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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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3. 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

4. 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

5. 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. 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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11. 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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12. 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

13. 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

14. 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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15. 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

17. 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, Westerdijk Fungal Biodiversity Institute, and Westerdijk Fungal Biodiversity Institute - Evolutionary Phytopathology

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

20. 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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22. 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

23. 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, 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 Laszlo, 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, Laszlo, Nagy, László Laszlo, 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

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

24. 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

25. 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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26. 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

28. Efficient improvement of silage additives by using genetic algorithms

Author

Davies, Zoe S., Gilbert, Richard J., Merry, Roger J., Kell, Douglas B., Theodorou, Michael K., and Griffith, Gareth W.

Subjects
Silage -- Additives, Genetic algorithms -- Usage, Biological sciences
Abstract

Using 50 silage additive combinations, researchers were able to find one that produced 4.6 times more lactic acid than untreated silage. Silage for farm animals is often acidified by lactic acid bacteria to preserve it and prohibit spoilage.

Published
2000

30. A Multi-Kingdom Study Reveals the Plasticity of the Rumen Microbiota in Response to a Shift From Non-grazing to Grazing Diets in Sheep

Author

Belanche, Alejandro, Kingston-Smith, Alison H., Griffith, Gareth W., and Newbold, Charles J.

Subjects
animal structures, rumen microbiota, taxa abundance, grazing, core microbes, Microbiology, network analysis, Original Research
Abstract

Increasing feed efficiency is a key target in ruminant science which requires a better understanding of rumen microbiota. This study investigated the effect of a shift from a non-grazing to a grazing diet on the rumen bacterial, methanogenic archaea, fungal, and protozoal communities. A systems biology approach based on a description of the community structure, core microbiota, network analysis, and taxon abundance linked to the rumen fermentation was used to explore the benefits of increasing depth of the community analysis. A total of 24 sheep were fed ryegrass hay supplemented with concentrate (CON) and subsequently ryegrass pasture (PAS) following a straight through experimental design. Results showed that concentrate supplementation in CON-fed animals (mainly starch) promoted a simplified rumen microbiota in terms of network density and bacterial, methanogen and fungal species richness which favored the proliferation of amylolytic microbes and VFA production (+48%), but led to a lower (ca. 4-fold) ammonia concentration making the N availability a limiting factor certain microbes. The adaptation process from the CON to the PAS diet consisted on an increase in the microbial concentration (biomass of bacteria, methanogens, and protozoa), diversity (+221, +3, and +21 OTUs for bacteria, methanogens, and fungi, respectively), microbial network complexity (+18 nodes and +86 edges) and in the abundance of key microbes involved in cellulolysis (Ruminococcus, Butyrivibrio, and Orpinomyces), proteolysis (Prevotella and Entodiniinae), lactate production (Streptococcus and Selenomonas), as well as methylotrophic archaea (Methanomassiliicoccaceae). This microbial adaptation indicated that pasture degradation is a complex process which requires a diverse consortium of microbes working together. The correlations between the abundance of microbial taxa and rumen fermentation parameters were not consistent across diets suggesting a metabolic plasticity which allowed microbes to adapt to different substrates and to shift their fermentation products. The core microbiota was composed of 34, 9, and 13 genera for bacteria, methanogens, and fungi, respectively, which were shared by all sheep, independent of diet. This systems biology approach adds a new dimension to our understanding of the rumen microbial interactions and may provide new clues to describe the mode of action of future nutritional interventions.

Published
2019

31. Polymorphisms in Phytophthora infestans: four mitochondrial haplotypes are detected after PCR amplification of DNA from pure cultures or from host lesions

Author

Griffith, Gareth W. and Shaw, David S.

Subjects
Polymerase chain reaction -- Usage, Genetic polymorphisms -- Research, Mitochondrial DNA -- Research, Biological sciences
Abstract

A study was conducted to analyze a polymerase chain reaction-based technique for the rapid detection of mtDNA polymorphisms in Phytophthora infestans. Fungi from agar cultures or infected host tissues were utilized to carry out the analysis. Leaf and stem lesions of late blight were obtained from naturally infected crops while DNA was determined by cutting slabs of agar-containing mycelium. In addition, polymerase chain reaction was carried out with the PC2 PCR thermal cycler.

Published
1998

32. Assessing aerial tree pollen composition via metabarcoding analysis of environmental DNA

Author

de Vere, Natasha, Rafiq, Abdullah M., Brennan, Georgina L, Griffith, Gareth W., Skjoth, Carsten Ambelas, Osborne, Nicholas J, Wheeler, Benedict W, McInnes, Rachel N, Clewlow, Yolanda, Barber, Adam, Hanlon, Helen M., Hegarty, Matt, Jones, Laura, Kurganskiy, Alexander, Rowney, Francis, Armitage, Charlotte, Adams-Groom, Beverley, Ford, Col R, Petch, Geoff M., Creer, Simon, de Vere, Natasha, Rafiq, Abdullah M., Brennan, Georgina L, Griffith, Gareth W., Skjoth, Carsten Ambelas, Osborne, Nicholas J, Wheeler, Benedict W, McInnes, Rachel N, Clewlow, Yolanda, Barber, Adam, Hanlon, Helen M., Hegarty, Matt, Jones, Laura, Kurganskiy, Alexander, Rowney, Francis, Armitage, Charlotte, Adams-Groom, Beverley, Ford, Col R, Petch, Geoff M., and Creer, Simon

Abstract

Background: Airborne pollen is ranked as the world’s most harmful aeroallergen, with pollen allergy presenting a significant socioeconomic burden. Contributing factors influencing allergenic reactions include the aeroallergen concentration and the taxonomic origin of pollen grains. In the UK, current pollen monitoring protocols aim to reduce this burden by monitoring and forecasting regional atmospheric pollen concentrations. However, due to morphological features being largely conserved across taxa, traditional palynological techniques are unable to discriminate between species of grass and tree pollen, and the ability to accurately characterise the taxonomic composition of airborne pollen remains an Achilles heel of pollen forecasting. Results: Using aerial environmental DNA (eDNA) sampling and DNA metabarcoding (with two complementary DNA barcode markers, rbcL and ITS2), we aim to explore the composition of airborne pollen across the tree allergy season, at two sites in Great Britain. We will compare traditional palynological techniques and targeted high-throughput sequencing to assess the accuracy of pollen identification via DNA metabarcoding and the ability to detect rare species. Furthermore, we will investigate the influences of bias involved in pollen DNA metabarcoding and test measures of association between species’ abundances to explore cross-utility of the different approaches for measuring pollen abundance. Significance: We anticipate that this research will increase our understanding of the ecology of airborne pollen in time and space and demonstrate the usefulness of DNA metabarcoding in pollen monitoring and aerobiology research.

Published
2019

33. Temperate airborne grass pollen defined by spatio-temporal shifts in community composition

Author

Brennan, Georgina L., Potter, Caitlin, de Vere, Natasha, Griffith, Gareth W., Skjøth, Carsten A., Osborne, Nicholas J., Wheeler, Benedict W., McInnes, Rachel N., Clewlow, Yolanda, Barber, Adam, Hanlon, Helen M., Hegarty, Matthew, Jones, Laura, Kurganskiy, Alexander, Rowney, Francis M., Armitage, Charlotte, Adams-Groom, Beverley, Ford, Col R., Petch, Geoff M., Elliot, Angela, Frisk, Carl A., Neilson, Roy, Potter, Stephen, Rafiq, Abdullah M., Roy, David B., Selby, Katherine, Steinberg, Natascha, Creer, Simon, Brennan, Georgina L., Potter, Caitlin, de Vere, Natasha, Griffith, Gareth W., Skjøth, Carsten A., Osborne, Nicholas J., Wheeler, Benedict W., McInnes, Rachel N., Clewlow, Yolanda, Barber, Adam, Hanlon, Helen M., Hegarty, Matthew, Jones, Laura, Kurganskiy, Alexander, Rowney, Francis M., Armitage, Charlotte, Adams-Groom, Beverley, Ford, Col R., Petch, Geoff M., Elliot, Angela, Frisk, Carl A., Neilson, Roy, Potter, Stephen, Rafiq, Abdullah M., Roy, David B., Selby, Katherine, Steinberg, Natascha, and Creer, Simon

Abstract

Grass pollen is the world’s most harmful outdoor aeroallergen. However, it is unknown how airborne pollen assemblages change across time and space. Human sensitivity varies between different species of grass that flower at different times, but it is not known whether temporal turnover in species composition match terrestrial flowering or whether species richness steadily accumulates over the grass pollen season. Here, using targeted, high-throughput sequencing, we demonstrate that all grass genera displayed discrete, temporally restricted peaks of incidence, which varied with latitude and longitude throughout Great Britain, revealing that the taxonomic composition of grass pollen exposure changes substantially across the grass pollen season.

Published
2019

34. Temperate grass allergy season defined by spatio-temporal shifts in airborne pollen communities

Author

Brennan, Georgina L, Potter, Caitlin, de Vere, Natasha, Griffith, Gareth W., Skjoth, Carsten Ambelas, Osborne, Nicholas J, Wheeler, Benedict W, McInnes, Rachel N, Clewlow, Yolanda, Barber, Adam, Hanlon, Helen M., Hegarty, Matt, Jones, Laura, Kurganskiy, Alexander, Rowney, Francis, Armitage, Charlotte, Adams-Groom, Beverley, Ford, Col R, Petch, Geoff M., Creer, Simon, Brennan, Georgina L, Potter, Caitlin, de Vere, Natasha, Griffith, Gareth W., Skjoth, Carsten Ambelas, Osborne, Nicholas J, Wheeler, Benedict W, McInnes, Rachel N, Clewlow, Yolanda, Barber, Adam, Hanlon, Helen M., Hegarty, Matt, Jones, Laura, Kurganskiy, Alexander, Rowney, Francis, Armitage, Charlotte, Adams-Groom, Beverley, Ford, Col R, Petch, Geoff M., and Creer, Simon

Abstract

Background: Grass pollen is the world’s most harmful outdoor aeroallergen, yet it is not known how airborne assemblages change in time and space. Human sensitivity towards grass pollen varies between species, of which there are over 150 in the UK that flower at different times across the allergy season. However, due to few unique morphological features, grass pollen of different genera cannot be discriminated using traditional observational methods. Currently there is no way of detecting, modelling, or forecasting the atmospheric dispersion of pollen from the biodiversity of grasses, and it is unknown if temporal turnover in species composition match terrestrial flowering or if species richness steadily accumulates over the grass pollen season. Using two complementary DNA barcode markers (rbcL and ITS2), we aim to identify how the taxonomic composition of grass pollen exposure changes across the temperate grass allergy season. Results: Here we show that all grass genera display discrete, temporally restricted peaks of incidence which vary with latitude and longitude across Britain. We reveal that the taxonomic composition of airborne grass pollen changes substantially across the grass allergy season, and changes in total grass pollen concentration, measured using traditional observational methods, are the result of many grassspecies and not a single flowering species of grass. We also demonstrate that local flowering events, with appropriate temporal delays, may be useful for predicting the incidence of particular species of grass pollen in the air. Significance: Our results demonstrate how targeted, high-throughput sequencing can be used to understand the biodiversity of airborne pollen communities and fill a substantial knowledge gap that has persisted over the past 50 years of aerobiology research. By developing more refined aeroallergen profiling, we anticipate that our findings will facilitate the exploration of links between taxon-specific exposure of

Published
2019

35. Metabarcoding-based assessment of airborne pollen assemblages

Author

Potter, Caitlin, Brennan, Georgina L, Creer, Simon, de Vere, Natasha, Skjoth, Carsten Ambelas, Osborne, Nicholas J, Wheeler, Benedict W, McInnes, Rachel N, Clewlow, Yolanda, Barber, Adam, Hanlon, Helen M., Hegarty, Matt, Jones, Laura, Kurganskiy, Alexander, Rowney, Francis, Armitage, Charlotte, Adams-Groom, Beverley, Ford, Col R, Petch, Geoff M., Griffith, Gareth W., Potter, Caitlin, Brennan, Georgina L, Creer, Simon, de Vere, Natasha, Skjoth, Carsten Ambelas, Osborne, Nicholas J, Wheeler, Benedict W, McInnes, Rachel N, Clewlow, Yolanda, Barber, Adam, Hanlon, Helen M., Hegarty, Matt, Jones, Laura, Kurganskiy, Alexander, Rowney, Francis, Armitage, Charlotte, Adams-Groom, Beverley, Ford, Col R, Petch, Geoff M., and Griffith, Gareth W.

Abstract

Background: Airborne pollen is a common trigger for both allergic rhinitis (hay fever) and asthma, which globally affect 400 million and 300 million people, respectively. Accurate pollen forecasts are important in managing these conditions, enabling sufferers to minimise their exposure. However, current UK pollen forecasts are based on counting individual grains under a light microscope, which is time consuming and requires highly trained personnel. Moreover, it is often not possible to morphologically identify pollen grains to the species or genus level, and counts may not be consistent between different collectors. Here, we assess the use of DNA metabarcoding as an alternative to light microscopy that avoids these drawbacks. Results: In this study, pollen was collected at up to 12 sites across the UK over multiple years and analysed using both metabarcoding and light microscopy. Airborne pollen was dominated by a few groups of wind-pollinated species, but in some instances high levels of pollen from insect-pollinated plants were also present. Pollen assemblages varied considerably across the season, but also differed between sampling sites. We demonstrate that metabarcoding and light microscopy were broadly in agreement about the time window over which pollen of a given family was present in the air. Significance: These results suggest the potential for high-throughput sequencing to be incorporated into current workflows for generating pollen forecasts, reducing costs and avoiding the limitations of microscopy-based pollen counts. By contributing to improved pollen forecasts and a better understanding of seasonal pollen dynamics, a better understanding can be developed of the impact of airborne pollen on human health.

Published
2019

39. Linking aerial grass pollen biodiversity and human health: an environmental genomic approach

Author

Brennan, Georgina L, Adams-Groom, Beverley, Barber, Adam, Clewlow, Yolanda, de Vere, Natasha, Griffith, Gareth W., Hegarty, Matt, McInnes, Rachel N, Osborne, Nicholas J, Petch, Geoffrey M., Skjoth, Carsten Ambelas, Wheeler, Benedict W, Creer, Simon, Brennan, Georgina L, Adams-Groom, Beverley, Barber, Adam, Clewlow, Yolanda, de Vere, Natasha, Griffith, Gareth W., Hegarty, Matt, McInnes, Rachel N, Osborne, Nicholas J, Petch, Geoffrey M., Skjoth, Carsten Ambelas, Wheeler, Benedict W, and Creer, Simon

Abstract

In Europe and the UK, grass pollen is the single most important outdoor aeroallergen; 27% of the population are sensitised to grass pollen. Grass pollen allergy has been linked to increased risk of allergic asthma exacerbations, which can lead to hospitalisation and fatalities. Sensitivity towards grass pollen varies with species, of which there are over 150 in the UK. However, due to few unique morphological features, grass pollen from different species cannot be discriminated using traditional observational methods. Currently, there is no way of detecting, modelling or forecasting the aerial-dispersion of pollen from the biodiversity of UK grasses and so they are coalesced into a single group in the UK forecast. PollerGEN is an interdisciplinary NERC project with the aim of revolutionising the way that pollen dispersion is measured and forecast, and to increase our understanding of the ecology of aerial dispersed pollen. In collaboration with the UK Met Office, a key goal of the project is to build a more accurate forecast of individual grass pollen species. Using environmental genomics (shotgun sequencing, DNA metabarcoding, and qPCR), we will identify which species of grass pollen are present during the summer months across 16 specific collection sites in the UK, with the aim of measuring the abundance of different allergenic species of grass. The information will be used to model the spatial and temporal deposition of grass pollen and identify linkages to human health. The project therefore aims to provide a paradigm shift in our understanding of the ecology of windborne pollen in time and space and inform the public about the timing and environmental factors that put them at risk of exposure to pollen they are allergic to, a key strategy in the prevention of allergy and asthma attacks.

Published
2017

40. Hodophilus (Clavariaceae, Agaricales) species with dark dots on the stipe:more than one species in Europe

Author

Adamčík, Slavomír, Jančovičová, Soňa, Looney, Brian P., Adamčíková, Katarína, Griffith, Gareth W., Læssøe, Thomas, Moreau, Pierre-Arthur, Vizzini, Alfredo, Matheny, P. Brandon, Adamčík, Slavomír, Jančovičová, Soňa, Looney, Brian P., Adamčíková, Katarína, Griffith, Gareth W., Læssøe, Thomas, Moreau, Pierre-Arthur, Vizzini, Alfredo, and Matheny, P. Brandon

Published
2017

41. PCR and omics based techniques to study the diversity, ecology and biology of anaerobic fungi : Insights, challenges and opportunities

Author

Edwards, Joan E., Forster, Robert J., Callaghan, Tony M., Dollhofer, Veronika, Dagar, Sumit S., Cheng, Yanfen, Chang, Jongsoo, Kittelmann, Sandra, Fliegerova, Katerina, Puniya, Anil K., Henske, John K., Gilmore, Sean P., O'Malley, Michelle A., Griffith, Gareth W., Smidt, Hauke, Edwards, Joan E., Forster, Robert J., Callaghan, Tony M., Dollhofer, Veronika, Dagar, Sumit S., Cheng, Yanfen, Chang, Jongsoo, Kittelmann, Sandra, Fliegerova, Katerina, Puniya, Anil K., Henske, John K., Gilmore, Sean P., O'Malley, Michelle A., Griffith, Gareth W., and Smidt, Hauke

Abstract

Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however

Published
2017

42. PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities

Author

Edwards, Joan E., primary, Forster, Robert J., additional, Callaghan, Tony M., additional, Dollhofer, Veronika, additional, Dagar, Sumit S., additional, Cheng, Yanfen, additional, Chang, Jongsoo, additional, Kittelmann, Sandra, additional, Fliegerova, Katerina, additional, Puniya, Anil K., additional, Henske, John K., additional, Gilmore, Sean P., additional, O'Malley, Michelle A., additional, Griffith, Gareth W., additional, and Smidt, Hauke, additional

Published
2017
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44. High-throughput metabolic fingerprinting of legume silage fermentations via fourier transform infrared spectroscopy and chemometrics

Author

Johnson, Helen E., Broadhurst, David, Kell, Douglas B., Theodorou, Michael K., Merry, Roger J., and Griffith, Gareth W.

Subjects
Fermentation -- Research, Infrared spectroscopy -- Research, Biological sciences
Abstract

A study about how a metabolic fingerprinting approach can be applied to studies of model fermentation dynamics in red clover to identify the presence of an inoculation and to discriminate between the effects of different LAB inoculants over time is presented. The results of three experiments studying grass and red clover juice fermentation in response to inoculation with a range of different LAB are reported.

Published
2004

45. A fungal perspective on conservation biology

Author

Jacob, HEILMANN-CLAUSEN, Barron, ELIZABETH S., Lynne, Boddy, Anders, Dahlberg, Griffith, GARETH W., Jenni, Nord´en, Otso, Ovaskainen, Perini, Claudia, Beatrice, SENN-IRLET, and Panu, Halme

Subjects
indicator species, mycorrhizal fungi, Conservation of Natural Resources, non-timber forest products, Fungi, decomposers, ecosystem services, forest ecology, lichens, pathogens, Biodiversity, Ecosystem
Abstract

Hitherto fungi have rarely been considered in conservation biology, but this is changing as the field moves from addressing single species issues to an integrative ecosystem-based approach. The current emphasis on biodiversity as a provider of ecosystem services throws the spotlight on the vast diversity of fungi, their crucial roles in terrestrial ecosystems, and the benefits of considering fungi in concert with animals and plants. We reviewed the role of fungi in ecosystems and composed an overview of the current state of conservation of fungi. There are 5 areas in which fungi can be readily integrated into conservation: as providers of habitats and processes important for other organisms; as indicators of desired or undesired trends in ecosystem functioning; as indicators of habitats of conservation value; as providers of powerful links between human societies and the natural world because of their value as food, medicine, and biotechnological tools; and as sources of novel tools and approaches for conservation of megadiverse organism groups. We hope conservation professionals will value the potential of fungi, engage mycologists in their work, and appreciate the crucial role of fungi in nature.

Published
2014

47. 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, Luecking, 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, Regis, Young, Anthony, Binder, Manfred, Minnis, Andrew M., Lindner, Daniel L., Ortiz-Santana, Beatriz, Haight, John, Læssøe, Thomas, Baroni, Timothy J., Geml, Jozsef, Hattori, Tsutomu, 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, Luecking, 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, Regis, Young, Anthony, Binder, Manfred, Minnis, Andrew M., Lindner, Daniel L., Ortiz-Santana, Beatriz, Haight, John, Læssøe, Thomas, Baroni, Timothy J., Geml, Jozsef, and Hattori, Tsutomu

Published
2014

48. A fungal perspective on conservation biology

Author

Heilmann‐Clausen, Jacob, primary, Barron, Elizabeth S., additional, Boddy, Lynne, additional, Dahlberg, Anders, additional, Griffith, Gareth W., additional, Nordén, Jenni, additional, Ovaskainen, Otso, additional, Perini, Claudia, additional, Senn‐Irlet, Beatrice, additional, and Halme, Panu, additional

Published
2014
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49. Anaerobic fungi (phylumNeocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential

Author

Gruninger, Robert J., primary, Puniya, Anil K., additional, Callaghan, Tony M., additional, Edwards, Joan E., additional, Youssef, Noha, additional, Dagar, Sumit S., additional, Fliegerova, Katerina, additional, Griffith, Gareth W., additional, Forster, Robert, additional, Tsang, Adrian, additional, McAllister, Tim, additional, and Elshahed, Mostafa S., additional

Published
2014
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50. The ascomycota tree of life:a phylum-wide phylogeny clarifies the origin and evolutionof fundamental reproductive and ecological traits

Author

Schoch, Conrad L., Sung, Gi-Ho, López-Giráldez, Francesc, Townsend, Jeffrey P., Miadlikowska, Jolanta, Hoffstetter, Valérie, Robbertse, Barbara, Matheny, P. Brandon, Kauff, Frank, Wang, Zheng, Gueidan, Cécile, Andrie, Rachael M., Trippe, Kristin, Ciufetti, Linda M., Wynns, Anja Amtoft, Fraker, Emily, Hodkinson, Brendan P., Bonito, Gregory, Groenewald, Johannes Z., Arzanlou, Mahdi, Hoog, G. Sybren de, Crous, Pedro W., Hewitt, David, Pfister, Donald H., Peterson, Kristin, Grysenhout, 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, Francois Lutzoni, Spatafora, Joseph W., Schoch, Conrad L., Sung, Gi-Ho, López-Giráldez, Francesc, Townsend, Jeffrey P., Miadlikowska, Jolanta, Hoffstetter, Valérie, Robbertse, Barbara, Matheny, P. Brandon, Kauff, Frank, Wang, Zheng, Gueidan, Cécile, Andrie, Rachael M., Trippe, Kristin, Ciufetti, Linda M., Wynns, Anja Amtoft, Fraker, Emily, Hodkinson, Brendan P., Bonito, Gregory, Groenewald, Johannes Z., Arzanlou, Mahdi, Hoog, G. Sybren de, Crous, Pedro W., Hewitt, David, Pfister, Donald H., Peterson, Kristin, Grysenhout, 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, Francois Lutzoni, and Spatafora, Joseph W.

Published
2009

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