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1. Airborne DNA reveals predictable spatial and seasonal dynamics of fungi

Author

Abrego, Nerea, Furneaux, Brendan, Hardwick, Bess, Somervuo, Panu, Palorinne, Isabella, Aguilar-Trigueros, Carlos A., Andrew, Nigel R., Babiy, Ulyana V., Bao, Tan, Bazzano, Gisela, Bondarchuk, Svetlana N., Bonebrake, Timothy C., Brennan, Georgina L., Bret-Harte, Syndonia, Bässler, Claus, Cagnolo, Luciano, Cameron, Erin K., Chapurlat, Elodie, Creer, Simon, D’Acqui, Luigi P., de Vere, Natasha, Desprez-Loustau, Marie-Laure, Dongmo, Michel A. K., Jacobsen, Ida B. Dyrholm, Fisher, Brian L., Flores de Jesus, Miguel, Gilbert, Gregory S., Griffith, Gareth W., Gritsuk, Anna A., Gross, Andrin, Grudd, Håkan, Halme, Panu, Hanna, Rachid, Hansen, Jannik, Hansen, Lars Holst, Hegbe, Apollon D. M. T., Hill, Sarah, Hogg, Ian D., Hultman, Jenni, Hyde, Kevin D., Hynson, Nicole A., Ivanova, Natalia, Karisto, Petteri, Kerdraon, Deirdre, Knorre, Anastasia, Krisai-Greilhuber, Irmgard, Kurhinen, Juri, Kuzmina, Masha, Lecomte, Nicolas, Lecomte, Erin, Loaiza, Viviana, Lundin, Erik, Meire, Alexander, Mešić, Armin, Miettinen, Otto, Monkhouse, Norman, Mortimer, Peter, Müller, Jörg, Nilsson, R. Henrik, Nonti, Puani Yannick C., Nordén, Jenni, Nordén, Björn, Norros, Veera, Paz, Claudia, Pellikka, Petri, Pereira, Danilo, Petch, Geoff, Pitkänen, Juha-Matti, Popa, Flavius, Potter, Caitlin, Purhonen, Jenna, Pätsi, Sanna, Rafiq, Abdullah, Raharinjanahary, Dimby, Rakos, Niklas, Rathnayaka, Achala R., Raundrup, Katrine, Rebriev, Yury A., Rikkinen, Jouko, Rogers, Hanna M. K., Rogovsky, Andrey, Rozhkov, Yuri, Runnel, Kadri, Saarto, Annika, Savchenko, Anton, Schlegel, Markus, Schmidt, Niels Martin, Seibold, Sebastian, Skjøth, Carsten, Stengel, Elisa, Sutyrina, Svetlana V., Syvänperä, Ilkka, Tedersoo, Leho, Timm, Jebidiah, Tipton, Laura, Toju, Hirokazu, Uscka-Perzanowska, Maria, van der Bank, Michelle, van der Bank, F. Herman, Vandenbrink, Bryan, Ventura, Stefano, Vignisson, Solvi R., Wang, Xiaoyang, Weisser, Wolfgang W., Wijesinghe, Subodini N., Wright, S. Joseph, Yang, Chunyan, Yorou, Nourou S., Young, Amanda, Yu, Douglas W., Zakharov, Evgeny V., Hebert, Paul D. N., Roslin, Tomas, and Ovaskainen, Otso

Published
2024
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2. Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA

Author

Ovaskainen, Otso, Abrego, Nerea, Furneaux, Brendan, Hardwick, Bess, Somervuo, Panu, Palorinne, Isabella, Andrew, Nigel R., Babiy, Ulyana V., Bao, Tan, Bazzano, Gisela, Bondarchuk, Svetlana N., Bonebrake, Timothy C., Brennan, Georgina L., Bret-Harte, Syndonia, Bässler, Claus, Cagnolo, Luciano, Cameron, Erin K., Chapurlat, Elodie, Creer, Simon, D’Acqui, Luigi P., de Vere, Natasha, Desprez-Loustau, Marie-Laure, Dongmo, Michel A. K., Dyrholm Jacobsen, Ida B., Fisher, Brian L., Flores de Jesus, Miguel, Gilbert, Gregory S., Griffith, Gareth W., Gritsuk, Anna A., Gross, Andrin, Grudd, Håkan, Halme, Panu, Hanna, Rachid, Hansen, Jannik, Hansen, Lars Holst, Hegbe, Apollon D. M. T., Hill, Sarah, Hogg, Ian D., Hultman, Jenni, Hyde, Kevin D., Hynson, Nicole A., Ivanova, Natalia, Karisto, Petteri, Kerdraon, Deirdre, Knorre, Anastasia, Krisai-Greilhuber, Irmgard, Kurhinen, Juri, Kuzmina, Masha, Lecomte, Nicolas, Lecomte, Erin, Loaiza, Viviana, Lundin, Erik, Meire, Alexander, Mešić, Armin, Miettinen, Otto, Monkhause, Norman, Mortimer, Peter, Müller, Jörg, Nilsson, R. Henrik, Nonti, Puani Yannick C., Nordén, Jenni, Nordén, Björn, Paz, Claudia, Pellikka, Petri, Pereira, Danilo, Petch, Geoff, Pitkänen, Juha-Matti, Popa, Flavius, Potter, Caitlin, Purhonen, Jenna, Pätsi, Sanna, Rafiq, Abdullah, Raharinjanahary, Dimby, Rakos, Niklas, Rathnayaka, Achala R., Raundrup, Katrine, Rebriev, Yury A., Rikkinen, Jouko, Rogers, Hanna M. K., Rogovsky, Andrey, Rozhkov, Yuri, Runnel, Kadri, Saarto, Annika, Savchenko, Anton, Schlegel, Markus, Schmidt, Niels Martin, Seibold, Sebastian, Skjøth, Carsten, Stengel, Elisa, Sutyrina, Svetlana V., Syvänperä, Ilkka, Tedersoo, Leho, Timm, Jebidiah, Tipton, Laura, Toju, Hirokazu, Uscka-Perzanowska, Maria, van der Bank, Michelle, Herman van der Bank, F., Vandenbrink, Bryan, Ventura, Stefano, Vignisson, Solvi R., Wang, Xiaoyang, Weisser, Wolfgang W., Wijesinghe, Subodini N., Joseph Wright, S., Yang, Chunyan, Yorou, Nourou S., Young, Amanda, Yu, Douglas W., Zakharov, Evgeny V., Hebert, Paul D. N., and Roslin, Tomas

Published
2024
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4. Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage

Author

Murphy, Chelsea L, Youssef, Noha H, Hanafy, Radwa A, Couger, MB, Stajich, Jason E, Wang, Yan, Baker, Kristina, Dagar, Sumit S, Griffith, Gareth W, Farag, Ibrahim F, Callaghan, TM, and Elshahed, Mostafa S

Subjects
Microbiology, Biological Sciences, Infectious Diseases, Genetics, Animals, Biological Evolution, Cattle, Evolution, Molecular, Gastrointestinal Microbiome, Gastrointestinal Tract, Gene Transfer, Horizontal, Genome, Fungal, Goats, Neocallimastigomycota, Sheep, anaerobic gut fungi, horizontal gene transfer, Medical microbiology
Abstract

Survival and growth of the anaerobic gut fungi (AGF; Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. The patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 277 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. The majority of HGT events were AGF specific (91.7%) and wide (70.8%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This study strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.IMPORTANCE The anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryote-dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. We assess here the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota postsequestration in the herbivorous gut. Analysis of 27 transcriptomes that represent the broad diversity of Neocallimastigomycota identified 277 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This study represents a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.

Published
2019

5. Horizontal gene transfer as an indispensable driver for Neocallimastigomycota evolution into a distinct gut-dwelling fungal lineage

Author

Murphy, Chelsea L, Youssef, Noha H, Hanafy, Radwa A, Couger, MB, Stajich, Jason E, Wang, Y, Baker, Kristina, Dagar, Sumit S, Griffith, Gareth W, Farag, Ibrahim F, Callaghan, TM, and Elshahed, Mostafa S

Subjects
Microbiology, Biological Sciences, Genetics
Abstract

Abstract Survival and growth of the anaerobic gut fungi (AGF, Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. Patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 283 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2.1-3.6% in AGF genomes. The majority of HGT events were AGF specific (91.5%) and wide (70.7%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This work strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high rank taxonomic eukaryotic lineage. Importance The anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryotes dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. This manuscript assesses the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota post sequestration in the herbivorous gut. Analysis of twenty-seven transcriptomes that represent the broad Neocallimastigomycota diversity identified 283 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2.1-3.6% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This work represents a unique example of the role of HGT in shaping the evolution of a high rank taxonomic eukaryotic lineage.

Published
2018

6. The Biotechnological Potential of Anaerobic Gut Fungi

Author

Flad, Veronika, Young, Diana, Seppälä, Susanna, Hooker, Casey, Youssef, Noha, Podmirseg, Sabine M., Nagler, Magdalena, Reilly, Matthew, Li, Yuanfei, Fliegerová, Kateřina, Cheng, Yanfen, Griffith, Gareth W., Elshahed, Mostafa, Solomon, Kevin V., O’Malley, Michelle A., Theodorou, Michael K., Esser, Karl, Series Editor, Carter, Dee, Series Editor, Chowdhary, Anuradha, Series Editor, Heitman, Joe, Series Editor, Kück, Ulrich, Series Editor, Benz, J. Philipp, editor, and Schipper, Kerstin, editor

Published
2020
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7. Early-diverging fungal phyla: taxonomy, species concept, ecology, distribution, anthropogenic impact, and novel phylogenetic proposals

Author

Voigt, Kerstin, James, Timothy Y., Kirk, Paul M., Santiago, André L. C. M. de A., Waldman, Bruce, Griffith, Gareth W., Fu, Minjie, Radek, Renate, Strassert, Jürgen F. H., Wurzbacher, Christian, Jerônimo, Gustavo Henrique, Simmons, David R., Seto, Kensuke, Gentekaki, Eleni, Hurdeal, Vedprakash G., Hyde, Kevin D., Nguyen, Thuong T. T., and Lee, Hyang Burm

Published
2021
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8. Global Spore Sampling Project:A global, standardized dataset of airborne fungal DNA

Author

Ovaskainen, Otso, Abrego, Nerea, Furneaux, Brendan, Hardwick, Bess, Somervuo, Panu, Palorinne, Isabella, Andrew, Nigel R, Babiy, Ulyana V, Bao, Tan, Bazzano, Gisela, Bondarchuk, Svetlana N, Bonebrake, Timothy C, Brennan, Georgina L, Bret-Harte, Syndonia, Bässler, Claus, Cagnolo, Luciano, Cameron, Erin K, Chapurlat, Elodie, Creer, Simon, D'Acqui, Luigi P, de Vere, Natasha, Desprez-Loustau, Marie-Laure, Dongmo, Michel A K, Dyrholm Jacobsen, Ida B, Fisher, Brian L, Flores de Jesus, Miguel, Gilbert, Gregory S, Griffith, Gareth W, Gritsuk, Anna A, Gross, Andrin, Grudd, Håkan, Halme, Panu, Hanna, Rachid, Hansen, Jannik, Hansen, Lars Holst, Hegbe, Apollon D M T, Hill, Sarah, Hogg, Ian D, Hultman, Jenni, Hyde, Kevin D, Hynson, Nicole A, Ivanova, Natalia, Karisto, Petteri, Kerdraon, Deirdre, Knorre, Anastasia, Krisai-Greilhuber, Irmgard, Kurhinen, Juri, Kuzmina, Masha, Lecomte, Nicolas, Lecomte, Erin, Loaiza, Viviana, Lundin, Erik, Meire, Alexander, Mešić, Armin, Miettinen, Otto, Monkhause, Norman, Mortimer, Peter, Müller, Jörg, Nilsson, R Henrik, Nonti, Puani Yannick C, Nordén, Jenni, Nordén, Björn, Paz, Claudia, Pellikka, Petri, Pereira, Danilo, Petch, Geoff, Pitkänen, Juha-Matti, Popa, Flavius, Potter, Caitlin, Purhonen, Jenna, Pätsi, Sanna, Rafiq, Abdullah, Raharinjanahary, Dimby, Rakos, Niklas, Rathnayaka, Achala R, Raundrup, Katrine, Rebriev, Yury A, Rikkinen, Jouko, Rogers, Hanna M K, Rogovsky, Andrey, Rozhkov, Yuri, Runnel, Kadri, Saarto, Annika, Savchenko, Anton, Schlegel, Markus, Schmidt, Niels Martin, Seibold, Sebastian, Skjøth, Carsten, Stengel, Elisa, Sutyrina, Svetlana V, Syvänperä, Ilkka, Tedersoo, Leho, Timm, Jebidiah, Tipton, Laura, Toju, Hirokazu, Uscka-Perzanowska, Maria, van der Bank, Michelle, Herman van der Bank, F, Vandenbrink, Bryan, Ventura, Stefano, Vignisson, Solvi R, Wang, Xiaoyang, Weisser, Wolfgang W, Wijesinghe, Subodini N, Joseph Wright, S, Yang, Chunyan, Yorou, Nourou S, Young, Amanda, Yu, Douglas W, Zakharov, Evgeny V, Hebert, Paul D N, Roslin, Tomas, Ovaskainen, Otso, Abrego, Nerea, Furneaux, Brendan, Hardwick, Bess, Somervuo, Panu, Palorinne, Isabella, Andrew, Nigel R, Babiy, Ulyana V, Bao, Tan, Bazzano, Gisela, Bondarchuk, Svetlana N, Bonebrake, Timothy C, Brennan, Georgina L, Bret-Harte, Syndonia, Bässler, Claus, Cagnolo, Luciano, Cameron, Erin K, Chapurlat, Elodie, Creer, Simon, D'Acqui, Luigi P, de Vere, Natasha, Desprez-Loustau, Marie-Laure, Dongmo, Michel A K, Dyrholm Jacobsen, Ida B, Fisher, Brian L, Flores de Jesus, Miguel, Gilbert, Gregory S, Griffith, Gareth W, Gritsuk, Anna A, Gross, Andrin, Grudd, Håkan, Halme, Panu, Hanna, Rachid, Hansen, Jannik, Hansen, Lars Holst, Hegbe, Apollon D M T, Hill, Sarah, Hogg, Ian D, Hultman, Jenni, Hyde, Kevin D, Hynson, Nicole A, Ivanova, Natalia, Karisto, Petteri, Kerdraon, Deirdre, Knorre, Anastasia, Krisai-Greilhuber, Irmgard, Kurhinen, Juri, Kuzmina, Masha, Lecomte, Nicolas, Lecomte, Erin, Loaiza, Viviana, Lundin, Erik, Meire, Alexander, Mešić, Armin, Miettinen, Otto, Monkhause, Norman, Mortimer, Peter, Müller, Jörg, Nilsson, R Henrik, Nonti, Puani Yannick C, Nordén, Jenni, Nordén, Björn, Paz, Claudia, Pellikka, Petri, Pereira, Danilo, Petch, Geoff, Pitkänen, Juha-Matti, Popa, Flavius, Potter, Caitlin, Purhonen, Jenna, Pätsi, Sanna, Rafiq, Abdullah, Raharinjanahary, Dimby, Rakos, Niklas, Rathnayaka, Achala R, Raundrup, Katrine, Rebriev, Yury A, Rikkinen, Jouko, Rogers, Hanna M K, Rogovsky, Andrey, Rozhkov, Yuri, Runnel, Kadri, Saarto, Annika, Savchenko, Anton, Schlegel, Markus, Schmidt, Niels Martin, Seibold, Sebastian, Skjøth, Carsten, Stengel, Elisa, Sutyrina, Svetlana V, Syvänperä, Ilkka, Tedersoo, Leho, Timm, Jebidiah, Tipton, Laura, Toju, Hirokazu, Uscka-Perzanowska, Maria, van der Bank, Michelle, Herman van der Bank, F, Vandenbrink, Bryan, Ventura, Stefano, Vignisson, Solvi R, Wang, Xiaoyang, Weisser, Wolfgang W, Wijesinghe, Subodini N, Joseph Wright, S, Yang, Chunyan, Yorou, Nourou S, Young, Amanda, Yu, Douglas W, Zakharov, Evgeny V, Hebert, Paul D N, and Roslin, Tomas

Abstract

Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m 3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition.

Published
2024

9. Correction to: FungalTraits: a user friendly traits database of fungi and fungus-like stramenopiles

Author

Põlme, Sergei, Abarenkov, Kessy, Henrik Nilsson, R., Lindahl, Björn D., Clemmensen, Karina Engelbrecht, Kauserud, Havard, Nguyen, Nhu, Kjøller, Rasmus, Bates, Scott T., Baldrian, Petr, Frøslev, Tobias Guldberg, Adojaan, Kristjan, Vizzini, Alfredo, Suija, Ave, Pfister, Donald, Baral, Hans-Otto, Järv, Helle, Madrid, Hugo, Nordén, Jenni, Liu, Jian-Kui, Pawlowska, Julia, Põldmaa, Kadri, Pärtel, Kadri, Runnel, Kadri, Hansen, Karen, Larsson, Karl-Henrik, Hyde, Kevin David, Sandoval-Denis, Marcelo, Smith, Matthew E., Toome-Heller, Merje, Wijayawardene, Nalin N., Menolli, Jr., Nelson, Reynolds, Nicole K., Drenkhan, Rein, Maharachchikumbura, Sajeewa S. N., Gibertoni, Tatiana B., Læssøe, Thomas, Davis, William, Tokarev, Yuri, Corrales, Adriana, Soares, Adriene Mayra, Agan, Ahto, Machado, Alexandre Reis, Argüelles-Moyao, Andrés, Detheridge, Andrew, de Meiras-Ottoni, Angelina, Verbeken, Annemieke, Dutta, Arun Kumar, Cui, Bao-Kai, Pradeep, C. K., Marín, César, Stanton, Daniel, Gohar, Daniyal, Wanasinghe, Dhanushka N., Otsing, Eveli, Aslani, Farzad, Griffith, Gareth W., Lumbsch, Thorsten H., Grossart, Hans-Peter, Masigol, Hossein, Timling, Ina, Hiiesalu, Inga, Oja, Jane, Kupagme, John Y., Geml, József, Alvarez-Manjarrez, Julieta, Ilves, Kai, Loit, Kaire, Adamson, Kalev, Nara, Kazuhide, Küngas, Kati, Rojas-Jimenez, Keilor, Bitenieks, Krišs, Irinyi, László, Nagy, László G., Soonvald, Liina, Zhou, Li-Wei, Wagner, Lysett, Aime, M. Catherine, Öpik, Maarja, Mujica, María Isabel, Metsoja, Martin, Ryberg, Martin, Vasar, Martti, Murata, Masao, Nelsen, Matthew P., Cleary, Michelle, Samarakoon, Milan C., Doilom, Mingkwan, Bahram, Mohammad, Hagh-Doust, Niloufar, Dulya, Olesya, Johnston, Peter, Kohout, Petr, Chen, Qian, Tian, Qing, Nandi, Rajasree, Amiri, Rasekh, Perera, Rekhani Hansika, dos Santos Chikowski, Renata, Mendes-Alvarenga, Renato L., Garibay-Orijel, Roberto, Gielen, Robin, Phookamsak, Rungtiwa, Jayawardena, Ruvishika S., Rahimlou, Saleh, Karunarathna, Samantha C., Tibpromma, Saowaluck, Brown, Shawn P., Sepp, Siim-Kaarel, Mundra, Sunil, Luo, Zhu-Hua, Bose, Tanay, Vahter, Tanel, Netherway, Tarquin, Yang, Teng, May, Tom, Varga, Torda, Li, Wei, Coimbra, Victor Rafael Matos, de Oliveira, Virton Rodrigo Targino, de Lima, Vitor Xavier, Mikryukov, Vladimir S., Lu, Yongzhong, Matsuda, Yosuke, Miyamoto, Yumiko, Kõljalg, Urmas, and Tedersoo, Leho

Published
2021
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10. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles

Author

Põlme, Sergei, Abarenkov, Kessy, Henrik Nilsson, R., Lindahl, Björn D., Clemmensen, Karina Engelbrecht, Kauserud, Havard, Nguyen, Nhu, Kjøller, Rasmus, Bates, Scott T., Baldrian, Petr, Frøslev, Tobias Guldberg, Adojaan, Kristjan, Vizzini, Alfredo, Suija, Ave, Pfister, Donald, Baral, Hans-Otto, Järv, Helle, Madrid, Hugo, Nordén, Jenni, Liu, Jian-Kui, Pawlowska, Julia, Põldmaa, Kadri, Pärtel, Kadri, Runnel, Kadri, Hansen, Karen, Larsson, Karl-Henrik, Hyde, Kevin David, Sandoval-Denis, Marcelo, Smith, Matthew E., Toome-Heller, Merje, Wijayawardene, Nalin N., Menolli, Jr., Nelson, Reynolds, Nicole K., Drenkhan, Rein, Maharachchikumbura, Sajeewa S. N., Gibertoni, Tatiana B., Læssøe, Thomas, Davis, William, Tokarev, Yuri, Corrales, Adriana, Soares, Adriene Mayra, Agan, Ahto, Machado, Alexandre Reis, Argüelles-Moyao, Andrés, Detheridge, Andrew, de Meiras-Ottoni, Angelina, Verbeken, Annemieke, Dutta, Arun Kumar, Cui, Bao-Kai, Pradeep, C. K., Marín, César, Stanton, Daniel, Gohar, Daniyal, Wanasinghe, Dhanushka N., Otsing, Eveli, Aslani, Farzad, Griffith, Gareth W., Lumbsch, Thorsten H., Grossart, Hans-Peter, Masigol, Hossein, Timling, Ina, Hiiesalu, Inga, Oja, Jane, Kupagme, John Y., Geml, József, Alvarez-Manjarrez, Julieta, Ilves, Kai, Loit, Kaire, Adamson, Kalev, Nara, Kazuhide, Küngas, Kati, Rojas-Jimenez, Keilor, Bitenieks, Krišs, Irinyi, Laszlo, Nagy, László G., Soonvald, Liina, Zhou, Li-Wei, Wagner, Lysett, Aime, M. Catherine, Öpik, Maarja, Mujica, María Isabel, Metsoja, Martin, Ryberg, Martin, Vasar, Martti, Murata, Masao, Nelsen, Matthew P., Cleary, Michelle, Samarakoon, Milan C., Doilom, Mingkwan, Bahram, Mohammad, Hagh-Doust, Niloufar, Dulya, Olesya, Johnston, Peter, Kohout, Petr, Chen, Qian, Tian, Qing, Nandi, Rajasree, Amiri, Rasekh, Perera, Rekhani Hansika, dos Santos Chikowski, Renata, Mendes-Alvarenga, Renato L., Garibay-Orijel, Roberto, Gielen, Robin, Phookamsak, Rungtiwa, Jayawardena, Ruvishika S., Rahimlou, Saleh, Karunarathna, Samantha C., Tibpromma, Saowaluck, Brown, Shawn P., Sepp, Siim-Kaarel, Mundra, Sunil, Luo, Zhu-Hua, Bose, Tanay, Vahter, Tanel, Netherway, Tarquin, Yang, Teng, May, Tom, Varga, Torda, Li, Wei, Coimbra, Victor Rafael Matos, de Oliveira, Virton Rodrigo Targino, de Lima, Vitor Xavier, Mikryukov, Vladimir S., Lu, Yongzhong, Matsuda, Yosuke, Miyamoto, Yumiko, Kõljalg, Urmas, and Tedersoo, Leho

Published
2020
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12. 17 The Biotechnological Potential of Anaerobic Gut Fungi

Author

Flad, Veronika, primary, Young, Diana, additional, Seppälä, Susanna, additional, Hooker, Casey, additional, Youssef, Noha, additional, Podmirseg, Sabine M., additional, Nagler, Magdalena, additional, Reilly, Matthew, additional, Li, Yuanfei, additional, Fliegerová, Kateřina, additional, Cheng, Yanfen, additional, Griffith, Gareth W., additional, Elshahed, Mostafa, additional, Solomon, Kevin V., additional, O’Malley, Michelle A., additional, and Theodorou, Michael K., additional

Published
2020
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19. Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats

Author

Joshi, Akshay, primary, Young, Diana, additional, Huang, Liren, additional, Mosberger, Lona, additional, Munk, Bernhard, additional, Vinzelj, Julia, additional, Flad, Veronika, additional, Sczyrba, Alexander, additional, Griffith, Gareth W., additional, Podmirseg, Sabine Marie, additional, Warthmann, Rolf, additional, Lebuhn, Michael, additional, and Insam, Heribert, additional

Published
2022
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21. Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages

Author

Young, Diana, primary, Joshi, Akshay, additional, Huang, Liren, additional, Munk, Bernhard, additional, Wurzbacher, Christian, additional, Youssef, Noha H., additional, Elshahed, Mostafa S., additional, Moon, Christina D., additional, Ochsenreither, Katrin, additional, Griffith, Gareth W., additional, Callaghan, Tony M., additional, Sczyrba, Alexander, additional, Lebuhn, Michael, additional, and Flad, Veronika, additional

Published
2022
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22. Characterization and rank assignment criteria for the anaerobic fungi (Neocallimastigomycota)

Author

Elshahed, Mostafa S., primary, Hanafy, Radwa A., additional, Cheng, Yanfen, additional, Dagar, Sumit S., additional, Edwards, Joan E., additional, Flad, Veronika, additional, Fliegerová, Kateřina Olša, additional, Griffith, Gareth W., additional, Kittelmann, Sandra, additional, Lebuhn, Michael, additional, O'Malley, Michelle A., additional, Podmirseg, Sabine Marie, additional, Solomon, Kevin V., additional, Vinzelj, Julia, additional, Young, Diana, additional, and Youssef, Noha H., additional

Published
2022
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24. Effect of growth media on the diversity of Neocallimastigomycetes from non-rumen habitats

Author

Joshi, Akshay, Young, Diana, Huang, Liren, Mosberger, Lona, Munk, Bernhard, Vinzelj, Julia, Flad, Veronika, Sczyrba, Alexander, Griffith, Gareth W., Podmirseg, Sabine Marie, Warthmann, Rolf, Lebuhn, Michael, Insam, Heribert, Joshi, Akshay, Young, Diana, Huang, Liren, Mosberger, Lona, Munk, Bernhard, Vinzelj, Julia, Flad, Veronika, Sczyrba, Alexander, Griffith, Gareth W., Podmirseg, Sabine Marie, Warthmann, Rolf, Lebuhn, Michael, and Insam, Heribert

Abstract

Anaerobic fungi (AF), belonging to the phylum Neocallimastigomycota, are a pivotal component of the digestive tract microbiome of various herbivorous animals. In the last decade, the diversity of AF has rapidly expanded due to the exploration of numerous (novel) habitats. Studies aiming at understanding the role of AF require robust and reliable isolation and cultivation techniques, many of which remained unchanged for decades. Using amplicon sequencing, we compared three different media: medium with rumen fluid (RF), depleted rumen fluid (DRF), and no rumen fluid (NRF) to enrich the AF from the feces of yak, as a rumen control; and Przewalski’s horse, llama, guanaco, and elephant, as a non-rumen habitats. The results revealed the selective enrichment of Piromyces and Neocallimastix from the feces of elephant and llama, respectively, in the RF medium. Similarly, the enrichment culture in DRF medium explicitly manifested Piromyces-related sequences from elephant feces. Five new clades (MM1-5) were defined from llama, guanaco, yak, and elephant feces that could as well be enriched from llama and elephant samples using non-conventional DRF and NRF media. This study presents evidence for the selective enrichment of certain genera in medium with RF and DRF from rumen as well as from non-rumen samples. NRF medium is suggested for the isolation of AF from non-rumen environments.

Published
2022

25. Simultaneous metabarcoding and quantification of neocallimastigomycetes from environmental samples : insights into community composition and novel lineages

Author

Young, Diana, Joshi, Akshay, Huang, Liren, Munk, Bernhard, Wurzbacher, Christian, Youssef, Noha H, Elshahed, Mostafa S, Moon, Christina D, Ochsenreither, Katrin, Griffith, Gareth W, Callaghan, Tony M, Sczyrba, Alexander, Lebuhn, Michael, Flad, Veronika, Young, Diana, Joshi, Akshay, Huang, Liren, Munk, Bernhard, Wurzbacher, Christian, Youssef, Noha H, Elshahed, Mostafa S, Moon, Christina D, Ochsenreither, Katrin, Griffith, Gareth W, Callaghan, Tony M, Sczyrba, Alexander, Lebuhn, Michael, and Flad, Veronika

Abstract

Anaerobic fungi from the herbivore digestive tract (Neocallimastigomycetes) are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. We developed and validated a Neocallimastigomycetes-specific PCR primer pair targeting the D2 region of the ribosomal large subunit suitable for screening, quantifying, and sequencing. We evaluated this primer pair in silico on sequences from all known genera, in vitro with pure cultures covering 16 of the 20 known genera, and on environmental samples with highly diverse microbiomes. The amplified region allowed phylogenetic differentiation of all known genera and most species. The amplicon is about 350 bp long, suitable for short-read high-throughput sequencing as well as qPCR assays. Sequencing of herbivore fecal samples verified the specificity of the primer pair and recovered highly diverse and so far unknown anaerobic gut fungal taxa. As the chosen barcoding region can be easily aligned and is taxonomically informative, the sequences can be used for classification and phylogenetic inferences. Several new Neocallimastigomycetes clades were obtained, some of which represent putative novel lineages such as a clade from feces of the rodent Dolichotis patagonum (mara).

Published
2022

26. Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa

Author

Ariyawansa, Hiran A., Hyde, Kevin D., Jayasiri, Subashini C., Buyck, Bart, Chethana, K. W. Thilini, Dai, Dong Qin, Dai, Yu Cheng, Daranagama, Dinushani A., Jayawardena, Ruvishika S., Lücking, Robert, Ghobad-Nejhad, Masoomeh, Niskanen, Tuula, Thambugala, Kasun M., Voigt, Kerstin, Zhao, Rui Lin, Li, Guo-Jie, Doilom, Mingkwan, Boonmee, Saranyaphat, Yang, Zhu L., Cai, Qing, Cui, Yang-Yang, Bahkali, Ali H., Chen, Jie, Cui, Bao Kai, Chen, Jia Jia, Dayarathne, Monika C., Dissanayake, Asha J., Ekanayaka, Anusha H., Hashimoto, Akira, Hongsanan, Sinang, Jones, E. B. Gareth, Larsson, Ellen, Li, Wen Jing, Li, Qi-Rui, Liu, Jian Kui, Luo, Zong Long, Maharachchikumbura, Sajeewa S. N., Mapook, Ausana, McKenzie, Eric H. C., Norphanphoun, Chada, Konta, Sirinapa, Pang, Ka Lai, Perera, Rekhani H., Phookamsak, Rungtiwa, Phukhamsakda, Chayanard, Pinruan, Umpava, Randrianjohany, Emile, Singtripop, Chonticha, Tanaka, Kazuaki, Tian, Cheng Ming, Tibpromma, Saowaluck, Abdel-Wahab, Mohamed A., Wanasinghe, Dhanushka N., Wijayawardene, Nalin N., Zhang, Jin-Feng, Zhang, Huang, Abdel-Aziz, Faten A., Wedin, Mats, Westberg, Martin, Ammirati, Joseph F., Bulgakov, Timur S., Lima, Diogo X., Callaghan, Tony M., Callac, Philipp, Chang, Cheng-Hao, Coca, Luis F., Dal-Forno, Manuela, Dollhofer, Veronika, Fliegerová, Kateřina, Greiner, Katrin, Griffith, Gareth W., Ho, Hsiao-Man, Hofstetter, Valerie, Jeewon, Rajesh, Kang, Ji Chuan, Wen, Ting-Chi, Kirk, Paul M., Kytövuori, Ilkka, Lawrey, James D., Xing, Jia, Li, Hong, Liu, Zou Yi, Liu, Xing Zhong, Liimatainen, Kare, Lumbsch, H. Thorsten, Matsumura, Misato, Moncada, Bibiana, Nuankaew, Salilaporn, Parnmen, Sittiporn, de Azevedo Santiago, André L. C. M., Sommai, Sujinda, Song, Yu, de Souza, Carlos A. F., de Souza-Motta, Cristina M., Su, Hong Yan, Suetrong, Satinee, Wang, Yong, Wei, Syuan-Fong, Wen, Ting Chi, Yuan, Hai Sheng, Zhou, Li Wei, Réblová, Martina, Fournier, Jacques, Camporesi, Erio, Luangsa-ard, J. Jennifer, Tasanathai, Kanoksri, Khonsanit, Artit, Thanakitpipattana, Donnaya, Somrithipol, Sayanh, Diederich, Paul, Millanes, Ana M., Common, Ralph S., Stadler, Marc, Yan, Ji Ye, Li, XingHong, Lee, Hye Won, Nguyen, Thi T. T., Lee, Hyang Burm, Battistin, Eliseo, Marsico, Orlando, Vizzini, Alfredo, Vila, Jordi, Ercole, Enrico, Eberhardt, Ursula, Simonini, Giampaolo, Wen, Hua-An, Chen, Xin-Hua, Miettinen, Otto, Spirin, Viacheslav, and Hernawati

Published
2015
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27. On the characterization and rank assignment criteria for the anaerobic gut fungi (Neocallimastigomycota)

Author

Elshahed, Mostafa, Radwa Hanafy, Yanfen Cheng, Dagar, Sumit S., Edwards, Joan E., Flad, Veronika, Kate��ina Ol��a Fliegerov��, Griffith, Gareth W., Kittelmann, Sandra, Lebuhn, Michael, O'Malley, Michelle, Podmirseg, Sabine, Solomon, Kevin V., Vinzelj, Julia, Young, Diana, and Youssef, Noha

Subjects
Anaerobic fungi, Neocallimastigomycota, taxonomy
Abstract

Within a specific lineage, establishing a solid taxonomic framework is crucial for enabling discovery and documentation efforts. This ensures effective communication between scientists as well as reproducibility of results between laboratories, and facilitates the exchange and preservation of biological material. Such framework can only be achieved by establishing clear criteria for taxa characterization and rank assignment. Within the anaerobic fungi (Phylum Neocallimastigomycota), the need for such criteria is especially vital. Difficulties associated with their isolation, maintenance, and long-term storage often result in limited availability and loss of previously described taxa. To this end, we provide here a list of morphological, microscopic, phylogenetic, and phenotypic criteria for assessment and documentation when characterizing newly obtained Neocallimastigomycota isolates. We also recommend a polyphasic rank-assignment scheme for novel genus, species, and strain level designations for newly obtained Neocallimastigomycota isolates.Within a specific lineage, establishing a solid taxonomic framework is crucial for enabling discovery and documentation efforts. This ensures effective communication between scientists as well as reproducibility of results between laboratories, and facilitates the exchange and preservation of biological material. Such framework can only be achieved by establishing clear criteria for taxa characterization and rank assignment. Within the anaerobic fungi (Phylum Neocallimastigomycota), the need for such criteria is especially vital. Difficulties associated with their isolation, maintenance, and long-term storage often result in limited availability and loss of previously described taxa. To this end, we provide here a list of morphological, microscopic, phylogenetic, and phenotypic criteria for assessment and documentation when characterizing newly obtained Neocallimastigomycota isolates. We also recommend a polyphasic rank-assignment scheme for novel genus, species, and strain level designations for newly obtained Neocallimastigomycota isolates.

Published
2021
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28. The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits

Author

Schoch, Conrad L., Sung, Gi-Ho, López-Giráldez, Francesc, Townsend, Jeffrey P., Miadlikowska, Jolanta, Hofstetter, Valérie, Robbertse, Barbara, Matheny, P. Brandon, Kauff, Frank, Wang, Zheng, Gueidan, Cécile, Andrie, Rachael M., Trippe, Kristin, Ciufetti, Linda M., Wynns, Anja, Fraker, Emily, Hodkinson, Brendan P., Bonito, Gregory, Groenewald, Johannes Z., Arzanlou, Mahdi, de Hoog, G. Sybren, Crous, Pedro W., Hewitt, David, Pfister, Donald H., Peterson, Kristin, Gryzenhout, Marieka, Wingfield, Michael J., Aptroot, André, Suh, Sung-Oui, Blackwell, Meredith, Hillis, David M., Griffith, Gareth W., Castlebury, Lisa A., Rossman, Amy Y., Lumbsch, H. Thorsten, Lücking, Robert, Büdel, Burkhard, Rauhut, Alexandra, Diederich, Paul, Ertz, Damien, Geiser, David M., Hosaka, Kentaro, Inderbitzin, Patrik, Kohlmeyer, Jan, Volkmann-Kohlmeyer, Brigitte, Mostert, Lizel, O'Donnell, Kerry, Sipman, Harrie, Rogers, Jack D., Shoemaker, Robert A., Sugiyama, Junta, Summerbell, Richard C., Untereiner, Wendy, Johnston, Peter R., Stenroos, Soili, Zuccaro, Alga, Dyer, Paul S., Crittenden, Peter D., Cole, Mariette S., Hansen, Karen, Trappe, James M., Yahr, Rebecca, Lutzoni, François, and Spatafora, Joseph W.

Published
2009

31. Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales)

Author

Lodge, D. Jean, Padamsee, Mahajabeen, Matheny, P. Brandon, Aime, M. Catherine, Cantrell, Sharon A., Boertmann, David, Kovalenko, Alexander, Vizzini, Alfredo, Dentinger, Bryn T. M., Kirk, Paul M., Ainsworth, A. Martyn, Moncalvo, Jean-Marc, Vilgalys, Rytas, Larsson, Ellen, Lücking, Robert, Griffith, Gareth W., Smith, Matthew E., Norvell, Lorelei L., Desjardin, Dennis E., Redhead, Scott A., Ovrebo, Clark L., Lickey, Edgar B., Ercole, Enrico, Hughes, Karen W., Courtecuisse, Régis, Young, Anthony, Binder, Manfred, Minnis, Andrew M., Lindner, Daniel L., Ortiz-Santana, Beatriz, Haight, John, Læssøe, Thomas, Baroni, Timothy J., Geml, József, and Hattori, Tsutomu

Published
2014
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32. Erratum to: Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa

Author

Ariyawansa, Hiran A., Hyde, Kevin D., Jayasiri, Subashini C., Buyck, Bart, Chethana, K. W. Thilini, Dai, Dong Qin, Dai, Yu Cheng, Daranagama, Dinushani A., Jayawardena, Ruvishika S., Lücking, Robert, Ghobad-Nejhad, Masoomeh, Niskanen, Tuula, Thambugala, Kasun M., Voigt, Kerstin, Zhao, Rui Lin, Li, Guo-Jie, Doilom, Mingkwan, Boonmee, Saranyaphat, Yang, Zhu L., Cai, Qing, Cui, Yang-Yang, Bahkali, Ali H., Chen, Jie, Cui, Bao Kai, Chen, Jia Jia, Dayarathne, Monika C., Dissanayake, Asha J., Ekanayaka, Anusha H., Hashimoto, Akira, Hongsanan, Sinang, Jones, E. B. Gareth, Larsson, Ellen, Li, Wen Jing, Li, Qi-Rui, Liu, Jian Kui, Luo, Zong Long, Maharachchikumbura, Sajeewa S. N., Mapook, Ausana, McKenzie, Eric H. C., Norphanphoun, Chada, Konta, Sirinapa, Pang, Ka Lai, Perera, Rekhani H., Phookamsak, Rungtiwa, Phukhamsakda, Chayanard, Pinruan, Umpava, Randrianjohany, Emile, Singtripop, Chonticha, Tanaka, Kazuaki, Tian, Cheng Ming, Tibpromma, Saowaluck, Abdel-Wahab, Mohamed A., Wanasinghe, Dhanushka N., Wijayawardene, Nalin N., Zhang, Jin-Feng, Zhang, Huang, Abdel-Aziz, Faten A., Wedin, Mats, Westberg, Martin, Ammirati, Joseph F., Bulgakov, Timur S., Lima, Diogo X., Callaghan, Tony M., Callac, Philipp, Chang, Cheng-Hao, Coca, Luis F., Dal-Forno, Manuela, Dollhofer, Veronika, Fliegerová, Kateřina, Greiner, Katrin, Griffith, Gareth W., Ho, Hsiao-Man, Hofstetter, Valerie, Jeewon, Rajesh, Kang, Ji Chuan, Wen, Ting-Chi, Kirk, Paul M., Kytövuori, Ilkka, Lawrey, James D., Xing, Jia, Li, Hong, Liu, Zou Yi, Liu, Xing Zhong, Liimatainen, Kare, Lumbsch, H. Thorsten, Matsumura, Misato, Moncada, Bibiana, Nuankaew, Salilaporn, Parnmen, Sittiporn, de Azevedo Santiago, André L. C. M., Sommai, Sujinda, Song, Yu, de Souza, Carlos A. F., de Souza-Motta, Cristina M., Su, Hong Yan, Suetrong, Satinee, Wang, Yong, Wei, Syuan-Fong, Wen, Ting Chi, Yuan, Hai Sheng, Zhou, Li Wei, Réblová, Martina, Fournier, Jacques, Camporesi, Erio, Luangsa-ard, J. Jennifer, Tasanathai, Kanoksri, Khonsanit, Artit, Thanakitpipattana, Donnaya, Somrithipol, Sayanh, Diederich, Paul, Millanes, Ana M., Common, Ralph S., Stadler, Marc, Yan, Ji Ye, Li, XingHong, Lee, Hye Won, Nguyen, Thi T. T., Lee, Hyang Burm, Battistin, Eliseo, Marsico, Orlando, Vizzini, Alfredo, Vila, Jordi, Ercole, Enrico, Eberhardt, Ursula, Simonini, Giampaolo, Wen, Hua-An, Chen, Xin-Hua, Miettinen, Otto, Spirin, Viacheslav, and Hernawati

Published
2015
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34. Correction to: FungalTraits: a user friendly traits database of fungi and fungus-like stramenopiles (Fungal Diversity, (2020), 105, 1, (1-16), 10.1007/s13225-020-00466-2)

Author

Põlme, Sergei, Abarenkov, Kessy, Henrik Nilsson, R., Lindahl, Björn D., Clemmensen, Karina Engelbrecht, Kauserud, Havard, Nguyen, Nhu, Kjøller, Rasmus, Bates, Scott T., Baldrian, Petr, Frøslev, Tobias Guldberg, Adojaan, Kristjan, Vizzini, Alfredo, Suija, Ave, Pfister, Donald, Baral, Hans Otto, Järv, Helle, Madrid, Hugo, Nordén, Jenni, Liu, Jian Kui, Pawlowska, Julia, Põldmaa, Kadri, Pärtel, Kadri, Runnel, Kadri, Hansen, Karen, Larsson, Karl Henrik, Hyde, Kevin David, Sandoval-Denis, Marcelo, Smith, Matthew E., Toome-Heller, Merje, Wijayawardene, Nalin N., Menolli, Nelson, Reynolds, Nicole K., Drenkhan, Rein, Maharachchikumbura, Sajeewa S.N., Gibertoni, Tatiana B., Læssøe, Thomas, Davis, William, Tokarev, Yuri, Corrales, Adriana, Soares, Adriene Mayra, Agan, Ahto, Machado, Alexandre Reis, Argüelles-Moyao, Andrés, Detheridge, Andrew, de Meiras-Ottoni, Angelina, Verbeken, Annemieke, Dutta, Arun Kumar, Cui, Bao Kai, Pradeep, C. K., Marín, César, Stanton, Daniel, Gohar, Daniyal, Wanasinghe, Dhanushka N., Otsing, Eveli, Aslani, Farzad, Griffith, Gareth W., Lumbsch, Thorsten H., Grossart, Hans Peter, Masigol, Hossein, Timling, Ina, Hiiesalu, Inga, Oja, Jane, Kupagme, John Y., Geml, József, Alvarez-Manjarrez, Julieta, Ilves, Kai, Loit, Kaire, Adamson, Kalev, Nara, Kazuhide, Küngas, Kati, Rojas-Jimenez, Keilor, Bitenieks, Krišs, Irinyi, László, Nagy, László G., Soonvald, Liina, Zhou, Li Wei, Wagner, Lysett, Aime, M. Catherine, Öpik, Maarja, Mujica, María Isabel, Metsoja, Martin, Ryberg, Martin, Vasar, Martti, Murata, Masao, Nelsen, Matthew P., Cleary, Michelle, Samarakoon, Milan C., Doilom, Mingkwan, Bahram, Mohammad, Hagh-Doust, Niloufar, Dulya, Olesya, Johnston, Peter, Kohout, Petr, Chen, Qian, Tian, Qing, Nandi, Rajasree, Amiri, Rasekh, Perera, Rekhani Hansika, dos Santos Chikowski, Renata, Mendes-Alvarenga, Renato L., Garibay-Orijel, Roberto, Gielen, Robin, Phookamsak, Rungtiwa, Jayawardena, Ruvishika S., Rahimlou, Saleh, Karunarathna, Samantha C., Tibpromma, Saowaluck, Brown, Shawn P., Sepp, Siim Kaarel, Mundra, Sunil, Luo, Zhu Hua, Bose, Tanay, Vahter, Tanel, Netherway, Tarquin, Yang, Teng, May, Tom, Varga, Torda, Li, Wei, Coimbra, Victor Rafael Matos, de Oliveira, Virton Rodrigo Targino, de Lima, Vitor Xavier, Mikryukov, Vladimir S., Lu, Yongzhong, Matsuda, Yosuke, Miyamoto, Yumiko, Kõljalg, Urmas, Tedersoo, Leho, Põlme, Sergei, Abarenkov, Kessy, Henrik Nilsson, R., Lindahl, Björn D., Clemmensen, Karina Engelbrecht, Kauserud, Havard, Nguyen, Nhu, Kjøller, Rasmus, Bates, Scott T., Baldrian, Petr, Frøslev, Tobias Guldberg, Adojaan, Kristjan, Vizzini, Alfredo, Suija, Ave, Pfister, Donald, Baral, Hans Otto, Järv, Helle, Madrid, Hugo, Nordén, Jenni, Liu, Jian Kui, Pawlowska, Julia, Põldmaa, Kadri, Pärtel, Kadri, Runnel, Kadri, Hansen, Karen, Larsson, Karl Henrik, Hyde, Kevin David, Sandoval-Denis, Marcelo, Smith, Matthew E., Toome-Heller, Merje, Wijayawardene, Nalin N., Menolli, Nelson, Reynolds, Nicole K., Drenkhan, Rein, Maharachchikumbura, Sajeewa S.N., Gibertoni, Tatiana B., Læssøe, Thomas, Davis, William, Tokarev, Yuri, Corrales, Adriana, Soares, Adriene Mayra, Agan, Ahto, Machado, Alexandre Reis, Argüelles-Moyao, Andrés, Detheridge, Andrew, de Meiras-Ottoni, Angelina, Verbeken, Annemieke, Dutta, Arun Kumar, Cui, Bao Kai, Pradeep, C. K., Marín, César, Stanton, Daniel, Gohar, Daniyal, Wanasinghe, Dhanushka N., Otsing, Eveli, Aslani, Farzad, Griffith, Gareth W., Lumbsch, Thorsten H., Grossart, Hans Peter, Masigol, Hossein, Timling, Ina, Hiiesalu, Inga, Oja, Jane, Kupagme, John Y., Geml, József, Alvarez-Manjarrez, Julieta, Ilves, Kai, Loit, Kaire, Adamson, Kalev, Nara, Kazuhide, Küngas, Kati, Rojas-Jimenez, Keilor, Bitenieks, Krišs, Irinyi, László, Nagy, László G., Soonvald, Liina, Zhou, Li Wei, Wagner, Lysett, Aime, M. Catherine, Öpik, Maarja, Mujica, María Isabel, Metsoja, Martin, Ryberg, Martin, Vasar, Martti, Murata, Masao, Nelsen, Matthew P., Cleary, Michelle, Samarakoon, Milan C., Doilom, Mingkwan, Bahram, Mohammad, Hagh-Doust, Niloufar, Dulya, Olesya, Johnston, Peter, Kohout, Petr, Chen, Qian, Tian, Qing, Nandi, Rajasree, Amiri, Rasekh, Perera, Rekhani Hansika, dos Santos Chikowski, Renata, Mendes-Alvarenga, Renato L., Garibay-Orijel, Roberto, Gielen, Robin, Phookamsak, Rungtiwa, Jayawardena, Ruvishika S., Rahimlou, Saleh, Karunarathna, Samantha C., Tibpromma, Saowaluck, Brown, Shawn P., Sepp, Siim Kaarel, Mundra, Sunil, Luo, Zhu Hua, Bose, Tanay, Vahter, Tanel, Netherway, Tarquin, Yang, Teng, May, Tom, Varga, Torda, Li, Wei, Coimbra, Victor Rafael Matos, de Oliveira, Virton Rodrigo Targino, de Lima, Vitor Xavier, Mikryukov, Vladimir S., Lu, Yongzhong, Matsuda, Yosuke, Miyamoto, Yumiko, Kõljalg, Urmas, and Tedersoo, Leho

Abstract

There were errors in the name of author László G. Nagy and in affiliation no. 31 in the original publication. The original article has been corrected.

Published
2021

38. Environmental DNA reveals links between abundance and composition of airborne grass pollen and respiratory health

Author

Rowney, Francis M., primary, Brennan, Georgina L., additional, Skjøth, Carsten A., additional, Griffith, Gareth W., additional, McInnes, Rachel N., additional, Clewlow, Yolanda, additional, Adams-Groom, Beverley, additional, Barber, Adam, additional, de Vere, Natasha, additional, Economou, Theo, additional, Hegarty, Matthew, additional, Hanlon, Helen M., additional, Jones, Laura, additional, Kurganskiy, Alexander, additional, Petch, Geoffrey M., additional, Potter, Caitlin, additional, Rafiq, Abdullah M., additional, Warner, Amena, additional, Wheeler, Benedict, additional, Osborne, Nicholas J., additional, and Creer, Simon, additional

Published
2021
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40. Isotopic evidence of biotrophy and unusual nitrogen nutrition in soil‐dwelling Hygrophoraceae

Author

Halbwachs, Hans, Easton, Gary L., Bol, Roland, Hobbie, Erik A., Garnett, Mark H, Peršoh, Derek, Dixon, Liz, Ostle, Nick, Karasch, Peter, and Griffith, Gareth W.

Subjects
Nitrogen, ddc:570, Mycorrhizae, Fruiting Bodies, Fungal, Agaricales, Research Articles, Soil Microbiology, Research Article
Abstract

Summary Several lines of evidence suggest that the agaricoid, non‐ectomycorrhizal members of the family Hygrophoraceae (waxcaps) are biotrophic with unusual nitrogen nutrition. However, methods for the axenic culture and lab‐based study of these organisms remain to be developed, so our current knowledge is limited to field‐based investigations. Addition of nitrogen, lime or organophosphate pesticide at an experimental field site (Sourhope) suppressed fruiting of waxcap basidiocarps. Furthermore, stable isotope natural abundance in basidiocarps were unusually high in 15N and low in 13C, the latter consistent with mycorrhizal nutritional status. Similar patterns were found in waxcap basidiocarps from diverse habitats across four continents. Additional data from 14C analysis of basidiocarps and 13C pulse label experiments suggest that these fungi are not saprotrophs but rather biotrophic endophytes and possibly mycorrhizal. The consistently high but variable δ15N values (10–20‰) of basidiocarps further indicate that N acquisition or processing differ from other fungi; we suggest that N may be derived from acquisition of N via soil fauna high in the food chain.

Published
2018

41. FungalTraits:a user-friendly traits database of fungi and fungus-like stramenopiles

Author

Põlme, Sergei, Abarenkov, Kessy, Nilsson, R. Henrik, Lindahl, Björn D., Clemmensen, Karina Engelbrecht, Kauserud, Havard, Nguyen, Nhu, Kjøller, Rasmus, Bates, Scott T., Baldrian, Petr, Frøslev, Tobias Guldberg, Adojaan, Kristjan, Vizzini, Alfredo, Suija, Ave, Pfister, Donald, Baral, Hans Otto, Järv, Helle, Madrid, Hugo, Nordén, Jenni, Liu, Jian-Kui, Pawlowska, Julia, Põldmaa, Kadri, Pärtel, Kadri, Runnel, Kadri, Hansen, Karen, Larsson, Karl-Henrik, Hyde, Kevin David, Sandoval-Denis, Marcelo, Smith, Matthew E., Toome-Heller, Merje, Wijayawardene, Nalin N., Menolli, Nelson, Reynolds, Nicole K., Drenkhan, Rein, Maharachchikumbura, Sajeewa S. N., Gibertoni, Tatiana B., Læssøe, Thomas, Davis, William, Tokarev, Yuri, Corrales, Adriana, Soares, Adriene Mayra, Agan, Ahto, Machado, Alexandre Reis, Argüelles-Moyao, Andrés, Detheridge, Andrew, de Meiras-Ottoni, Angelina, Verbeken, Annemieke, Dutta, Arun Kumar, Cui, Bao-Kai, Pradeep, C. K., Marín, César, Stanton, Daniel, Gohar, Daniyal, Wanasinghe, Dhanushka N., Otsing, Eveli, Aslani, Farzad, Griffith, Gareth W., Lumbsch, Thorsten H., Grossart, Hans-Peter, Masigol, Hossein, Timling, Ina, Hiiesalu, Inga, Oja, Jane, Kupagme, John Y., Geml, József, Alvarez-Manjarrez, Julieta, Ilves, Kai, Loit, Kaire, Adamson, Kalev, Nara, Kazuhide, Küngas, Kati, Rojas-Jimenez, Keilor, Bitenieks, Krišs, Irinyi, Laszlo, Nagy, László G., Soonvald, Liina, Zhou, Li-Wei, Wagner, Lysett, Aime, M. Catherine, Öpik, Maarja, Mujica, María Isabel, Metsoja, Martin, Ryberg, Martin, Vasar, Martti, Murata, Masao, Nelsen, Matthew P., Cleary, Michelle, Samarakoon, Milan C., Doilom, Mingkwan, Bahram, Mohammad, Hagh-Doust, Niloufar, Dulya, Olesya, Johnston, Peter, Kohout, Petr, Chen, Qian, Tian, Qing, Nandi, Rajasree, Amiri, Rasekh, Perera, Rekhani Hansika, Chikowski, Renata dos Santos, Mendes-Alvarenga, Renato L., Garibay-Orijel, Roberto, Gielen, Robin, Phookamsak, Rungtiwa, Jayawardena, Ruvishika S., Rahimlou, Saleh, Karunarathna, Samantha C., Tibpromma, Saowaluck, Brown, Shawn P., Sepp, Siim-Kaarel, Mundra, Sunil, Luo, Zhu-Hua, Bose, Tanay, Vahter, Tanel, Netherway, Tarquin, Yang, Teng, May, Tom, Varga, Torda, Li, Wei, Coimbra, Victor Rafael Matos, de Oliveira, Virton Rodrigo Targino, de Lima, Vitor Xavier, Mikryukov, Vladimir S., Lu, Yongzhong, Matsuda, Yosuke, Miyamoto, Yumiko, Kõljalg, Urmas, Tedersoo, Leho, Põlme, Sergei, Abarenkov, Kessy, Nilsson, R. Henrik, Lindahl, Björn D., Clemmensen, Karina Engelbrecht, Kauserud, Havard, Nguyen, Nhu, Kjøller, Rasmus, Bates, Scott T., Baldrian, Petr, Frøslev, Tobias Guldberg, Adojaan, Kristjan, Vizzini, Alfredo, Suija, Ave, Pfister, Donald, Baral, Hans Otto, Järv, Helle, Madrid, Hugo, Nordén, Jenni, Liu, Jian-Kui, Pawlowska, Julia, Põldmaa, Kadri, Pärtel, Kadri, Runnel, Kadri, Hansen, Karen, Larsson, Karl-Henrik, Hyde, Kevin David, Sandoval-Denis, Marcelo, Smith, Matthew E., Toome-Heller, Merje, Wijayawardene, Nalin N., Menolli, Nelson, Reynolds, Nicole K., Drenkhan, Rein, Maharachchikumbura, Sajeewa S. N., Gibertoni, Tatiana B., Læssøe, Thomas, Davis, William, Tokarev, Yuri, Corrales, Adriana, Soares, Adriene Mayra, Agan, Ahto, Machado, Alexandre Reis, Argüelles-Moyao, Andrés, Detheridge, Andrew, de Meiras-Ottoni, Angelina, Verbeken, Annemieke, Dutta, Arun Kumar, Cui, Bao-Kai, Pradeep, C. K., Marín, César, Stanton, Daniel, Gohar, Daniyal, Wanasinghe, Dhanushka N., Otsing, Eveli, Aslani, Farzad, Griffith, Gareth W., Lumbsch, Thorsten H., Grossart, Hans-Peter, Masigol, Hossein, Timling, Ina, Hiiesalu, Inga, Oja, Jane, Kupagme, John Y., Geml, József, Alvarez-Manjarrez, Julieta, Ilves, Kai, Loit, Kaire, Adamson, Kalev, Nara, Kazuhide, Küngas, Kati, Rojas-Jimenez, Keilor, Bitenieks, Krišs, Irinyi, Laszlo, Nagy, László G., Soonvald, Liina, Zhou, Li-Wei, Wagner, Lysett, Aime, M. Catherine, Öpik, Maarja, Mujica, María Isabel, Metsoja, Martin, Ryberg, Martin, Vasar, Martti, Murata, Masao, Nelsen, Matthew P., Cleary, Michelle, Samarakoon, Milan C., Doilom, Mingkwan, Bahram, Mohammad, Hagh-Doust, Niloufar, Dulya, Olesya, Johnston, Peter, Kohout, Petr, Chen, Qian, Tian, Qing, Nandi, Rajasree, Amiri, Rasekh, Perera, Rekhani Hansika, Chikowski, Renata dos Santos, Mendes-Alvarenga, Renato L., Garibay-Orijel, Roberto, Gielen, Robin, Phookamsak, Rungtiwa, Jayawardena, Ruvishika S., Rahimlou, Saleh, Karunarathna, Samantha C., Tibpromma, Saowaluck, Brown, Shawn P., Sepp, Siim-Kaarel, Mundra, Sunil, Luo, Zhu-Hua, Bose, Tanay, Vahter, Tanel, Netherway, Tarquin, Yang, Teng, May, Tom, Varga, Torda, Li, Wei, Coimbra, Victor Rafael Matos, de Oliveira, Virton Rodrigo Targino, de Lima, Vitor Xavier, Mikryukov, Vladimir S., Lu, Yongzhong, Matsuda, Yosuke, Miyamoto, Yumiko, Kõljalg, Urmas, and Tedersoo, Leho

Abstract

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.

Published
2020

42. Reconstructing the early evolution of Fungi using a six-gene phylogeny

Author

James, Timothy Y., Kauff, Frank, Schoch, Conrad L., Matheny, P. Brandon, Hofstetter, Valerie, Cox, Cymon J., Celio, Gail, Gueidan, Cecile, Fraker, Emily, Miadlikowska, Jolanta, Lumbsch, H. Thorsten, Rauhut, Alexandra, Reeb, Valerie, Arnold, A. Elizabeth, Amtoft, Anja, Stajich, Jason E., Hosaka, Kentaro, Sung, Gi-Ho, Johnson, Desiree, O'Rourke, Ben, Crockett, Michael, Binder, Manfred, Curtis, Judd M., Slot, Jason C., Wang, Zheng, Wilson, Andrew W., Schußler, Arthur, Longcore, Joyce E., O'Donnell, Kerry, Mozley-Standridge, Sharon, Porter, David, Letcher, Peter M., Powell, Martha J., Taylor, John W., White, Merlin M., Griffith, Gareth W., Davies, David R., Humber, Richard A., Morton, Joseph B., Sugiyama, Junta, Rossman, Amy Y., Rogers, Jack D., Pfister, Don H., Hewitt, David, Hansen, Karen, Hambleton, Sarah, Shoemaker, Robert A., Kohlmeyer, Jan, Volkmann-Kohlmeyer, Brigitte, Spotts, Robert A., Serdani, Maryna, Crous, Pedro W., Hughes, Karen W., Matsuura, Kenji, Langer, Ewald, Langer, Gitta, Untereiner, Wendy A., Lucking, Robert, Budel, Burkhard, Geiser, David M., Aptroot, Andre, Diederich, Paul, Schmitt, Imke, Schultz, Matthias, Yahr, Rebecca, Hibbett, David S., Lutzoni, Francois, McLaughlin, David J., Spatafora, Joseph W., and Vilgalys, Rytas

Abstract

Author(s): Timothy Y. James (corresponding author) [1]; Frank Kauff [1]; Conrad L. Schoch [2, 36]; P. Brandon Matheny [3, 36]; Valérie Hofstetter [1, 36]; Cymon J. Cox [1, 37]; Gail [...]

Published
2006
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43. Differentiation of Phytophthora infestans sporangia from other airborne biological particles by flow cytometry

Author

Day, Jennifer P., Kell, Douglas B., and Griffith, Gareth W.

Subjects
Spores (Botany) -- Measurement, Flow cytometry -- Evaluation, Potatoes -- Diseases and pests, Biological sciences
Abstract

The PAS-III flow cytometer from Partec GmbH is more effective than the Microcyte flow cytometer from Optoflow AS in distinguishing air-borne sporangia of the late-blight of potato from other spores and pollens. This is somewhat unfortunate, because PAS-III is a large benchtop system whereas Microcyte is portable and battery-powered and could be used in the field.

Published
2002

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