97 results on '"Griffith, GW"'
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2. Chapter 37 The intangible made tangible in Wales
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Young, Einir M., Griffith, Gwenan H., Evans, Marc, and Jones, S. Arwel
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Cultural Heritage ,ICH ,museum studies ,museums ,identity ,folklore ,cultural studies ,community ,place ,intellectual property ,UNESCO-ICH ,2003 Convention ,cultural tradition ,bic Book Industry Communication::H Humanities::HD Archaeology - Abstract
This collection provides an in-depth and up-to-date examination of the concept of Intangible Cultural Heritage and the issues surrounding its value to society. Critically engaging with the UNESCO 2003 Convention for the Safeguarding of the Intangible Cultural Heritage, the book also discusses local-level conceptualizations of living cultural traditions, practices and expressions, and reflects on the efforts that seek to safeguard them. Exploring a global range of case studies, the book considers the diverse perspectives currently involved with intangible cultural heritage and presents a rich picture of the geographic, socioeconomic and political contexts impacting research in this area. With contributions from established and emerging scholars, public servants, professionals, students and community members, this volume is also deeply enhanced by an interdisciplinary approach which draws on the theories and practices of heritage and museum studies, anthropology, folklore studies, ethnomusicology, and the study of cultural policy and related law. The Routledge Companion to Intangible Cultural Heritage undoubtedly broadens the international heritage discourse and is an invaluable learning tool for instructors, students and practitioners in the field.
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- 2017
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3. Airborne DNA reveals predictable spatial and seasonal dynamics of fungi.
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Abrego N, Furneaux B, Hardwick B, Somervuo P, Palorinne I, Aguilar-Trigueros CA, Andrew NR, Babiy UV, Bao T, Bazzano G, Bondarchuk SN, Bonebrake TC, Brennan GL, Bret-Harte S, Bässler C, Cagnolo L, Cameron EK, Chapurlat E, Creer S, D'Acqui LP, de Vere N, Desprez-Loustau ML, Dongmo MAK, Jacobsen IBD, Fisher BL, Flores de Jesus M, Gilbert GS, Griffith GW, Gritsuk AA, Gross A, Grudd H, Halme P, Hanna R, Hansen J, Hansen LH, Hegbe ADMT, Hill S, Hogg ID, Hultman J, Hyde KD, Hynson NA, Ivanova N, Karisto P, Kerdraon D, Knorre A, Krisai-Greilhuber I, Kurhinen J, Kuzmina M, Lecomte N, Lecomte E, Loaiza V, Lundin E, Meire A, Mešić A, Miettinen O, Monkhouse N, Mortimer P, Müller J, Nilsson RH, Nonti PYC, Nordén J, Nordén B, Norros V, Paz C, Pellikka P, Pereira D, Petch G, Pitkänen JM, Popa F, Potter C, Purhonen J, Pätsi S, Rafiq A, Raharinjanahary D, Rakos N, Rathnayaka AR, Raundrup K, Rebriev YA, Rikkinen J, Rogers HMK, Rogovsky A, Rozhkov Y, Runnel K, Saarto A, Savchenko A, Schlegel M, Schmidt NM, Seibold S, Skjøth C, Stengel E, Sutyrina SV, Syvänperä I, Tedersoo L, Timm J, Tipton L, Toju H, Uscka-Perzanowska M, van der Bank M, van der Bank FH, Vandenbrink B, Ventura S, Vignisson SR, Wang X, Weisser WW, Wijesinghe SN, Wright SJ, Yang C, Yorou NS, Young A, Yu DW, Zakharov EV, Hebert PDN, Roslin T, and Ovaskainen O
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- Mycorrhizae genetics, Mycorrhizae classification, Mycorrhizae isolation & purification, Phylogeny, Spores, Fungal classification, Spores, Fungal isolation & purification, Temperature, Tropical Climate, Geographic Mapping, Air Microbiology, Biodiversity, DNA, Fungal analysis, DNA, Fungal genetics, Fungi genetics, Fungi classification, Fungi isolation & purification, Seasons, Spatio-Temporal Analysis
- Abstract
Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions
1,2 . To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores3 . The vast majority of operational taxonomic units were detected within only one climatic zone, and the spatiotemporal patterns of species richness and community composition were mostly explained by annual mean air temperature. Tropical regions hosted the highest fungal diversity except for lichenized, ericoid mycorrhizal and ectomycorrhizal fungi, which reached their peak diversity in temperate regions. The sensitivity in climatic responses was associated with phylogenetic relatedness, suggesting that large-scale distributions of some fungal groups are partially constrained by their ancestral niche. There was a strong phylogenetic signal in seasonal sensitivity, suggesting that some groups of fungi have retained their ancestral trait of sporulating for only a short period. Overall, our results show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude. Our study reports patterns resembling those described for other major groups of organisms, thus making a major contribution to the long-standing debate on whether organisms with a microbial lifestyle follow the global biodiversity paradigms known for macroorganisms4,5 ., (© 2024. The Author(s).)- Published
- 2024
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4. Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA.
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Ovaskainen O, Abrego N, Furneaux B, Hardwick B, Somervuo P, Palorinne I, Andrew NR, Babiy UV, Bao T, Bazzano G, Bondarchuk SN, Bonebrake TC, Brennan GL, Bret-Harte S, Bässler C, Cagnolo L, Cameron EK, Chapurlat E, Creer S, D'Acqui LP, de Vere N, Desprez-Loustau ML, Dongmo MAK, Dyrholm Jacobsen IB, Fisher BL, Flores de Jesus M, Gilbert GS, Griffith GW, Gritsuk AA, Gross A, Grudd H, Halme P, Hanna R, Hansen J, Hansen LH, Hegbe ADMT, Hill S, Hogg ID, Hultman J, Hyde KD, Hynson NA, Ivanova N, Karisto P, Kerdraon D, Knorre A, Krisai-Greilhuber I, Kurhinen J, Kuzmina M, Lecomte N, Lecomte E, Loaiza V, Lundin E, Meire A, Mešić A, Miettinen O, Monkhause N, Mortimer P, Müller J, Nilsson RH, Nonti PYC, Nordén J, Nordén B, Paz C, Pellikka P, Pereira D, Petch G, Pitkänen JM, Popa F, Potter C, Purhonen J, Pätsi S, Rafiq A, Raharinjanahary D, Rakos N, Rathnayaka AR, Raundrup K, Rebriev YA, Rikkinen J, Rogers HMK, Rogovsky A, Rozhkov Y, Runnel K, Saarto A, Savchenko A, Schlegel M, Schmidt NM, Seibold S, Skjøth C, Stengel E, Sutyrina SV, Syvänperä I, Tedersoo L, Timm J, Tipton L, Toju H, Uscka-Perzanowska M, van der Bank M, Herman van der Bank F, Vandenbrink B, Ventura S, Vignisson SR, Wang X, Weisser WW, Wijesinghe SN, Joseph Wright S, Yang C, Yorou NS, Young A, Yu DW, Zakharov EV, Hebert PDN, and Roslin T
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- Fungi genetics, Fungi classification, Biodiversity, Air Microbiology, Spores, Fungal, DNA, Fungal analysis
- 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., (© 2024. The Author(s).)- Published
- 2024
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5. Editorial: Rising stars in systems microbiology: 2021.
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Puniya AK, Griffith GW, and Ungerfeld EM
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Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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- 2023
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6. Portable HEPA filtration successfully augments natural-ventilation-mediated airborne particle clearance in a legacy design hospital ward.
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Fennelly M, Hellebust S, Wenger J, O'Connor D, Griffith GW, Plant BJ, and Prentice MB
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- Humans, Respiratory Aerosols and Droplets, Hospitals, Ventilation, Infection Control, Filtration, COVID-19 prevention & control, Air Pollution, Indoor analysis
- Abstract
As the severe acute respiratory syndrome coronavirus-2 pandemic has proceeded, ventilation has been recognized increasingly as an important tool in infection control. Many hospitals in Ireland and the UK do not have mechanical ventilation and depend on natural ventilation. The effectiveness of natural ventilation varies with atmospheric conditions and building design. In a challenge test of a legacy design ward, this study showed that portable air filtration significantly increased the clearance of pollutant aerosols of respirable size compared with natural ventilation, and reduced spatial variation in particle persistence. A combination of natural ventilation and portable air filtration is significantly more effective for particle clearance than either intervention alone., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
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- 2023
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7. Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats.
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Joshi A, Young D, Huang L, Mosberger L, Munk B, Vinzelj J, Flad V, Sczyrba A, Griffith GW, Podmirseg SM, Warthmann R, Lebuhn M, and Insam H
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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.
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- 2022
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8. Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages.
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Young D, Joshi A, Huang L, Munk B, Wurzbacher C, Youssef NH, Elshahed MS, Moon CD, Ochsenreither K, Griffith GW, Callaghan TM, Sczyrba A, Lebuhn M, and Flad V
- 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).
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- 2022
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9. Characterization and rank assignment criteria for the anaerobic fungi (Neocallimastigomycota).
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Elshahed MS, Hanafy RA, Cheng Y, Dagar SS, Edwards JE, Flad V, Fliegerová KO, Griffith GW, Kittelmann S, Lebuhn M, O'Malley MA, Podmirseg SM, Solomon KV, Vinzelj J, Young D, and Youssef NH
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- Anaerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Fungi genetics, Phylogeny, RNA, Ribosomal, 16S genetics, Reproducibility of Results, Sequence Analysis, DNA, Neocallimastigomycota
- Abstract
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.
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- 2022
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10. Taxonomy of the anaerobic gut fungi ( Neocallimastigomycota ): a review of classification criteria and description of current taxa.
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Hanafy RA, Dagar SS, Griffith GW, Pratt CJ, Youssef NH, and Elshahed MS
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- Anaerobiosis, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Fungi genetics, Mammals, Phylogeny, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Neocallimastigomycota
- Abstract
Members of the anaerobic gut fungi ( Neocallimastigomycota ) reside in the rumen and alimentary tract of larger mammalian and some reptilian, marsupial and avian herbivores. The recent decade has witnessed a significant expansion in the number of described Neocallimastigomycota genera and species. However, the difficulties associated with the isolation and maintenance of Neocallimastigomycota strains has greatly complicated comparative studies to resolve inter- and intra-genus relationships. Here, we provide an updated outline of Neocallimastigomycota taxonomy. We critically evaluate various morphological, microscopic and phylogenetic traits previously and currently utilized in Neocallimastigomycota taxonomy, and provide an updated key for quick characterization of all genera. We then synthesize data from taxa description manuscripts, prior comparative efforts and molecular sequence data to present an updated list of Neocallimastigomycota genera and species, with an emphasis on resolving relationships and identifying synonymy between recent and historic strains. We supplement data from published manuscripts with information and illustrations from strains in the authors' collections. Twenty genera and 36 species are recognized, but the status of 10 species in the genera Caecomyces, Piromyces , Anaeromyces and Cyllamyces remains uncertain due to the unavailability of culture and conferre ( cf .) strains, lack of sequence data, and/or inadequacy of available microscopic and phenotypic data. Six cases of synonymy are identified in the genera Neocallimastix and Caecomyces , and two names in the genus Piromyces are rejected based on apparent misclassification.
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- 2022
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11. Earthworm-Collembola interactions affecting water-soluble nutrients, fauna and physiochemistry in a mesocosm manure-straw composting experiment.
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Jacques RG, Allison G, Shaw P, Griffith GW, and Scullion J
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- Animals, Manure, Nutrients, Soil, Water, Composting, Oligochaeta
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A mesocosm fermentation experiment was undertaken to investigate interactions between Eisenia fetida and Collembola affecting composting processes. Earthworms, Collembola, respiration, water soluble nutrients and compost characteristics (near infrared spectra - NIRS) were monitored on four occasions over 136 days. Earthworms were the main drivers of early changes in composts, increasing the general abundance of Collembola, although responses varied with species. Earthworms accelerated substrate mineralisation and release of soluble nutrients whilst also changing compost characteristics. Collembola alone had little direct effect on soluble nutrient concentrations or respiration; they did however alter compost characteristics (NIR spectra). Earthworm-Collembola interactions affecting respiration and soluble nutrients were mainly antagonistic in the early stages of composting but synergistic in later stages. In the later stages of composting, the higher abundance of Collembola when combined with earthworms resulted in greater concentrations of soluble nitrate and phosphate. These findings emphasise the importance in vermicomposting practice of different invertebrate groups having access to feedstock at appropriate stages of the process. The high concentrations of soluble nutrients released during vermicomposting indicate the need for control measures to avoid off-site pollution and loss of this resource., (Copyright © 2021 Elsevier Ltd. All rights reserved.)
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- 2021
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12. Crystallicutis gen. nov. (Irpicaceae, Basidiomycota), including C. damiettensis sp. nov., found on Phoenix dactylifera (date palm) trunks in the Nile Delta of Egypt.
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El-Gharabawy HM, Leal-Dutra CA, and Griffith GW
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- DNA, Fungal genetics, Egypt, Phylogeny, Polyporales classification, Polyporales genetics, Species Specificity, Basidiomycota classification, Basidiomycota genetics, Phoeniceae microbiology
- Abstract
The taxonomy of Polyporales is complicated by the variability in key morphological characters across families and genera, now being gradually resolved through molecular phylogenetic analyses. Here a new resupinate species, Crystallicutis damiettensis sp. nov. found on the decayed trunks of date palm (Phoenix dactylifera) trees in the fruit orchards of the Nile Delta region of Egypt is reported. Multigene phylogenetic analyses based on ITS, LSU, EF1α, RPB1 and RPB2 loci place this species in Irpicaceae, and forming a distinct clade with Ceraceomyces serpens and several other hitherto unnamed taxa, which we also incorporate into a new genus Crystallicutis. We name two of these species, Crystallicutis huangshanensis sp. nov. and Crystallicutis rajchenbergii sp. nov. The distinctive feature of Crystallicutis gen. nov. is the presence of crystal-encrusted hyphae in the hymenium and subiculum. Basidiomes are usually honey-yellow with white margins but there is variability in the presence of clamp connections and cystidia, as noted for other genera within Irpicacae. C. damiettensis is hitherto consistently associated with date palms killed by the red palm weevil Rhynchophorus ferrugineus, a highly damaging and invasive pest, recently spread to the Mediterranean region. C. damiettensis causes rapid wood decay by a potentially unusual white-rot mechanism and may play a role in the damage caused by R. ferrugineus., (Copyright © 2021 British Mycological Society. Published by Elsevier Ltd. All rights reserved.)
- Published
- 2021
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13. Environmental DNA reveals links between abundance and composition of airborne grass pollen and respiratory health.
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Rowney FM, Brennan GL, Skjøth CA, Griffith GW, McInnes RN, Clewlow Y, Adams-Groom B, Barber A, de Vere N, Economou T, Hegarty M, Hanlon HM, Jones L, Kurganskiy A, Petch GM, Potter C, Rafiq AM, Warner A, Wheeler B, Osborne NJ, and Creer S
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- Allergens, Humans, Poaceae, Pollen, Asthma epidemiology, Asthma genetics, DNA, Environmental, Rhinitis, Allergic, Seasonal epidemiology
- Abstract
Grass (Poaceae) pollen is the most important outdoor aeroallergen,
1 exacerbating a range of respiratory conditions, including allergic asthma and rhinitis ("hay fever").2-5 Understanding the relationships between respiratory diseases and airborne grass pollen with a view to improving forecasting has broad public health and socioeconomic relevance. It is estimated that there are over 400 million people with allergic rhinitis6 and over 300 million with asthma, globally,7 often comorbidly.8 In the UK, allergic asthma has an annual cost of around US$ 2.8 billion (2017).9 The relative contributions of the >11,000 (worldwide) grass species (C. Osborne et al., 2011, Botany Conference, abstract) to respiratory health have been unresolved,10 as grass pollen cannot be readily discriminated using standard microscopy.11 Instead, here we used novel environmental DNA (eDNA) sampling and qPCR12-15 to measure the relative abundances of airborne pollen from common grass species during two grass pollen seasons (2016 and 2017) across the UK. We quantitatively demonstrate discrete spatiotemporal patterns in airborne grass pollen assemblages. Using a series of generalized additive models (GAMs), we explore the relationship between the incidences of airborne pollen and severe asthma exacerbations (sub-weekly) and prescribing rates of drugs for respiratory allergies (monthly). Our results indicate that a subset of grass species may have disproportionate influence on these population-scale respiratory health responses during peak grass pollen concentrations. The work demonstrates the need for sensitive and detailed biomonitoring of harmful aeroallergens in order to investigate and mitigate their impacts on human health., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2021
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14. Predicting the severity of the grass pollen season and the effect of climate change in Northwest Europe.
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Kurganskiy A, Creer S, de Vere N, Griffith GW, Osborne NJ, Wheeler BW, McInnes RN, Clewlow Y, Barber A, Brennan GL, Hanlon HM, Hegarty M, Potter C, Rowney F, Adams-Groom B, Petch GM, Pashley CH, Satchwell J, de Weger LA, Rasmussen K, Oliver G, Sindt C, Bruffaerts N, and Skjøth CA
- Abstract
Allergic rhinitis is an inflammation in the nose caused by overreaction of the immune system to allergens in the air. Managing allergic rhinitis symptoms is challenging and requires timely intervention. The following are major questions often posed by those with allergic rhinitis: How should I prepare for the forthcoming season? How will the season's severity develop over the years? No country yet provides clear guidance addressing these questions. We propose two previously unexplored approaches for forecasting the severity of the grass pollen season on the basis of statistical and mechanistic models. The results suggest annual severity is largely governed by preseasonal meteorological conditions. The mechanistic model suggests climate change will increase the season severity by up to 60%, in line with experimental chamber studies. These models can be used as forecasting tools for advising individuals with hay fever and health care professionals how to prepare for the grass pollen season., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)
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- 2021
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15. Early-diverging fungal phyla: taxonomy, species concept, ecology, distribution, anthropogenic impact, and novel phylogenetic proposals.
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Voigt K, James TY, Kirk PM, Santiago ALCMA, Waldman B, Griffith GW, Fu M, Radek R, Strassert JFH, Wurzbacher C, Jerônimo GH, Simmons DR, Seto K, Gentekaki E, Hurdeal VG, Hyde KD, Nguyen TTT, and Lee HB
- Abstract
The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa, has dramatically changed the classification system of early-diverging fungi over the past several decades. The number of phyla established for non-Dikarya fungi has increased from 2 to 17. However, to date, both the classification and phylogeny of the basal fungi are still unresolved. In this article, we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal phyla. We also provide information on the ecology and distribution in Mucoromycota and highlight the impact of chytrids on amphibian populations. Species concepts in Chytridiomycota , Aphelidiomycota , Rozellomycota , Neocallimastigomycota are discussed in this paper. To preserve the current application of the genus Nephridiophaga ( Chytridiomycota : Nephridiophagales ) , a new type species, Nephridiophaga blattellae , is proposed., (© The Author(s) 2021.)
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- 2021
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16. Seven new Neocallimastigomycota genera from wild, zoo-housed, and domesticated herbivores greatly expand the taxonomic diversity of the phylum.
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Hanafy RA, Lanjekar VB, Dhakephalkar PK, Callaghan TM, Dagar SS, Griffith GW, Elshahed MS, and Youssef NH
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- Anaerobiosis, Animals, DNA, Fungal genetics, DNA, Ribosomal genetics, Deer microbiology, Feces microbiology, Female, Goats microbiology, Horses microbiology, Male, Neocallimastigomycota isolation & purification, Sheep microbiology, Swine microbiology, Animals, Domestic microbiology, Animals, Wild microbiology, Animals, Zoo microbiology, Herbivory classification, Neocallimastigomycota classification, Neocallimastigomycota genetics, Phylogeny
- Abstract
We isolated and characterized 65 anaerobic gut fungal (AGF; Neocallimastigomycota) strains from fecal samples of five wild (W, axis deer, white-tailed deer, Boer goat, mouflon, and Nilgiri tahr), one zoo-housed (Z, zebra), and three domesticated (D, horse, sheep, and goat) herbivores in the US states of Texas (TX) and Oklahoma (OK), Wales (WA), and the Indian states of Kerala (KE) and Haryana (HA). Phylogenetic assessment using the D1-D2 regions of the large subunit (28S) rDNA and internal transcribed spacer 1 (ITS1) identified seven monophyletic clades that are distinct from all currently recognized AGF genera. All strains displayed monocentric thalli and produced exclusively or predominantly monoflagellate zoospores, with the exception of axis deer strains, which produced polyflagellate zoospores. Analysis of amplicon-based AGF diversity surveys indicated that zebra and horse strains are representatives of uncultured AL1 group, whereas domesticated goat and sheep strains are representatives of uncultured AL5 group, previously encountered in fecal and rumen samples of multiple herbivores. The other five lineages, all of which were isolated from wild herbivores, have not been previously encountered in such surveys. Our results significantly expand the genus-level diversity within the Neocallimastigomycota and strongly suggest that wild herbivores represent a yet-untapped reservoir of AGF diversity. We propose seven novel genera and eight novel Neocallimastigomycota species to comprise these strains, for which we propose the names Agriosomyces longus (mouflon and wild Boer goat), Aklioshbomyces papillarum (white-tailed deer), Capellomyces foraminis (wild Boar goat), and C. elongatus (domesticated goat), Ghazallomyces constrictus (axis deer), Joblinomyces apicalis (domesticated goat and sheep), Khoyollomyces ramosus (zebra-horse), and Tahromyces munnarensis (Nilgiri tahr).
- Published
- 2020
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17. Reclassification of Pterulaceae Corner (Basidiomycota: Agaricales) introducing the ant-associated genus Myrmecopterula gen. nov., Phaeopterula Henn. and the corticioid Radulomycetaceae fam. nov.
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Leal-Dutra CA, Griffith GW, Neves MA, McLaughlin DJ, McLaughlin EG, Clasen LA, and Dentinger BTM
- Abstract
Pterulaceae was formally proposed to group six coralloid and dimitic genera: Actiniceps (= Dimorphocystis) , Allantula , Deflexula , Parapterulicium , Pterula, and Pterulicium . Recent molecular studies have shown that some of the characters currently used in Pterulaceae do not distinguish the genera. Actiniceps and Parapterulicium have been removed, and a few other resupinate genera were added to the family. However, none of these studies intended to investigate the relationship between Pterulaceae genera. In this study, we generated 278 sequences from both newly collected and fungarium samples. Phylogenetic analyses supported with morphological data allowed a reclassification of Pterulaceae where we propose the introduction of Myrmecopterula gen. nov. and Radulomycetaceae fam. nov., the reintroduction of Phaeopterula , the synonymisation of Deflexula in Pterulicium, and 53 new combinations. Pterula is rendered polyphyletic requiring a reclassification; thus, it is split into Pterula , Myrmecopterula gen. nov., Pterulicium and Phaeopterula . Deflexula is recovered as paraphyletic alongside several Pterula species and Pterulicium, and is sunk into the latter genus. Phaeopterula is reintroduced to accommodate species with darker basidiomes. The neotropical Myrmecopterula gen. nov. forms a distinct clade adjacent to Pterula , and most members of this clade are associated with active or inactive attine ant nests. The resupinate genera Coronicium and Merulicium are recovered in a strongly supported clade close to Pterulicium . The other resupinate genera previously included in Pterulaceae , and which form basidiomes lacking cystidia and with monomitic hyphal structure ( Radulomyces , Radulotubus and Aphanobasidium ), are reclassified into Radulomycetaceae fam. nov. Allantula is still an enigmatic piece in this puzzle known only from the type specimen that requires molecular investigation. A key for the genera of Pterulaceae and Radulomycetaceae fam. nov. is also provided here., Competing Interests: Competing interestsThe authors declare that they have no competing interests., (© The Author(s) 2020.)
- Published
- 2020
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18. Variation in Soil Fungal Composition Associated with the Invasion of Stellera chamaejasme L. in Qinghai-Tibet Plateau Grassland.
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He W, Detheridge A, Liu Y, Wang L, Wei H, Griffith GW, Scullion J, and Wei Y
- Abstract
Stellera chamaejasme L. is the most problematic weed in China's grasslands. Its root exudates affect co-occurring plants and thus may also affect soil fungi. Soils (0-20 cm depth) on two adjacent sites, one invaded the other uninvaded, were compared for a range of physiochemical parameters and by DNA sequencing of fungal communities. At the invaded site, relationships between S. chamaejasme abundance, soil physiochemical factors, and fungal communities were further investigated to determine whether these relationships corroborated conclusions on the basis of site differences that could be translated into functional variation. Results showed that the invaded soils had lower N, P, organic matter, fungal alpha diversity, and relative abundance of arbuscular mycorrhizal fungi (AMF), but greater abundance of pathogenic fungi. Organic matter and P were the edaphic factors most strongly linked to site differences in total fungal communities. Within the invaded site, organic matter rather than S. chamaejasme cover was closely linked to total fungal composition. However, on this site, a number of fungal species that had various ecological functions and that differentiated the two sites were related to S. chamaejasme cover. This study indicates that lower fertility soils may be more susceptible to invasion by S. chamaejasme. Although the influence of S. chamaejasme on total fungal community composition was limited, there was evidence of effects on particular fungal species. Further research is needed to determine whether these effects influence S. chamaejasme invasiveness., Competing Interests: The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.
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- 2019
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19. Maternal versus artificial rearing shapes the rumen microbiome having minor long-term physiological implications.
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Belanche A, Yáñez-Ruiz DR, Detheridge AP, Griffith GW, Kingston-Smith AH, and Newbold CJ
- Subjects
- Animals, Diet veterinary, Female, Male, Weaning, Microbiota, Milk, Rumen microbiology, Sheep microbiology
- Abstract
Increasing productivity is a key target in ruminant science which requires better understanding of the rumen microbiota. This study investigated how maternal versus artificial rearing shapes the rumen microbiota using 24 sets of triplet lambs. Lambs within each sibling set were randomly assigned to natural rearing on the ewe (NN); ewe colostrum for 24 h followed by artificial milk feeding (NA); and colostrum alternative and artificial milk feeding (AA). Maternal colostrum feeding enhanced VFA production at weaning but not thereafter. At weaning, lambs reared on milk replacer had no rumen protozoa and lower microbial diversity, whereas natural rearing accelerated the rumen microbial development and facilitated the transition to solid diet. Differences in the rumen prokaryotic communities disappear later in life when all lambs were grouped on the same pasture up to 23 weeks of age. However, NN animals retained higher fungal diversity and abundances of Piromyces, Feramyces and Diplodiniinae protozoa as well as higher feed digestibility (+4%) and animal growth (+6.5%) during the grazing period. Nevertheless, no correlations were found between rumen microbiota and productive outcomes. These findings suggest that the early life nutritional intervention determine the initial rumen microbial community, but the persistence of these effects later in life is weak., (© 2019 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.)
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- 2019
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20. Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage.
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Murphy CL, Youssef NH, Hanafy RA, Couger MB, Stajich JE, Wang Y, Baker K, Dagar SS, Griffith GW, Farag IF, Callaghan TM, and Elshahed MS
- Subjects
- Animals, Biological Evolution, Cattle microbiology, Gastrointestinal Tract microbiology, Genome, Fungal, Goats microbiology, Neocallimastigomycota physiology, Sheep microbiology, Evolution, Molecular, Gastrointestinal Microbiome, Gene Transfer, Horizontal, Neocallimastigomycota genetics
- 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., (Copyright © 2019 American Society for Microbiology.)
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- 2019
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21. Temperate airborne grass pollen defined by spatio-temporal shifts in community composition.
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Brennan GL, Potter C, de Vere N, Griffith GW, Skjøth CA, Osborne NJ, Wheeler BW, McInnes RN, Clewlow Y, Barber A, Hanlon HM, Hegarty M, Jones L, Kurganskiy A, Rowney FM, Armitage C, Adams-Groom B, Ford CR, Petch GM, and Creer S
- Subjects
- Flowers, Humans, Poaceae, Seasons, Allergens, Pollen
- 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.
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- 2019
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22. A Multi-Kingdom Study Reveals the Plasticity of the Rumen Microbiota in Response to a Shift From Non-grazing to Grazing Diets in Sheep.
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Belanche A, Kingston-Smith AH, Griffith GW, and Newbold CJ
- 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.
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- 2019
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23. Genome Sequence Analysis of Two Pseudomonas putida Strains to Identify a 17-Hydroxylase Putatively Involved in Sparteine Degradation.
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Detheridge AP, Griffith GW, and Hopper DJ
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- Alkaloids genetics, Oxidoreductases Acting on CH-NH Group Donors genetics, Sequence Analysis methods, Sparteine analogs & derivatives, Whole Genome Sequencing methods, Bacterial Proteins genetics, Genome, Bacterial genetics, Pseudomonas putida genetics, Sparteine genetics, Steroid 17-alpha-Hydroxylase genetics
- Abstract
Two strains of Pseudomonas putida, Psp-LUP and Psp-SPAR, capable of growth on the quinolizidine alkaloids, lupanine and sparteine respectively, were studied here. We report the isolation of Psp-SPAR and the complete genome sequencing of both bacteria. Both were confirmed to belong to P. putida, Psp-LUP close to the type isolate of the species (NBRC14164
T ) and Psp-SPAR close to strains KT2440 and F1. Psp-SPAR did not grow on lupanine but did contain a gene encoding a putative quinolizidine-17-hydroxylase peptide which exhibited high similarity (76%identity) to the lupanine-17-hydroxylase characterised from Psp-LUP.- Published
- 2018
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24. Liebetanzomycespolymorphus gen. et sp. nov., a new anaerobic fungus (Neocallimastigomycota) isolated from the rumen of a goat.
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Joshi A, Lanjekar VB, Dhakephalkar PK, Callaghan TM, Griffith GW, and Dagar SS
- Abstract
An extended incubation strategy to culture slow growing members of anaerobic fungi resulted in the isolation of a novel anaerobic fungus from the rumen of a goat after 15 days. The novel genus, represented by type strain G1SC, showed filamentous monocentric thallus development and produced uniflagellate zoospores, hence, showing morphological similarity to the genera Piromyces , Buwchfawromyces , Oontomyces and Pecoramyces . However, strain G1SC showed genetic similarity to the genus Anaeromyces , which, though produces uniflagellate zoospore, also exhibits polycentric thallus development. Moreover, unlike Anaeromyces , strain G1SC did not show hyphal constrictions, instead produced a branched, determinate and anucleate rhizoidal system. This fungus also displayed extensive sporangial variations, both exogenous and endogenous type of development, short and long sporangiophores and produced septate sporangia. G1SC utilised various complex and simple substrates, including rice straw and wheat straw and produced H
2 , CO2 , formate, acetate, lactate, succinate and ethanol. Phylogenetic analysis, using internal transcribed spacer 1 (ITS1) and D1/D2 domain of large-subunit (LSU) rRNA locus, clearly showed a separate lineage for this strain, near Anaeromyces . The ITS1 based geographical distribution studies indicated detection of environmental sequences similar (93-96%) to this strain from cattle faeces. Based on morphological and molecular characterisation results of strain G1SC, we propose a novel anaerobic fungus Liebetanzomycespolymorphus gen. et sp. nov. , in the phylum Neocallimastigomycota .- Published
- 2018
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25. Isotopic evidence of biotrophy and unusual nitrogen nutrition in soil-dwelling Hygrophoraceae.
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Halbwachs H, Easton GL, Bol R, Hobbie EA, Garnett MH, Peršoh D, Dixon L, Ostle N, Karasch P, and Griffith GW
- Subjects
- Fruiting Bodies, Fungal metabolism, Mycorrhizae metabolism, Agaricales metabolism, Nitrogen metabolism, Soil Microbiology
- Abstract
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
15 N and low in13 C, the latter consistent with mycorrhizal nutritional status. Similar patterns were found in waxcap basidiocarps from diverse habitats across four continents. Additional data from14 C analysis of basidiocarps and13 C pulse label experiments suggest that these fungi are not saprotrophs but rather biotrophic endophytes and possibly mycorrhizal. The consistently high but variable δ15 N 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., (© 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.)- Published
- 2018
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26. Dose-dependent behavioural fever responses in desert locusts challenged with the entomopathogenic fungus Metarhizium acridum.
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Clancy LM, Jones R, Cooper AL, Griffith GW, and Santer RD
- Subjects
- Animals, Body Temperature physiology, Spores, Fungal physiology, Fever microbiology, Fever physiopathology, Grasshoppers microbiology, Grasshoppers physiology, Metarhizium physiology
- Abstract
Behavioural fever is a common response to immune challenge in ectotherms and confers survival benefits. However, costs accrue rapidly as body temperature rises. Thus, the magnitude of adaptive fever responses might reflect the balance of costs and benefits. We investigated behavioural fever in desert locusts, Schistocerca gregaria, infected with the entomopathogenic fungus Metarhizium acridum. We first tracked the time course of behavioural fever in infected locusts, demonstrating that body temperatures rose on the day following inoculation (day 1), and reached peak intensity on the day after that (day 2). Subsequently, the magnitude of fever responses varied during a day, and locusts tended to exhibit high-intensity fever responses in the mornings when basking was first possible. We speculate that this may have resulted from increased fungal load caused by unimpeded growth overnight when locusts could not fever. We next inoculated locusts with different M. acridum doses ranging from 0 to ca. 75,000 conidia. The magnitude of their behavioural fever responses on day 2 post-inoculation was positively related to fungal dose. Thus, we demonstrate dose-dependency in the behavioural fever responses of desert locusts and suggest that this may reflect the adaptive deployment of behavioural fever to minimize costs relative to benefits.
- Published
- 2018
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27. Reclassification of Parapterulicium Corner (Pterulaceae, Agaricales), contributions to Lachnocladiaceae and Peniophoraceae (Russulales) and introduction of Baltazaria gen. nov.
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Leal-Dutra CA, Neves MA, Griffith GW, Reck MA, Clasen LA, and Dentinger BTM
- Abstract
The genus Parapterulicium was first introduced to accommodate two Brazilian species of coralloid fungi with affinities to Pterulaceae (Agaricales). Despite the coralloid habit and the presence of skeletal hyphae, other features, notably the presence of gloeocystidia, dichophyses and papillate hyphal ends, differentiate this genus from Pterulaceae sensu stricto. Fieldwork in Brazil resulted in the rediscovery of two coralloid fungi identifiable as Parapterulicium , the first verified collections of this genus since Corner's original work in the 1950s. Molecular phylogenetic analyses of nrITS and nrLSU sequences from these modern specimens revealed affinities with the /peniophorales clade in the Russulales, rather than Pterulaceae. The presence of distinctive hyphal elements, homologous to the defining features of /peniophorales, is consistent with the phylogenetic evidence and thus clearly distinguished Parapterulicium and its type species P.subarbusculum from Pterulaceae, placing this genus within /peniophorales. Parapterulicium was also found to be polyphyletic so Baltazaria gen. nov. is proposed to accommodate P.octopodites , Scytinostromagalactinum , S.neogalactinum and S.eurasiaticogalactinum also within /peniophorales.
- Published
- 2018
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28. The use of extracellular DNA as a proxy for specific microbial activity.
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Nagler M, Podmirseg SM, Griffith GW, Insam H, and Ascher-Jenull J
- Subjects
- Aerobiosis, Anaerobiosis, Animals, Archaea genetics, Archaea metabolism, Bacteria genetics, Bacteria metabolism, Cluster Analysis, DNA, Bacterial genetics, DNA, Fungal chemistry, DNA, Fungal genetics, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, Environmental Microbiology, Fungi genetics, Fungi metabolism, Microbial Consortia, Phylogeny, RNA, Ribosomal, 28S genetics, Rumen microbiology, Sequence Analysis, DNA, Archaea growth & development, Bacteria growth & development, DNA, Archaeal analysis, DNA, Bacterial analysis, DNA, Fungal analysis, Fungi growth & development, Microbiological Techniques methods
- Abstract
The ubiquity and relevance of extracellular DNA (exDNA) are well-known and increasingly gaining importance in many fields of application such as medicine and environmental microbiology. Although sources and types of exDNA are manifold, ratios of specific DNA-molecules inside and outside of living cells can give reliable information about the activity of entire systems and of specific microbial groups or species. Here, we introduce a method to discriminate between internal (iDNA), as well as bound and free exDNA, and evaluate various DNA fractions and related ratios (ex:iDNA) regarding their applicability to be used as a fast, convenient, and reliable alternative to more tedious RNA-based activity measurements. In order to deal with microbial consortia that can be regulated regarding their activity, we tested and evaluated the proposed method in comparison to sophisticated dehydrogenase- and RNA-based activity measurements with two anaerobic microbial consortia (anaerobic fungi and syntrophic archaea and a microbial rumen consortium) and three levels of resolution (overall activity, total bacteria, methanogenic archaea). Furthermore, we introduce a 28S rRNA gene-specific primer set and qPCR protocol, targeting anaerobic fungi (Neocallimastigomycota). Our findings show that the amount of actively released free exDNA (fDNA) strongly correlates with different activity measurements and is thus suggested to serve as a proxy for microbial activity.
- Published
- 2018
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29. PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities.
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Edwards JE, Forster RJ, Callaghan TM, Dollhofer V, Dagar SS, Cheng Y, Chang J, Kittelmann S, Fliegerova K, Puniya AK, Henske JK, Gilmore SP, O'Malley MA, Griffith GW, and Smidt H
- 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, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.
- Published
- 2017
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30. Saprotrophic proteomes of biotypes of the witches' broom pathogen Moniliophthora perniciosa.
- Author
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Pierre S, Griffith GW, Morphew RM, Mur LAJ, and Scott IM
- Subjects
- Agaricales chemistry, Agaricales growth & development, Agaricales pathogenicity, Electrophoresis, Gel, Two-Dimensional, Fungal Proteins chemistry, Fungal Proteins genetics, Fungal Proteins isolation & purification, Multivariate Analysis, Mycelium chemistry, Mycological Typing Techniques, Spores, Fungal pathogenicity, Virulence, Agaricales classification, Cacao microbiology, Solanum lycopersicum microbiology, Proteome
- Abstract
Nine geographically diverse Moniliophthora perniciosa (witches' broom disease pathogen) isolates were cultured in vitro. They included six C-biotypes differing in virulence on cacao (Theobroma cacao), two S-biotypes (solanaceous hosts), and an L-biotype (liana hosts). Mycelial growth rates and morphologies differed considerably, but no characters were observed to correlate with virulence or biotype. In plant inoculations using basidiospores, one C-biotype caused symptoms on tomato (an S-biotype host), adding to evidence of limited host adaptation in these biotypes. Mycelial proteomes were analysed by two-dimensional gel electrophoresis (2-DE), and 619 gel spots were indexed on all replicate gels of at least one strain. Multivariate analysis of gel spots discriminated the L-biotype, but not the S-biotypes, from the remaining strains. The proteomic similarity of the S- and C-biotypes is consistent with their reported lack of phylogenetic distinction. Sequences from tandem mass spectrometry of tryptic peptides from major 2-DE spots were matched with Moniliophthora genome and transcript sequences on NCBI and WBD Transcriptome Atlas databases. Protein-spot identifications indicated that M. perniciosa saprotrophic mycelial proteomes expressed functions potentially connected with a 'virulence life-style', including peroxiredoxin, heat-shock proteins, nitrilase, formate dehydrogenase, a prominent complement of aldo-keto reductases, mannitol-1-phosphate dehydrogenase, and central metabolism enzymes with proposed pathogenesis functions., (Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.)
- Published
- 2017
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31. Increased Male-Male Mounting Behaviour in Desert Locusts during Infection with an Entomopathogenic Fungus.
- Author
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Clancy LM, Cooper AL, Griffith GW, and Santer RD
- Subjects
- Animals, Grasshoppers physiology, Host-Pathogen Interactions, Male, Grasshoppers microbiology, Metarhizium physiology, Sexual Behavior, Animal physiology
- Abstract
Same-sex sexual behaviour occurs across diverse animal taxa, but adaptive explanations can be difficult to determine. Here we investigate male-male mounting (MMM) behaviour in female-deprived desert locust males infected with the entomopathogenic fungus Metarhizium acridum. Over a four-week period, infected locusts performed more MMM behaviours than healthy controls. Among infected locusts, the probability of MMM, and the duration of time spent MMM, significantly increased with the mounting locust's proximity to death. In experimental trials, infected locusts were also significantly more likely than controls to attempt to mount healthy males. Therefore, we demonstrate that MMM is more frequent among infected than healthy male locusts, and propose that this may be explained by terminal reproductive effort and a lowered mate acceptance threshold in infected males. However, during experimental trials mounting attempts were more likely to be successful if the mounted locusts were experimentally manipulated to have a reduced capacity to escape. Thus, reduced escape capability resulting from infection may also contribute to the higher frequency of MMM among infected male locusts. Our data demonstrate that pathogen infection can affect same-sex sexual behaviour, and suggest that the impact of such behaviours on host and pathogen fitness will be a novel focus for future research.
- Published
- 2017
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32. Presence and transcriptional activity of anaerobic fungi in agricultural biogas plants.
- Author
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Dollhofer V, Callaghan TM, Griffith GW, Lebuhn M, and Bauer J
- Subjects
- Agriculture, Anaerobiosis, Fungi, Phylogeny, Biofuels microbiology, Bioreactors microbiology
- Abstract
Bioaugmentation with anaerobic fungi (AF) is promising for improved biogas generation from lignocelluloses-rich substrates. However, before implementing AF into biogas processes it is necessary to investigate their natural occurrence, community structure and transcriptional activity in agricultural biogas plants. Thus, AF were detected with three specific PCR based methods: (i) Copies of their 18S genes were found in 7 of 10 biogas plants. (ii) Transcripts of a GH5 endoglucanase gene were present at low level in two digesters, indicating transcriptional cellulolytic activity of AF. (iii) Phylogeny of the AF-community was inferred with the 28S gene. A new Piromyces species was isolated from a PCR-positive digester. Evidence for AF was only found in biogas plants operated with high proportions of animal feces. Thus, AF were most likely transferred into digesters with animal derived substrates. Additionally, high process temperatures in combination with long retention times seemed to impede AF survival and activity., (Copyright © 2017 Elsevier Ltd. All rights reserved.)
- Published
- 2017
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33. Pecoramyces ruminantium, gen. nov., sp. nov., an anaerobic gut fungus from the feces of cattle and sheep.
- Author
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Hanafy RA, Elshahed MS, Liggenstoffer AS, Griffith GW, and Youssef NH
- Subjects
- Animals, Cattle, DNA, Fungal genetics, DNA, Ribosomal genetics, DNA, Ribosomal Spacer genetics, Mycological Typing Techniques, Neocallimastigomycota cytology, Neocallimastigomycota genetics, Neocallimastigomycota ultrastructure, Phylogeny, Rumen microbiology, Sequence Analysis, DNA, Sheep, Sporangia ultrastructure, Spores, Fungal ultrastructure, Feces microbiology, Gastrointestinal Tract microbiology, Neocallimastigomycota classification
- Abstract
The anaerobic gut fungi (AGF) inhabit the rumen and alimentary tracts of multiple ruminant and nonruminant herbivores, belong to a distinct phylum-level lineage (Neocallimastigomycota), and play an important role in plant biomass degradation in many herbivores. As part of a wider effort to obtain AGF with high lignocellulolytic capacities, we isolated and characterized four different AGF strains from the feces of cattle and sheep. Microscopically, isolates produced monocentric thalli and monoflagellated zoospores. Phylogenetic analysis revealed that all isolates formed a monophyletic cluster with strong bootstrap support as a sister clade to the genus Orpinomyces and close to Neocallimastix, an unexpected result because these two genera of AGF form polyflagellated zoospores. Isolates displayed a smooth biofilm-like growth in liquid medium and formed small (0.5-1 mm) pinpoint circular colonies on agar roll tubes. Both endogenous and exogenous sporangia were observed with variable shapes and sizes. Zoospores were mainly spherical, with diameters ranging between 3.8 and 12.5 µm, and mostly a single flagellum. All strains exhibited similar substrate utilization patterns and comparable cellulolytic and xylanolytic activities. Similar ITS1 sequences falling within the same distinctive clade were found on GenBank, with all environmental samples obtained from diverse ruminant and pseudoruminant hosts from three continents, but not from any hindgut-fermenting hosts. Given the high level of sequence divergence between our strains and closest cultured representatives and their distinct microscopic/macroscopic features, we propose a new genus, Pecoramyces, from the name of the taxonomic infraorder Pecora ("horned ruminants" or "higher ruminants"; derived from the Latin word for horned livestock), and a new species, P. ruminantium (since occurrence seems to be specific to ruminant/pseudoruminant foregut, but not hindgut-fermenting mammals).
- Published
- 2017
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34. A new anaerobic fungus (Oontomyces anksri gen. nov., sp. nov.) from the digestive tract of the Indian camel (Camelus dromedarius).
- Author
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Dagar SS, Kumar S, Griffith GW, Edwards JE, Callaghan TM, Singh R, Nagpal AK, and Puniya AK
- Subjects
- Anaerobiosis, Animals, Cluster Analysis, DNA, Fungal chemistry, DNA, Fungal genetics, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, DNA, Ribosomal Spacer chemistry, DNA, Ribosomal Spacer genetics, Microscopy, Molecular Sequence Data, Neocallimastigales cytology, Neocallimastigales genetics, Phylogeny, RNA, Ribosomal genetics, Sequence Analysis, DNA, Camelus microbiology, Gastrointestinal Tract microbiology, Neocallimastigales classification, Neocallimastigales isolation & purification
- Abstract
Two cultures of anaerobic fungi were isolated from the forestomach of an Indian camel (Camelus dromedarius). Phylogenetic analysis using both the internal transcribed spacer (ITS) and large-subunit (LSU) regions of the rRNA locus demonstrated that these isolates were identical and formed a distinct clade within the anaerobic fungi (phylum Neocallimastigomycota). Morphological examination showed that these fungi formed monocentric thalli with filamentous rhizoids and uniflagellate zoospores, broadly similar to members of the genus Piromyces. However, distinctive morphological features were observed, notably the pinching of the cytoplasm in the sporangiophore and the formation of intercalary rhizoidal swellings. Since genetic analyses demonstrated this fungus was only distantly related to Piromyces spp. and closer to the polycentric Anaeromyces clade, we have assigned it to a new genus and species Oontomyces anksri gen. nov., sp. nov. Interrogation of the GenBank database identified several closely related ITS sequences, which were all environmental sequences obtained from camels, raising the possibility that this fungus may be specific to camelids., (Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.)
- Published
- 2015
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35. A fungal perspective on conservation biology.
- Author
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Heilmann-Clausen J, Barron ES, Boddy L, Dahlberg A, Griffith GW, Nordén J, Ovaskainen O, Perini C, Senn-Irlet B, and Halme P
- Subjects
- Biodiversity, Ecosystem, Conservation of Natural Resources, Fungi physiology
- 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., (© 2014 Society for Conservation Biology.)
- Published
- 2015
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36. Anaerobic Fungi and Their Potential for Biogas Production.
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Dollhofer V, Podmirseg SM, Callaghan TM, Griffith GW, and Fliegerová K
- Subjects
- Anaerobiosis, Fungi classification, Biofuels, Fungi metabolism
- Abstract
Plant biomass is the largest reservoir of environmentally friendly renewable energy on earth. However, the complex and recalcitrant structure of these lignocellulose-rich substrates is a severe limitation for biogas production. Microbial pro-ventricular anaerobic digestion of ruminants can serve as a model for improvement of converting lignocellulosic biomass into energy. Anaerobic fungi are key players in the digestive system of various animals, they produce a plethora of plant carbohydrate hydrolysing enzymes. Combined with the invasive growth of their rhizoid system their contribution to cell wall polysaccharide decomposition may greatly exceed that of bacteria. The cellulolytic arsenal of anaerobic fungi consists of both secreted enzymes, as well as extracellular multi-enzyme complexes called cellulosomes. These complexes are extremely active, can degrade both amorphous and crystalline cellulose and are probably the main reason of cellulolytic efficiency of anaerobic fungi. The synergistic use of mechanical and enzymatic degradation makes anaerobic fungi promising candidates to improve biogas production from recalcitrant biomass. This chapter presents an overview about their biology and their potential for implementation in the biogas process.
- Published
- 2015
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37. Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential.
- Author
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Gruninger RJ, Puniya AK, Callaghan TM, Edwards JE, Youssef N, Dagar SS, Fliegerova K, Griffith GW, Forster R, Tsang A, McAllister T, and Elshahed MS
- Subjects
- Animals, Biotechnology, Ecological and Environmental Phenomena, Gastrointestinal Tract microbiology, Genome, Fungal, Neocallimastigomycota classification, Neocallimastigomycota enzymology, Neocallimastigomycota growth & development, Proteomics, Rumen microbiology, Neocallimastigomycota physiology
- Abstract
Anaerobic fungi (phylum Neocallimastigomycota) inhabit the gastrointestinal tract of mammalian herbivores, where they play an important role in the degradation of plant material. The Neocallimastigomycota represent the earliest diverging lineage of the zoosporic fungi; however, understanding of the relationships of the different taxa (both genera and species) within this phylum is in need of revision. Issues exist with the current approaches used for their identification and classification, and recent evidence suggests the presence of several novel taxa (potential candidate genera) that remain to be characterised. The life cycle and role of anaerobic fungi has been well characterised in the rumen, but not elsewhere in the ruminant alimentary tract. Greater understanding of the 'resistant' phase(s) of their life cycle is needed, as is study of their role and significance in other herbivores. Biotechnological application of anaerobic fungi, and their highly active cellulolytic and hemi-cellulolytic enzymes, has been a rapidly increasing area of research and development in the last decade. The move towards understanding of anaerobic fungi using -omics based (genomic, transcriptomic and proteomic) approaches is starting to yield valuable insights into the unique cellular processes, evolutionary history, metabolic capabilities and adaptations that exist within the Neocallimastigomycota., (© 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.)
- Published
- 2014
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38. Coupled cryoconite ecosystem structure-function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciers.
- Author
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Edwards A, Mur LA, Girdwood SE, Anesio AM, Stibal M, Rassner SM, Hell K, Pachebat JA, Post B, Bussell JS, Cameron SJ, Griffith GW, Hodson AJ, and Sattler B
- Subjects
- Arctic Regions, Austria, Biodiversity, Cyanobacteria metabolism, Geologic Sediments microbiology, Greenland, High-Throughput Nucleotide Sequencing, Polymorphism, Restriction Fragment Length, Proteobacteria metabolism, Sequence Analysis, DNA, Spectroscopy, Fourier Transform Infrared, Svalbard, Cyanobacteria genetics, Ice Cover microbiology, Proteobacteria genetics
- Abstract
Cryoconite holes are known as foci of microbial diversity and activity on polar glacier surfaces, but are virtually unexplored microbial habitats in alpine regions. In addition, whether cryoconite community structure reflects ecosystem functionality is poorly understood. Terminal restriction fragment length polymorphism and Fourier transform infrared metabolite fingerprinting of cryoconite from glaciers in Austria, Greenland and Svalbard demonstrated cryoconite bacterial communities are closely correlated with cognate metabolite fingerprints. The influence of bacterial-associated fatty acids and polysaccharides was inferred, underlining the importance of bacterial community structure in the properties of cryoconite. Thus, combined application of T-RFLP and FT-IR metabolite fingerprinting promises high throughput, and hence, rapid assessment of community structure-function relationships. Pyrosequencing revealed Proteobacteria were particularly abundant, with Cyanobacteria likely acting as ecosystem engineers in both alpine and Arctic cryoconite communities. However, despite these generalities, significant differences in bacterial community structures, compositions and metabolomes are found between alpine and Arctic cryoconite habitats, reflecting the impact of local and regional conditions on the challenges of thriving in glacial ecosystems., (© 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.)
- Published
- 2014
- Full Text
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39. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.
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Schoch CL, Robbertse B, Robert V, Vu D, Cardinali G, Irinyi L, Meyer W, Nilsson RH, Hughes K, Miller AN, Kirk PM, Abarenkov K, Aime MC, Ariyawansa HA, Bidartondo M, Boekhout T, Buyck B, Cai Q, Chen J, Crespo A, Crous PW, Damm U, De Beer ZW, Dentinger BT, Divakar PK, Dueñas M, Feau N, Fliegerova K, García MA, Ge ZW, Griffith GW, Groenewald JZ, Groenewald M, Grube M, Gryzenhout M, Gueidan C, Guo L, Hambleton S, Hamelin R, Hansen K, Hofstetter V, Hong SB, Houbraken J, Hyde KD, Inderbitzin P, Johnston PR, Karunarathna SC, Kõljalg U, Kovács GM, Kraichak E, Krizsan K, Kurtzman CP, Larsson KH, Leavitt S, Letcher PM, Liimatainen K, Liu JK, Lodge DJ, Luangsa-ard JJ, Lumbsch HT, Maharachchikumbura SS, Manamgoda D, Martín MP, Minnis AM, Moncalvo JM, Mulè G, Nakasone KK, Niskanen T, Olariaga I, Papp T, Petkovits T, Pino-Bodas R, Powell MJ, Raja HA, Redecker D, Sarmiento-Ramirez JM, Seifert KA, Shrestha B, Stenroos S, Stielow B, Suh SO, Tanaka K, Tedersoo L, Telleria MT, Udayanga D, Untereiner WA, Diéguez Uribeondo J, Subbarao KV, Vágvölgyi C, Visagie C, Voigt K, Walker DM, Weir BS, Weiß M, Wijayawardene NN, Wingfield MJ, Xu JP, Yang ZL, Zhang N, Zhuang WY, and Federhen S
- Subjects
- Cluster Analysis, DNA, Fungal, DNA, Intergenic, Genes, Fungal, Databases, Genetic, Fungi classification, Fungi genetics, Molecular Sequence Annotation methods, Sequence Analysis, DNA
- Abstract
DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353., (Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US.)
- Published
- 2014
- Full Text
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40. New aspects and strategies for methane mitigation from ruminants.
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Kumar S, Choudhury PK, Carro MD, Griffith GW, Dagar SS, Puniya M, Calabro S, Ravella SR, Dhewa T, Upadhyay RC, Sirohi SK, Kundu SS, Wanapat M, and Puniya AK
- Subjects
- Animals, Methane antagonists & inhibitors, Methane metabolism, Ruminants physiology
- Abstract
The growing demand for sustainable animal production is compelling researchers to explore the potential approaches to reduce emissions of greenhouse gases from livestock that are mainly produced by enteric fermentation. Some potential solutions, for instance, the use of chemical inhibitors to reduce methanogenesis, are not feasible in routine use due to their toxicity to ruminants, inhibition of efficient rumen function or other transitory effects. Strategies, such as use of plant secondary metabolites and dietary manipulations have emerged to reduce the methane emission, but these still require extensive research before these can be recommended and deployed in the livestock industry sector. Furthermore, immunization vaccines for methanogens and phages are also under investigation for mitigation of enteric methanogenesis. The increasing knowledge of methanogenic diversity in rumen, DNA sequencing technologies and bioinformatics have paved the way for chemogenomic strategies by targeting methane producers. Chemogenomics will help in finding target enzymes and proteins, which will further assist in the screening of natural as well chemical inhibitors. The construction of a methanogenic gene catalogue through these approaches is an attainable objective. This will lead to understand the microbiome function, its relation with the host and feeds, and therefore, will form the basis of practically viable and eco-friendly methane mitigation approaches, while improving the ruminant productivity.
- Published
- 2014
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- View/download PDF
41. Towards a unified paradigm for sequence-based identification of fungi.
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Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AF, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiss M, and Larsson KH
- Subjects
- DNA Barcoding, Taxonomic, DNA, Fungal genetics, DNA, Ribosomal Spacer genetics, Fungi genetics, Internet, Databases, Nucleic Acid, Fungi classification, Phylogeny
- Abstract
The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE., (© 2013 John Wiley & Sons Ltd.)
- Published
- 2013
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42. Above- and below-ground responses of Calamagrostis purpurea to UV-B radiation and elevated CO₂ under phosphorus limitation.
- Author
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Bussell JS, Gwynn-Jones D, Griffith GW, and Scullion J
- Subjects
- Biomass, Poaceae metabolism, Poaceae physiology, Carbon Dioxide metabolism, Phosphorus metabolism, Poaceae radiation effects, Ultraviolet Rays
- Abstract
UV-B radiation and elevated CO₂ may impact rhizosphere processes through altered below-ground plant resource allocation and root exudation, changes that may have implications for nutrient acquisition. As nutrients limit plant growth in many habitats, their supply may dictate plant response under elevated CO₂. This study investigated UV-B exposure and elevated CO₂ effects, including interactions, on plant growth, tissue chemistry and rooting responses relating to P acquisition. The sub-arctic grass Calamagrostis purpurea was subjected to UV-B (0 or 3.04 kJ m⁻² day⁻¹) and CO₂ (ambient 380 or 650 ppmv) treatments in a factorial glasshouse experiment, with sparingly soluble P (0 or 0.152 mg P per plant as FePO₄) a further factor. It was hypothesized that UV-B exposure and elevated CO₂would change plant resource allocation, with CO₂ mitigating adverse responses to UV-B exposure and aiding P uptake. Plant biomass and morphology, tissue composition and rhizosphere leachate properties were measured. UV-B directly affected chemical composition of shoots and interacted with CO₂ to give a greater root biomass. Elevated CO₂ altered the composition of both shoots and roots and increased shoot biomass and secondary root length, while leachate pH decreased. Below-ground responses to CO₂ did not affect P acquisition although P limitation progressively reduced leachate pH and increased secondary root length. Although direct plant growth, foliar composition and below-ground nutrient acquisition responses were dominated by CO₂ treatments, UV-B modified these CO₂ responses significantly. These interactions have implications for plant responses to future atmospheric conditions., (Copyright © Physiologia Plantarum 2012.)
- Published
- 2012
- Full Text
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43. Genome-wide analysis of longevity in nutrient-deprived Saccharomyces cerevisiae reveals importance of recycling in maintaining cell viability.
- Author
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Davey HM, Cross EJ, Davey CL, Gkargkas K, Delneri D, Hoyle DC, Oliver SG, Kell DB, and Griffith GW
- Subjects
- Autophagy genetics, Cell Survival genetics, Environment, Genome-Wide Association Study, Models, Biological, Phenotype, Saccharomyces cerevisiae genetics, Saccharomyces cerevisiae growth & development, Saccharomyces cerevisiae metabolism, Saccharomyces cerevisiae Proteins genetics, Genome, Fungal genetics, Saccharomyces cerevisiae physiology
- Abstract
Although typically cosseted in the laboratory with constant temperatures and plentiful nutrients, microbes are frequently exposed to much more stressful conditions in their natural environments where survival and competitive fitness depend upon both growth rate when conditions are favourable and on persistence in a viable and recoverable state when they are not. In order to determine the role of genetic heterogeneity in environmental fitness we present a novel approach that combines the power of fluorescence-activated cell sorting with barcode microarray analysis and apply this to determining the importance of every gene in the Saccharomyces cerevisiae genome in a high-throughput, genome-wide fitness screen. We have grown > 6000 heterozygous mutants together and exposed them to a starvation stress before using fluorescence-activated cell sorting to identify and isolate those individual cells that have not survived the stress applied. Barcode array analysis of the sorted and total populations reveals the importance of cellular recycling mechanisms (autophagy, pexophagy and ribosome breakdown) in maintaining cell viability during starvation and provides compelling evidence for an important role for fatty acid degradation in maintaining viability. In addition, we have developed a semi-batch fermentor system that is a more realistic model of environmental fitness than either batch or chemostat culture. Barcode array analysis revealed that arginine biosynthesis was important for fitness in semi-batch culture and modelling of this regime showed that rapid emergence from lag phase led to greatly increased fitness. One hundred and twenty-five strains with deletions in unclassified proteins were identified as being over-represented in the sorted fraction, while 27 unclassified proteins caused a haploinsufficient phenotype in semi-batch culture. These methods thus provide a screen to identifying other genes and pathways that have a role in maintaining cell viability., (© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.)
- Published
- 2012
- Full Text
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44. Do we need a global strategy for microbial conservation?
- Author
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Griffith GW
- Subjects
- Conservation of Natural Resources, International Cooperation, Microbiology
- Published
- 2012
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45. Enumeration of methanogens with a focus on fluorescence in situ hybridization.
- Author
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Kumar S, Dagar SS, Mohanty AK, Sirohi SK, Puniya M, Kuhad RC, Sangu KP, Griffith GW, and Puniya AK
- Subjects
- Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction, RNA, Ribosomal, 16S genetics, Ribonuclease H metabolism, Archaea physiology, In Situ Hybridization, Fluorescence, Microbiological Techniques methods
- Abstract
Methanogens, the members of domain Archaea are potent contributors in global warming. Being confined to the strict anaerobic environment, their direct cultivation as pure culture is quite difficult. Therefore, a range of culture-independent methods have been developed to investigate their numbers, substrate uptake patterns, and identification in complex microbial communities. Unlike other approaches, fluorescence in situ hybridization (FISH) is not only used for faster quantification and accurate identification but also to reveal the physiological properties and spatiotemporal dynamics of methanogens in their natural environment. Aside from the methodological aspects and application of FISH, this review also focuses on culture-dependent and -independent techniques employed in enumerating methanogens along with associated problems. In addition, the combination of FISH with micro-autoradiography that could also be an important tool in investigating the activities of methanogens is also discussed.
- Published
- 2011
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46. Possible interactions between bacterial diversity, microbial activity and supraglacial hydrology of cryoconite holes in Svalbard.
- Author
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Edwards A, Anesio AM, Rassner SM, Sattler B, Hubbard B, Perkins WT, Young M, and Griffith GW
- Subjects
- Arctic Regions, Geologic Sediments chemistry, Geologic Sediments microbiology, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S genetics, Svalbard, Bacteria classification, Bacteria genetics, Bacteria metabolism, Biodiversity, Ice Cover microbiology, Water Cycle
- Abstract
The diversity of highly active bacterial communities in cryoconite holes on three Arctic glaciers in Svalbard was investigated using terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA locus. Construction and sequencing of clone libraries allowed several members of these communities to be identified, with Proteobacteria being the dominant one, followed by Cyanobacteria and Bacteroidetes. T-RFLP data revealed significantly different communities in holes on the (cold) valley glacier Austre Brøggerbreen relative to two adjacent (polythermal) valley glaciers, Midtre Lovénbreen and Vestre Brøggerbreen. These population compositions correlate with differences in organic matter content, temperature and the metabolic activity of microbial communities concerned. No within-glacier spatial patterns were observed in the communities identified over the 2-year period and with the 1 km-spaced sampling. We infer that surface hydrology is an important factor in the development of cryoconite bacterial communities.
- Published
- 2011
- Full Text
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47. Anaerobic fungi: Neocallimastigomycota.
- Author
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Griffith GW, Baker S, Fliegerova K, Liggenstoffer A, van der Giezen M, Voigt K, and Beakes G
- Abstract
This contribution is based on the six oral presentations given at the Special Interest Group session on anaerobic fungi held during IMC9. These fungi, recently elevated to the status of a separate phylum (Neocallimastigomycota), distinct from the chytrid fungi, possess several unique traits that make their study both fascinating yet challenging to mycologists. There are several genome sequencing programs underway in the US but these are hampered by the highly AT-rich genomes. Next-generation sequencing has also allowed more detailed investigation of the ecology and diversity of these fungi, and it is apparent that several new taxa beyond the six genera already named exist within the digestive tracts of mammalian herbivores, with others potentially inhabiting other anaerobic niches. By increased collaboration between the various labs studying these fungi, it is hoped to develop a stable taxonomic backbone for these fungi and to facilitate exchange of both cultures and genetic data.
- Published
- 2010
- Full Text
- View/download PDF
48. Microbial diversity and activity are increased by compost amendment of metal-contaminated soil.
- Author
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Farrell M, Griffith GW, Hobbs PJ, Perkins WT, and Jones DL
- Subjects
- Amino Acids metabolism, Biomass, Glucose metabolism, Oxygen Consumption, Polymorphism, Restriction Fragment Length, Environmental Restoration and Remediation methods, Metals, Heavy toxicity, Soil analysis, Soil Microbiology, Soil Pollutants toxicity
- Abstract
Unlike organic pollutants, heavy metals cannot be degraded and can constitute a persistent environmental hazard. Here, we investigated the success of different remediation strategies in promoting microbial diversity and function with depth in an acidic soil heavily contaminated with Cu, Pb and Zn. Remediation involved the incorporation of either a high- or a low-quality compost or inorganic fertilizer into the topsoil and monitoring of microbial activity and diversity with soil depth over a 4-month period. While changes in topsoil microbial activity were expected, the possible effects on the subsurface microbial community due to the downward movement of metals, nutrients and/or soluble organic matter have not been examined previously. The results showed that both compost additions, especially the low-quality compost, resulted in significantly increased bacterial and fungal diversity (as assessed by terminal restriction fragment length polymorphism) and activity compared with the inorganic and control treatments in the topsoil. Although phospholipid fatty acid profiling indicated that compost addition had promoted enhanced microbial diversity in the subsoil, no concomitant increase in subsoil microbial activity was observed, suggesting that amelioration of the heavy metals remained localized in the topsoil. We conclude that although composts can successfully immobilize heavy metals and promote ecosystem diversity/function, surface incorporation had little remedial effect below the surface layer over the course of our short-term trial.
- Published
- 2010
- Full Text
- View/download PDF
49. Migration of heavy metals in soil as influenced by compost amendments.
- Author
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Farrell M, Perkins WT, Hobbs PJ, Griffith GW, and Jones DL
- Subjects
- Conservation of Natural Resources, Hydrogen-Ion Concentration, Biodegradation, Environmental, Environmental Monitoring, Metals, Heavy chemistry, Soil analysis, Soil Pollutants chemistry
- Abstract
Soils contaminated with heavy metals can pose a major risk to freshwaters and food chains. In this study, the success of organic and inorganic intervention strategies to alleviate toxicity in a highly acidic soil heavily contaminated with As, Cu, Pb, and Zn was evaluated over 112 d in a mesocosm trial. Amelioration of metal toxicity was assessed by measuring changes in soil solution chemistry, metal leaching, plant growth, and foliar metal accumulation. Either green waste- or MSW-derived composts increased plant yield and rooting depth, reduced plant metal uptake, and raised the pH and nutrient status of the soil. We conclude that composts are well suited for promoting the re-vegetation of contaminated sites; however, care must be taken to ensure that very short-term leaching pulses of heavy metals induced by compost amendment are not of sufficient magnitude to cause contamination of the wider environment.
- Published
- 2010
- Full Text
- View/download PDF
50. The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.
- Author
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Schoch CL, Sung GH, López-Giráldez F, Townsend JP, Miadlikowska J, Hofstetter V, Robbertse B, Matheny PB, Kauff F, Wang Z, Gueidan C, Andrie RM, Trippe K, Ciufetti LM, Wynns A, Fraker E, Hodkinson BP, Bonito G, Groenewald JZ, Arzanlou M, de Hoog GS, Crous PW, Hewitt D, Pfister DH, Peterson K, Gryzenhout M, Wingfield MJ, Aptroot A, Suh SO, Blackwell M, Hillis DM, Griffith GW, Castlebury LA, Rossman AY, Lumbsch HT, Lücking R, Büdel B, Rauhut A, Diederich P, Ertz D, Geiser DM, Hosaka K, Inderbitzin P, Kohlmeyer J, Volkmann-Kohlmeyer B, Mostert L, O'Donnell K, Sipman H, Rogers JD, Shoemaker RA, Sugiyama J, Summerbell RC, Untereiner W, Johnston PR, Stenroos S, Zuccaro A, Dyer PS, Crittenden PD, Cole MS, Hansen K, Trappe JM, Yahr R, Lutzoni F, and Spatafora JW
- Subjects
- Ascomycota classification, Ascomycota cytology, Ecosystem, Genes, Fungal, Reproduction, Ascomycota genetics, Phylogeny
- Abstract
We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.
- Published
- 2009
- Full Text
- View/download PDF
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