Arthrobotrys oligospora: a model organism for understanding the interaction between fungi and nematodes
TL;DR: It is argued for an increased role for A. oligospora in complementing other model systems in biological control research, and as a system to identify and characterize the ecology and biology of nematode-trapping fungi.
Abstract: Arthrobotrys oligospora, a predacious fungus of nematodes, has been very useful in understanding the relationship between nematophagous fungi and their nematode hosts. Arthrobotrys oligospora is by far the most common nematode-trapping fungus with the characteristic ability of forming adhesive trapping nets once in contact with nematodes. This review highlights the versatility and development of A. oligospora as a system to identify and characterize the ecology and biology of nematode-trapping fungi. Using A. oligospora, advances in our knowledge of nematophagous fungi have been made through the discovery of special traits and virulence determinants involved in the pathogenic process, or by creating new ways of presenting these factors to the target nematodes. We argue for an increased role for A. oligospora in complementing other model systems in biological control research.
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1,147 citations
TL;DR: This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi” published in 2013, which will be developed into a list of protected generic names.
Abstract: Knowledge of the relationships and thus the classification of fungi, has developed rapidly with increasingly widespread use of molecular techniques, over the past 10–15 years, and continues to accelerate. Several genera have been found to be polyphyletic, and their generic concepts have subsequently been emended. New names have thus been introduced for species which are phylogenetically distinct from the type species of particular genera. The ending of the separate naming of morphs of the same species in 2011, has also caused changes in fungal generic names. In order to facilitate access to all important changes, it was desirable to compile these in a single document. The present article provides a list of generic names of Ascomycota (approximately 6500 accepted names published to the end of 2016), including those which are lichen-forming. Notes and summaries of the changes since the last edition of ‘Ainsworth & Bisby’s Dictionary of the Fungi’ in 2008 are provided. The notes include the number of accepted species, classification, type species (with location of the type material), culture availability, life-styles, distribution, and selected publications that have appeared since 2008. This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi” published in 2013, which will be developed into a list of protected generic names. This will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists, and scrutiny by procedures determined by the Nomenclature Committee for Fungi (NCF). The previously invalidly published generic names Barriopsis, Collophora (as Collophorina), Cryomyces, Dematiopleospora, Heterospora (as Heterosporicola), Lithophila, Palmomyces (as Palmaria) and Saxomyces are validated, as are two previously invalid family names, Bartaliniaceae and Wiesneriomycetaceae. Four species of Lalaria, which were invalidly published are transferred to Taphrina and validated as new combinations. Catenomycopsis Tibell & Constant. is reduced under Chaenothecopsis Vain., while Dichomera Cooke is reduced under Botryosphaeria Ces. & De Not. (Art. 59).
243 citations
TL;DR: The genome of D. stenobrocha provides support for the hypothesis that nematode trapping fungi evolved from saprophytic fungi in a high carbon and low nitrogen environment and reveals the transition between saprophagy and predation of these fungi and also proves new insights into the mechanisms of mechanical trapping.
Abstract: Nematode-trapping fungi are a unique group of organisms that can capture nematodes using sophisticated trapping structures. The genome of Drechslerella stenobrocha, a constricting-ring-forming fungus, has been sequenced and reported, and provided new insights into the evolutionary origins of nematode predation in fungi, the trapping mechanisms, and the dual lifestyles of saprophagy and predation. The genome of the fungus Drechslerella stenobrocha, which mechanically traps nematodes using a constricting ring, was sequenced. The genome was 29.02 Mb in size and was found rare instances of transposons and repeat induced point mutations, than that of Arthrobotrys oligospora. The functional proteins involved in nematode-infection, such as chitinases, subtilisins, and adhesive proteins, underwent a significant expansion in the A. oligospora genome, while there were fewer lectin genes that mediate fungus-nematode recognition in the D. stenobrocha genome. The carbohydrate-degrading enzyme catalogs in both species were similar to those of efficient cellulolytic fungi, suggesting a saprophytic origin of nematode-trapping fungi. In D. stenobrocha, the down-regulation of saprophytic enzyme genes and the up-regulation of infection-related genes during the capture of nematodes indicated a transition between dual life strategies of saprophagy and predation. The transcriptional profiles also indicated that trap formation was related to the protein kinase C (PKC) signal pathway and regulated by Zn(2)–C6 type transcription factors. The genome of D. stenobrocha provides support for the hypothesis that nematode trapping fungi evolved from saprophytic fungi in a high carbon and low nitrogen environment. It reveals the transition between saprophagy and predation of these fungi and also proves new insights into the mechanisms of mechanical trapping.
71 citations
TL;DR: There is a need for further investigations on this ecologically important group of fungi to better understand their biology, ecological aspects, origin and divergence, host-specificity and application in biocontrol.
Abstract: Fungicolous fungi are a very large, diverse, ecological and trophic group of organisms that are associated with other fungi. This association occurs with species of different lineages across the fungal kingdom. They are recognized as symbionts, mycoparasites, saprotrophs, and even neutrals. Wherever fungi have been found, fungicolous taxa have also been found. Homogeneous environments favour the development of highly adapted and coevolved fungicolous species, which could have led to host-specificity aspects. As a primary consumer, fungicolous fungi decrease the turnaround time of certain nutrients in food webs, due to their special often-rapid life cycles. They may also significantly affect population dynamics and population sizes of their hosts in aquatic or terrestrial ecosystems. As mycoparasites of pathogenic fungi, some fungicolous fungi have been explored as biocontrol agents. They may also cause serious diseases of cultivated edible and medicinal mushrooms, decreasing both yield and quality. Fungicolous fungi could be used as model organisms that may help determine better understanding of species interactions, fungal evolution and divergence, and fungicolous mechanisms. This review summarizes our current understanding of fungicolous fungi, with a particular focus on the terminology, diversity, global distribution, and interaction with their hosts. We also provide a checklist including 1552 fungicolous fungal taxa so far recorded following the updated classification schemes. There is a need for further investigations on this ecologically important group of fungi to better understand their biology, ecological aspects, origin and divergence, host-specificity and application in biocontrol. Accurate identification of these fungi as pathogens and their significance in quarantine purposes on the mushroom industry need further evaluations so that efficient control measures can be developed for better disease management purposes.
64 citations
TL;DR: In this article, the authors performed high throughput sequencing enabled stable isotope probing (HTS-SIP) with 13C-cellulose to characterize the dynamics of fungi and bacteria during cellulose degradation in an agricultural soil.
Abstract: Soils represent one of the largest and most active pools of C in the biosphere, and soil respiration represents a major component of global C flux. Fungi are essential to soil carbon cycling due to their propensity for decomposing organic polymers such as cellulose. We performed high throughput sequencing enabled stable isotope probing (HTS-SIP) with 13C-cellulose to characterize the dynamics of fungi and bacteria during cellulose degradation in an agricultural soil. A total of 1900 fungal taxa were observed and 190 of these assimilated 13C-cellulose during a 30-day incubation. A majority of 13C-labeled fungi belonged to Ascomycota, Basidiomycota, and Mucoromycota. However, most 13C-labeled fungi could not be annotated at the species (71%, n = 134), or genus (49%, n = 93) level. Mucoromycota were 13C-labeled early, and by day 3 the most abundant 13C-labeled organism belonged to Mortierella. In contrast, 13C-labeled Ascomycota increased in diversity through day 14 and their relative abundance comprised more than 40% of fungal ITS sequences by day 30. These results show that: i) the majority of fungal taxa that assimilated 13C from 13C-cellulose are uncultivated and poorly characterized, ii) the beta-diversity of 13C-labeled fungi changed significantly over time during cellulose degradation, iii) a relatively small number of the 13C-labeled taxa dominated the community response to cellulose, and iv) fungi incorporated cellulose into DNA more rapidly and in greater numbers than did bacteria. These results show that fungi in a tilled agricultural field respond rapidly to new cellulose inputs, exhibiting complex temporal dynamics that likely drive carbon flow into diverse taxa within the soil community.
58 citations
References
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TL;DR: Version 4 of MEGA software expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses.
Abstract: We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at (http://www.megasoftware.net).
29,021 citations
"Arthrobotrys oligospora: a model or..." refers background or methods in this paper
...According to the phylogenetic tree (Figure 4) constructed on the basis of the deduced amino acid sequences from nematophagous and entomopathogenic fungi by the Mega program package (Tamura et al. 2007), six proteases (Mc1, Dv1, PII, Aoz1, Ac1, and Mlx) identified from nematode-trapping fungi formed a clade....
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...…to the phylogenetic tree (Figure 4) constructed on the basis of the deduced amino acid sequences from nematophagous and entomopathogenic fungi by the Mega program package (Tamura et al. 2007), six proteases (Mc1, Dv1, PII, Aoz1, Ac1, and Mlx) identified from nematode-trapping fungi formed a clade....
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TL;DR: The application of numerical methods are presented to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size.
Abstract: Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the Poisson-Boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. Here we present the application of numerical methods to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size. As a demonstration of this methodology, electrostatic potentials have been calculated for large microtubule and ribosome structures. The results point to the likely role of electrostatics in a variety of activities of these structures.
6,918 citations
"Arthrobotrys oligospora: a model or..." refers background in this paper
...The anionic substrate-binding regions could increase the local conformational flexibility and enhance catalytic efficiency (Baker et al. 2001), and the large positively charged areas on most of the molecular surface could increase the adsorption of the cuticle-degrading proteases to cuticles bearing abundant acidic residues....
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...The anionic substrate-binding regions could increase the local conformational flexibility and enhance catalytic efficiency (Baker et al. 2001), and the large positively charged areas on most of the molecular surface could increase the adsorption of the cuticle-degrading proteases to cuticles…...
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1,652 citations
"Arthrobotrys oligospora: a model or..." refers background in this paper
...The existence of specialized fungal proteins capable of binding to sugar and other substances suggests that fungi have developed a strategy to bind to host glycoconjugates by producing a type of protein called lectins, which target specific tissues (Sharon and Lis 1972)....
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TL;DR: The number of known species of fungi is estimated as at least 74 K, but could be as much as 120 K with allowances for ‘orphaned’ species as discussed by the authors, which is the current working hypothesis for the number of fungi on Earth.
1,444 citations
TL;DR: This work has shown thatectins on cell surfaces mediate cell-cell interactions by combining with complementary carbohydrates on apposing cells to form lectins, which play a key role in the control of various normal and pathological processes in living organisms.
Abstract: Lectins on cell surfaces mediate cell-cell interactions by combining with complementary carbohydrates on apposing cells. They play a key role in the control of various normal and pathological processes in living organisms.
1,158 citations
"Arthrobotrys oligospora: a model or..." refers background in this paper
...Lectins include a diverse group of carbohydrate-binding proteins commonly present in animals, plants and microorganisms (Sharon and Lis-Sharon 1989; Wimmerova et al. 2003)....
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