy economy. The green alga Scenedesmus dimorphus is a candidate for biofuel production, but is subject to parasitism and subsequent population crash when cultivated in open ponds. From an open pond cultivating S. dimorphus for biofuel production in New Mexico, USA, an amoeboid parasite was isolated, designated as isolate FD61, and its rDNA operon sequenced. A BLAST search for nuc 18S rDNA (18S) sequence similarity identified the parasite as Paraphysoderma sedebokerense (Blastocladiomycota). Here, we examine the ultrastructure of P. sedebokerense and compare it with that of a sister taxon, Physoderma maydis. The parasite has thin-walled vegetative sporangia and thick-walled resting sporangia. Our observations indicate that amoeboid swarmers are produced in the vegetative phase, while either amoeboid swarmers or zoospores are the product of meiosis in resting sporangia. Meiosis is confirmed by the presence of synaptonemal complexes in resting sporangia nuclei. Notably, P. sedebokerense has a Golgi apparatus with stacked cisternae, a feature reported for P. maydis, but which is absent in all other examined taxa in Blastocladiomycota. This report furthers our knowledge of the life cycle of P. sedebokerense.
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http://dx.doi.org/10.1016/j.funbio.2015.11.003DOI Listing
March 2016

A new family and four new genera in Rhizophydiales (Chytridiomycota).

Mycologia 2015 Jul-Aug;107(4):808-30. Epub 2015 Apr 24.

Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487.

Many chytrid phylogenies contain lineages representing a lone taxon or a few organisms. One such lineage in recent molecular phylogenies of Rhizophydiales contained two marine chytrids, Rhizophydium littoreum and Rhizophydium aestuarii. To better understand the relationship between these organisms, we increased sampling such that the R. littoreum/R. aestuarii lineage included 10 strains of interest. To place this lineage in Rhizophydiales, we constructed a molecular phylogeny from partial nuc 28S rDNA D1-D3 domains (28S) of these and 80 additional strains in Rhizophydiales and examined thallus morphology and zoospore ultrastructure of our strains of interest. We also analyzed sequences of the nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS) of our 10 strains of interest to assess sequence similarity and phylogenetic placement of strains within the lineage. The 10 strains grouped together in three well supported clades: (i) Rhizophydium littoreum+Phlyctochytrium mangrovei, (ii) three strains of Rhizophydium aestuarii and (iii) five previously unidentified strains. Light microscopic observations revealed four distinct thallus morphologies, and zoospore ultrastructural analyses revealed four distinct constellations of ultrastructural features. On the bases of morphological, ultrastructural and molecular evidence we place these strains in the new family Halomycetaceae and four new genera (Halomyces, Paludomyces, Ulkenomyces, Paranamyces) in Rhizophydiales.
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http://dx.doi.org/10.3852/14-280DOI Listing
September 2015

A new isolate of Amoeboaphelidium protococcarum, and Amoeboaphelidium occidentale, a new species in phylum Aphelida (Opisthosporidia).

Mycologia 2015 May-Jun;107(3):522-31. Epub 2015 Feb 6.

Crop Protection Group, Sapphire Energy, Inc., San Diego, California 92121.

Microalgae used in the production of biofuels represents an alternative to fossil fuels. One problem in the production of algae for biofuels is attacks by algal parasitoids that can cause population crashes when algae are cultivated in outdoor ponds (Greenwell et al. 2010). Integrated solutions are being sought to mitigate this problem, and an initial step is pest identification. We isolated an algal parasitoid from an open pond of Scenedesmus dimorphus used for biofuel production in New Mexico and examined its morphology, ultrastructure and molecular phylogeny. A phylogenetic analysis placed this organism in Aphelida as conspecific with Amoeboaphelidium protococcarum sensu Karpov et al. 2013. As a result we re-evaluated the taxonomy of Amoeboaphelidium protococcarum sensu Letcher et al. 2013 and here designate it as a new species, Amoeboaphelidium occidentale.
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http://dx.doi.org/10.3852/14-064DOI Listing
August 2015

A new genus and family for the misclassified chytrid, Rhizophlyctis harderi.

Mycologia 2015 Mar-Apr;107(2):419-31. Epub 2015 Jan 8.

Department of Botany, Miami University, Oxford, Ohio 45056.

A chytrid first discovered in Mediterranean sands and called Rhizophlyctis harderi was classified in the genus Rhizophlyctis based on its interbiotic vegetative thalli with multiple rhizoidal axes and resting thalli with tufts of rhizoid-like appendages. Developmental, electron microscopic and molecular analyses, however, have brought into question the proper placement of this chytrid. Because its original description was in German and not Latin, the name R. harderi is not validly published. We found that this chytrid produces three thallus forms that could place it in three different morpho-genera: Rhizophydium, Phlyctochytrium or Rhizophlyctis. The ultrastructural architecture of its zoospore is different from that of zoospores of Rhizophlyctis rosea, the type species for Rhizophlyctis, and shares zoospore ultrastructural characteristics with the Rhizophydiales. Zoospores of this chytrid exhibit a distinctive kinetosome-associated structure (KAS), a curved shield bridged to two of the kinetosomal triplets and a layered cap anterior to the kinetosome. Phylogenetic analyses of nuc rDNA also support the placement of this chytrid in the Rhizophydiales and not in the Rhizophlyctidales. Given its molecularly based phylogenetic placement and its distinctive zoospore architecture, we describe this chytrid in a new genus, Uebelmesseromyces, in the Rhizophydiales and erect Uebelmesseromycetaceae as a new family to accommodate it.
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http://dx.doi.org/10.3852/14-223DOI Listing
August 2015

Fayochytriomyces, a new genus within Chytridiales.

Mycologia 2015 Mar-Apr;107(2):432-9. Epub 2015 Jan 8.

Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487.

Chytriomyces is a complex genus in Chytridiales. The morphological concept of the genus expanded as new taxa were added, and studies of zoospore ultrastructure and molecular phylogenies have revealed the genus to be polyphyletic. One problematic taxon is C. spinosus Fay, a distinctive species characterized by whorls of spines on the zoosporangium and a large accumulation of vesicle material beneath the operculum. With light-, scanning-electron and transmission-electron microscopy, we examined a culture (WJD186) isolated from a muck sample collected from a temporary forest pond. We also analyzed the D1-D2 variable domains of the nuc 28S rDNA (28S) sequences to confirm the phylogenetic placement of the species relative to the type of Chytriomyces, C. hyalinus Karling. The morphology of culture WJD186 is consistent with features Fay described for C. spinosus, and the zoospore ultrastructure is consistent with the Group I-type zoospore characters of Chytriomycetaceae (Chytridiales). In our molecular phylogeny C. spinosus does not group with the type of Chytriomyces. Consequently, we erect a new genus in Chytriomycetaceae and present the new combination Fayochytriomyces spinosus.
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http://dx.doi.org/10.3852/14-265DOI Listing
August 2015

Irineochytrium, a new genus in Chytridiales having zoospores and aplanospores.

Mycologia 2014 Nov-Dec;106(6):1188-98. Epub 2014 Aug 20.

Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487.

Many described chytrids exhibit distinct morphological features that permit positive identification by light microscopy. Chytriomyces annulatus is one such species. It has a flap-like operculum and its sporangial wall is ornamented with multiple collar-like annulations proximal to the rhizoidal axis, features that, in combination, do not occur in any other described chytrid. Recent molecular phylogenies placed C. annulatus in the Chytridiaceae (Chytridiales) lineage, which is characterized by a Group II zoospore. Here we use light microscopy and transmission electron microscopy to examine thallus morphology of an isolate (JEL 729) of C. annulatus to confirm its identity and transmission electron microscopy to examine zoospore ultrastructure to confirm its phylogenetic placement. Light microscopic examinations confirmed its identity, and transmission electron microscopy analysis revealed both motile spores (zoospores) and nonmotile spores (aplanospores). Zoospores had a unique suite of ultrastructural features characteristic of the Group II zoospore; aplanospores had similar ultrastructure minus a flagellum. Chytriomyces annulatus does not group with the Chytriomycetaceae (Chytridiales) lineage containing the type of Chytriomyces, C. hyalinus, nor does it have a zoospore typical of that lineage. These arguments support the recognition of a distinct genus in Chytridiaceae, including one species, Irineochytrium annulatum.
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http://dx.doi.org/10.3852/14-057DOI Listing
May 2015

Unique odd-chain polyenoic phospholipid fatty acids present in chytrid fungi.

Lipids 2014 Sep 14;49(9):933-42. Epub 2014 Aug 14.

Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, USA.

Chytrid fungi are ubiquitous components of aquatic and terrestrial ecosystems yet they remain understudied. To investigate the use of phospholipid fatty acids as phenotypic characteristics in taxonomic studies and biomarkers for ecological studies, 18 chytrid fungi isolated from soil to freshwater samples were grown in defined media and their phospholipid fatty acid profile determined. Gas chromatographic/mass spectral analysis indicated the presence of fatty acids typically associated with fungi, such as 16:1(n-7), 16:0, 18:2(n-6), 18:3(n-3) 18:1(n-9), and 18:0, as well as, a number of odd-chain length fatty acids, including two polyunsaturated C-17 fatty acids. Conversion to their 3-pyridylcarbinol ester facilitated GC-MS determination of double-bond positions and these fatty acid were identified as 6,9-17:2 [17:2(n-8)] and 6,9,12-17:3 [17:3(n-5)]. To the best of our knowledge, this is the first report of polyunsaturated C-17 fatty acids isolated from the phospholipids of chytrid fungi. Cluster analysis of PLFA profiles showed sufficient correlation with chytrid phylogeny to warrant inclusion of lipid analysis in species descriptions and the presence of several phospholipid fatty acids of restricted phylogenetic distributions suggests their usefulness as biomarkers for ecological studies.
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http://dx.doi.org/10.1007/s11745-014-3934-3DOI Listing
September 2014

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, Department of Pharmaceutical Sciences - Microbiology, Università degli Studi di Perugia, Perugia, Italy, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, Muséum National d'Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, Real Jardín Botánico, RJB-CSIC,

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. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.
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http://dx.doi.org/10.1093/database/bau061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075928PMC
February 2015

Hypothesized evolutionary trends in zoospore ultrastructural characters in Chytridiales (Chytridiomycota).

Mycologia 2014 May-Jun;106(3):379-96

Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487.

Chytridiales is an order of zoosporic fungi currently comprising species representing 19 genera. Although morphologically and genetically diverse, these taxa have in common a zoospore with a suite of ultrastructural characters unique among Chytridiomycota. However, multiple states have been reported for almost every character that defines the Chytridiales zoospore. Two zoospore types have been recognized, each corresponding to a family. Here we examine zoospore ultrastructure of 52 isolates in Chytridiales and assess states for six characters to hypothesize evolutionary trends, using parsimony ancestral state reconstruction for evolutionary analysis. Based on suites of character states, we describe four additional zoospore types in Chytridiales. Five of the six characters ([i] location of the nucleus, [ii] morphology of the kinetosome-associated structure, [iii] complexity of the microtubular root, [iv] microbody-lipid globule complex cisterna structure and [v] thickness of the flagellar plug) revealed ancestral and derived states. The sixth character, structure of the paracrystalline inclusion, did not resolve ancestral and derived states. In each of the lineages within Chytridiales, the evolutionary trend appears to have been from a more complex zoospore to a less complex zoospore with reduced features. As we isolate and analyze additional taxa, we discover new ultrastructural character states that assist in taxon delineation and phylogenetic interpretation.
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http://dx.doi.org/10.3852/13-219DOI Listing
September 2014

Dendrochytridium crassum gen. et sp. nov., a taxon in Chytridiales with unique zoospore ultrastructure.

Mycologia 2014 Jan-Feb;106(1):145-53

Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487.

A water culture of detritus collected from an Australian tree canopy yielded multiple isolates (designated JEL 352, JEL 353, JEL 354) of an unidentified chytrid that grew on pollen bait and encysted spores of a Dictyuchus sp. oomycete. Morphological information from JEL 352 and genetic information from JEL 354 of this unidentified chytrid have been in several publications but the organism has not been named. Because isolates JEL 352 and JEL 354 are no longer viable, we sequenced partial SSU and LSU rDNA of isolate JEL 353, documented its thallus morphology with light microscopy and determined its zoospore ultrastructure via transmission electron microscopy. DNA evidence placed JEL 353 in Chytridiaceae, and its genetic composition was identical to that of JEL 354. Thallus morphology of JEL 353 was similar to that of JEL 352. Its zoospore ultrastructure is less complex compared to other members of Chytridiaceae. In pure culture, the rhizoidal system differed from other members of the family in being unevenly broad and not tapering to fine tips. Based on genetic, morphological and ultrastructural evidence, we place this chytrid in a new genus in Chytridiaceae and describe it as the new species Dendrochytridium crassum.
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http://dx.doi.org/10.3852/13-134DOI Listing
April 2014

Evidence for a facultative mutualist nutritional relationship between the green coccoid alga Bracteacoccus sp. (Chlorophyceae) and the zoosporic fungus Rhizidium phycophilum (Chytridiomycota).

Fungal Biol 2013 May 26;117(5):319-28. Epub 2013 Mar 26.

Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA.

Symbiotic interactions between fungi and photosynthetic partners are common among derived fungal lineages. The only fungal-phototroph interactions thus far reported from the early diverging zoosporic fungi are parasitic in nature. Rhizidium phycophilum is a terrestrial, saprotrophic chytrid, which appears to be able to enter a facultative mutualism with a coccoid green alga in the absence of refractory organic material, such as pollen and chitin. Liquid and solid culturing methods were used in a series of differential fitness experiments in conjunction with microscopic analyses to characterize the interaction between R. phycophilum and the alga. The alga in this partnership is identified as a member of the genus Bracteacoccus. Under certain culturing conditions, algal cells grown in coculture with R. phycophilum were shown to grow larger and more prolifically than when cultured axenically under the same conditions. Additionally, dialysis experiments demonstrate that R. phycophilum does not parasitize Bracteacoccus sp., and can be cultured in media infused with unknown algal exudates. Rhizidium phycophilum and Bracteacoccus sp. represent the first facultative positive interaction between a zoosporic fungus and a photoautotroph and may prove a tractable system for modelling interactions between early fungi and plants.
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http://dx.doi.org/10.1016/j.funbio.2013.03.003DOI Listing
May 2013

Three new genera in Chytridiales from aquatic habitats in Argentina.

Mycologia 2013 Sep-Oct;105(5):1251-65. Epub 2013 May 25.

Departamento de Biodiversidad y Biología, Experimental, Universidad de Buenos Aires, PRHIDEB-CONICET, C1428EHA Buenos Aires, Argentina.

Sampling for chytrids in a variety of habitats has resulted in pure cultures that when analyzed have yielded hypotheses of relationships based on molecular and zoospore ultrastructural markers. To extend our understanding of diversity of Chytridiales in eastern Argentina and USA, we isolated and examined the morphology, ultrastructure and 28S and ITS1-5.8S-ITS2 rDNA sequences of numerous chytrids from aquatic habitats from these two regions. Three family-level lineages (Chytridiaceae, Chytriomycetaceae, family incertae sedis) are represented in our molecular phylogeny, and three new genera (Avachytrium, Odontochytrium in Chytriomycetaceae, Delfinachytrium in family incertae sedis) are described. These findings of new genera and species emphasize the potential for discovery of additional diversity.
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http://dx.doi.org/10.3852/12-353DOI Listing
June 2014

Characterization of Amoeboaphelidium protococcarum, an algal parasite new to the cryptomycota isolated from an outdoor algal pond used for the production of biofuel.

PLoS One 2013 20;8(2):e56232. Epub 2013 Feb 20.

Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA.

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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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0056232PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577820PMC
August 2013

Pseudorhizidium is a new genus with distinct zoospore ultrastructure in the order Chytridiales.

Mycologia 2013 Mar-Apr;105(2):496-507. Epub 2012 Oct 25.

Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487, USA.

A chytrid isolate (JEL 221) we identified as the rarely reported species, Rhizidium endosporangiatum Karling, was cultured axenically for the first time. The purposes of this study are to characterize the developmental morphology of isolate JEL 221 and to elucidate its zoospore ultrastructural features. Thallus development and morphology of isolate JEL 221 are characteristic of R. endosporangiatum as it was originally described. However, thallus morphology of R. endosporangiatum is not entirely typical of the genus Rhizidium, especially that of the type R. mycophilum. The presence of an endosporangium, a layer of material encapsulating the edges of the protoplast protruding through multiple discharge pores, makes this a distinctive species. Consistent with its published molecular-based phylogenetic placement, we found that isolate JEL 221 shared ultrastructural features with the two major zoospore types described for the Chytridiales but had distinct zoospore architecture. A new genus, Pseudorhizidium, is erected for this chytrid based on its thallus morphology, molecular phylogenetic placement and unique zoospore ultrastructure. This new genus does not fit into either of the described families (Chytridiaceae or Chytriomycetaceae) in the Chytridiales because of its unique zoospore ultrastructure, especially the two-layered nature of the electron-opaque plug in the base of the flagellum.
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http://dx.doi.org/10.3852/12-269DOI Listing
June 2014