Fungal Diversity and Enzyme Activity Associated with the Macroalgae, Agarum clathratum

( Seobihn Lee ),( Myung Soo Park ),( Hanbyul Lee ),( Jae-jin Kim ),( John A. Eimes ),( Young Woon Lim ) 한국균학회 2019 Mycobiology Vol.47 No.1

Agarum clathratum, a brown macroalgae species, has recently become a serious environmental problem on the coasts of Korea. In an effort to solve this problem, fungal diversity associated with decaying A. clathratum was investigated and related b-glucosidase and endoglucanase activities were described. A total of 233 fungal strains were isolated from A. clathratum at 15 sites and identified 89 species based on morphology and a multigene analysis using the internal transcribed spacer region (ITS) and protein-coding genes including actin (act), b-tubulin (benA), calmodulin (CaM), and translation elongation factor (tef1). Acremonium, Corollospora, and Penicillium were the dominant genera, and Acremonium fuci and Corollospora gracilis were the dominant species. Fifty-one species exhibited cellulase activity, with A. fuci, Alfaria terrestris, Hypoxylon perforatum, P. madriti, and Pleosporales sp. Five showing the highest enzyme activities. Further enzyme quantification confirmed that these species had higher cellulase activity than P. crysogenum, a fungal species described in previous studies. This study lays the groundwork for bioremediation using fungi to remove decaying seaweed from populated areas and provides important background for potential industrial applications of environmentally friendly processes.

Diversity of fungi associated with roots of Calanthe orchid species in Korea

박명수,John A. Eimes,오상훈,서화정,오승윤,이서빈,박기형,권혁군,김소영,임영운 한국미생물학회 2018 The journal of microbiology Vol.56 No.1

While symbiotic fungi play a key role in the growth of endangered Calanthe orchid species, the relationship between fungal diversity and Calanthe species remains unclear. Here, we surveyed root associated fungal diversity of six Calanthe orchid species by sequencing the internal transcribed spacer (ITS) region using 454 pyrosequencing. Our results revealed that Paraboeremia and Coprinopsis are dominant fungal genera among Calanthe species. In terms of overall relative abundance, Paraboeremia was the most common fungal genus associated with Calanthe roots, followed by Coprinopsis. Overall fungal diversity showed a significant degree of variation depending on both location and Calanthe species. In terms of number of different fungal genera detected within Calanthe species, C. discolor had the most diverse fungal community, with 10 fungal genera detected. This study will contribute toward a better understanding of those fungi that are required for successful cultivation and conservation of Korean Calanthe species.

Major histocompatibility complex selection dynamics in pathogen-infected túngara frog ( <i>Physalaemus pustulosus</i> ) populations

Kosch, Tiffany A.,Bataille, Arnaud,Didinger, Chelsea,Eimes, John A.,Rodrí,guez-Brenes, Sofia,Ryan, Michael J.,Waldman, Bruce The Royal Society 2016 Biology letters Vol.12 No.8

<P> Pathogen-driven selection can favour major histocompatibility complex (MHC) alleles that confer immunological resistance to specific diseases. However, strong directional selection should deplete genetic variation necessary for robust immune function in the absence of balancing selection or challenges presented by other pathogens. We examined selection dynamics at one MHC class II (MHC-II) locus across Panamanian populations of the túngara frog, <I>Physalaemus pustulosus</I> , infected by the amphibian chytrid fungus <I>Batrachochytrium dendrobatidis</I> (Bd). We compared MHC-II diversity in highland túngara frog populations, where amphibian communities have experienced declines owing to Bd, with those in the lowland region that have shown no evidence of decline. Highland region frogs had MHC variants that confer resistance to Bd. Variant fixation appeared to occur by directional selection rather than inbreeding, as overall genetic variation persisted in populations. In Bd-infected lowland sites, however, selective advantage may accrue to individuals with only one Bd-resistance allele, which were more frequent. Environmental conditions in lowlands should be less favourable for Bd infection, which may reduce selection for specific Bd resistance in hosts. Our results suggest that MHC selection dynamics fluctuate in túngara frog populations as a function of the favourability of habitat to pathogen spread and the vulnerability of hosts to infection. </P>

Characterization of MHC class IA in the endangered southern corroboree frog

Kosch, Tiffany A.,Eimes, John A.,Didinger, Chelsea,Brannelly, Laura A.,Waldman, Bruce,Berger, Lee,Skerratt, Lee F. Springer-Verlag 2017 Immunogenetics Vol.69 No.3

<P>Southern corroboree frogs (Pseudophryne corroboree) have declined to near extinction in the wild after the emergence of the amphibian chytrid fungus Batrachochytrium dendrobatidis in southeastern Australia in the 1980s. A major captive breeding and reintroduction program is underway to preserve this iconic species, but improving resistance to B. dendrobatidis would help the wild population to be self-sustaining. Using 3' and 5' rapid amplification of complementary DNA ends (RACE), we characterized the major histocompatibility complex (MHC) class IA locus in this species. We then used sequences generated from RACE to design primers to amplify the peptide-binding region (PBR) of this functional genetic marker. Finally, we analysed the diversity, phylogeny, and selection patterns of PBR sequences from four P. corroboree populations and compared this with other amphibian species. We found moderately high MHC class IA genetic diversity in this species and evidence of strong positive and purifying selection at sites that are associated with putative PBR pockets in other species, indicating that this gene region may be under selection for resistance to Bd. Future studies should focus on identifying alleles associated with Bd resistance in P. corroboree by performing a Bd laboratory challenge study to confirm the functional importance of our genetic findings and explore their use in artificial selection or genetic engineering to increase resistance to chytridiomycosis.</P>

Multiple major histocompatibility complex class I genes in Asian anurans: Ontogeny and phylogeny

Didinger, Chelsea,Eimes, John A.,Lillie, Mette,Waldman, Bruce Elsevier 2017 DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY Vol.70 No.-

<P><B>Abstract</B></P> <P>Amphibians, as the first terrestrial vertebrates, offer a window into early major histocompatibility complex (MHC) evolution. We characterized the MHC class I of two Korean amphibians, the Asiatic toad (<I>Bufo gargarizans</I>) and the Japanese tree frog (<I>Hyla japonica</I>). We found at least four transcribed MHC class I (MHC I) loci, the highest number confirmed in any anuran to date. Furthermore, we identified MHC I transcripts in terrestrial adults, and possibly in aquatic larvae, of both species. We conducted a phylogenetic analysis based on MHC I sequence data and found that <I>B. gargarizans</I> and <I>H. japonica</I> cluster together in the superfamily Nobleobatrachia. We further identified three supertypes shared by the two species. Our results reveal substantial variation in the number of MHC I loci in anurans and suggest that certain supertypes have particular physiochemical properties that may confer pathogen resistance.</P> <P><B>Highlights</B></P> <P> <UL> <LI> We describe, for the first time, sequences of MHC class I from the Asian frogs <I>Bufo gargarizans</I> and <I>Hyla japonica.</I> </LI> <LI> We found at least four transcribed MHC class I loci in each species. </LI> <LI> MHC I transcription was found in larvae as well as adults. </LI> <LI> The two species shared supertypes based on their MHC I sequences. </LI> </UL> </P>

Re-evaluation of the taxonomy and diversity of <i>Russula</i> section <i>Foetentinae</i> (Russulales, Basidiomycota) in Korea

Lee, Hyun,Park, Myung Soo,Jung, Paul Eunil,Eimes, John A.,Seok, Soon Ja,Lim, Young Woon Mycological Society of Japan 2017 Mycoscience Vol.58 No.5

<P>Russula section Foetentinae is a group of ectomycorrhizal symbiont fungi that are integral in maintaining biodiversity in diverse ecosystems. Identification and accurate classification of these fungi has proven challenging because of significant similarities in morphology, particularly among fruiting bodies. The objective of this study was to re-evaluate the diversity and taxonomy of Russula section Foetentinae in Korea using both phylogenetic analysis and morphological characteristics. A phylogenetic tree was constructed using internal transcribed spacer sequences and compared against key morphological characteristics. Our results reassigned several taxa and established important ecological relationships among closely related species. The phylogenetic analysis produced strong support for seven species, two of which were previously identified, one was a new record to Korea, and one was an undescribed species which we propose to name R. catillus sp. nov. Russula section Foetentinae separated into four clades when molecular and morphological data were combined. An important finding of the study was that several taxonomic assignments based on morphological characters were inconsistent with more reliable molecular data. This study highlights the need for a genetic database that can be easily accessed and used in conjunction with morphological data in order to better resolve the evolutionary history of this important fungal group. (C) 2017 The Mycological Society of Japan. Published by Elsevier B. V. All rights reserved.</P>

Diversity of fungi associated with roots of Calanthe orchid species in Korea

Park, Myung Soo,Eimes, John A.,Oh, Sang Hoon,Suh, Hwa Jung,Oh, Seung-Yoon,Lee, Seobihn,Park, Ki Hyeong,Kwon, Hyuk Joon,Kim, Soo-Young,Lim, Young Woon MICROBIOLOGICAL SOCIETY OF KOREA 2018 JOURNAL OF MICROBIOLOGY -SEOUL- Vol.56 No.1

While symbiotic fungi play a key role in the growth of endangered Calanthe orchid species, the relationship between fungal diversity and Calanthe species remains unclear. Here, we surveyed root associated fungal diversity of six Calanthe orchid species by sequencing the internal transcribed spacer (ITS) region using 454 pyrosequencing. Our results revealed that Paraboeremia and Coprinopsis are dominant fungal genera among Calanthe species. In terms of overall relative abundance, Paraboeremia was the most common fungal genus associated with Calanthe roots, followed by Coprinopsis. Overall fungal diversity showed a significant degree of variation depending on both location and Calanthe species. In terms of number of different fungal genera detected within Calanthe species, C. discolor had the most diverse fungal community, with 10 fungal genera detected. This study will contribute toward a better understanding of those fungi that are required for successful cultivation and conservation of Korean Calanthe species.

Five New Wood Decay Fungi (Polyporales and Hymenochaetales) in Korea

( Nam Kyu Kim ),( Jae Young Park ),( Myung Soo Park ),( Hyun Lee ),( Hae Jin Cho ),( John A. Eimes ),( Changmu Kim ),( Young Woon Lim ) 한국균학회 2016 Mycobiology Vol.44 No.3

The wood decay fungi are a diverse taxonomic group that plays a pivotal role in forest carbon cycling. Wood decay fungi use various enzymatic pathways to digest dead or living wood in order to obtain carbon and other nutrients and these enzymatic systems have been exploited for both industrial and medical applications. Over 600 wood decay fungi species have been described in Korea; however, the recent application of molecular markers has dramatically altered the taxonomy of many of these wood decay fungi at both the genus and species levels. By combining molecular methods, specifically sequences of the internal transcribed spacer region, with traditional morphological characters, this study identified five new species records for Korea in five genera: Aurantiporus, Favolus, Neofavolus, Loweomyces, and Hymenochaetopsis. Three of these genera (Aurantiporus, Favolus, and Loweomyces) were previously unknown in Korea. The relatively simple morphology of the wood decay fungi often leads to ambiguous taxonomic assignment. Therefore, molecular markers are a necessary component of any taxonomic or evolutionary study of wood decay fungi. Our study highlights the need for a more robust and multifaceted approach in investigating new wood decay fungi in Korea.

Guild Patterns of Basidiomycetes Community Associated With Quercus mongolica in Mt. Jeombong, Republic of Korea

( Seung-yoon Oh ),( Hae Jin Cho ),( John A. Eimes ),( Sang-kuk Han ),( Chang Sun Kim ),( Young Woon Lim ) 한국균학회 2018 Mycobiology Vol.46 No.1

Depending on the mode of nutrition exploitation, major fungal guilds are distinguished as ectomycorrhizal and saprotrophic fungi. It is generally known that diverse environmental factors influence fungal communities; however, it is unclear how fungal communities respond differently to environment factors depend on fungal guilds. In this study, we investigated basidiomycetes communities associated with Quercus mongolica using 454 pyrosequencing. We attempted to detect guild pattern (ectomycorrhizal or saprotrophic fungal communities) by comparing the influence of geography and source (root and surrounding soil). A total of 515 mOTUs were detected from root (321) and soil (394) of Q. mongolica at three sites of Mt. Jeombong in Inje County. We found that patterns of diversity and community structure were different depending on the guilds. In terms of alpha diversity, only ectomycorrhizal fungi showed significant differences between sources. In terms of community structure, however, geography significantly influenced the ectomycorrhizal community, while source appeared to have a greater influence on the saprotrophic community. Therefore, a guildbased view will help to elucidates novel features of the relationship between environmental factors and fungal communities.

Seven New Recorded Species in Five Genera of the Strophariaceae in Korea

( Hae Jin Cho ),( Hyun Lee ),( Jae Young Park ),( Myung Soo Park ),( Nam Kyu Kim ),( John A. Eimes ),( Changmu Kim ),( Sang-kuk Han ),( Young Woon Lim ) 한국균학회 2016 Mycobiology Vol.44 No.3

Most known species in the Strophariaceae are decomposers and grow on various kind of organic matter. Approximately 18 genera and 1,316 species in the Strophariaceae have been reported worldwide. Through an ongoing survey of indigenous fungi in Korea, 29 specimens belonging to the Strophariaceae were collected from 2012 to 2016. These specimens were identified based on morphological characteristics and molecular analysis of internal transcribed spacer sequences. Fifteen taxa were confirmed, with eight species matching those previously recorded. Seven species in five genera were shown to be new records in Korea: Galerina marginata, Gymnopilus crociphyllus, Gymnopilus picreus, Hebeloma birrus, Hebeloma cavipes, Pholiota multicingulata, and Psilocybe thaizapoteca. In this study, we provide detailed morphological descriptions of these species and investigate their evolutionary relationships by constructing phylogenetic trees.